Annual Report 2011 - Center for Advanced Biotechnology and ...

CENTER FOR ADVANCED
BIOTECHNOLOGY AND MEDICINE
Annual Report 2011

CONTENTS
Director’s Overview 3
Research Programs and Laboratories 6
Cell & Developmental Biology 7
Molecular Chronobiology Isaac Edery 8
Tumor Virology Céline Gélinas 11
Bacterial Physiology and Protein Engineering Masayori Inouye 15
Growth and Differentiation Control Fang Liu 19
Protein Targeting Peter Lobel 22
Developmental Neurogenetics James Millonig 25
Viral Pathogenesis Arnold Rabson 29
Molecular Virology Aaron Shatkin 32
Molecular Neurodevelopment Mengqing Xiang 35
Structural Biology 39
Protein Engineering Stephen Anderson 40
Biomolecular Crystallography Eddy Arnold 42
Structural Biology and Bioinformatics Helen Berman 47
Structural Microbiology Joseph Marcotrigiano 51
Structural Bioinformatics Gaetano Montelione 54
Protein Design and Evolution Vikas Nanda 62
Protein Crystallography Ann Stock 65
Education, Training and Technology Transfer 68
Lectures and Seminars 69
CABM Lecture Series 70
Annual Retreat 71
25 th Annual Symposium 73
Undergraduate Students 76
Administrative and Support Staff 77
Patents 78
Scientific Advisory Board 81
Current Members 82
Past Members 84
Fiscal Information 86
Grants and Contracts 87
2

Director’s Overview
CABM—25 and counting.
CABM experienced a momentous 2011. It was remarkable as our 25 th anniversary year. Exciting
events to celebrate this milestone included a festive dinner attended by nearly 200 former students
and postdoctoral fellows who returned to CABM from around the country, Europe and Asia. This
enjoyable reunion was held on October 20 th . Announced at this event was the establishment of the
Aaron J. Shatkin Endowed Lectureship which will start in the spring of 2012 and the naming of the
CABM south atrium as the Shatkin Atrium – two overwhelming and highly appreciated honors.
The CABM Annual Symposium was held on the next day. The meeting attracted more than 450
participants and featured lectures by current and former CABM Scientific Advisory Board members
Bruce Alberts, Wayne Hendrickson, Robert Roeder and Phillip Sharp. In addition, several CABM
alumni from academia and industry gave talks, and many others described recent their recent work
in poster presentations.
Continuing the CABM Mission
The year was also noteworthy for the continued commitment to excellence of CABM faculty and
students. Their research success made possible the vigorous pursuit of our mission--the
advancement of basic knowledge to improve human health. CABM research programs were
supported by NIH and several additional federal and state granting agencies as well as other public
and private sources. The resulting research advanced our understanding of cancer, infectious
diseases and hereditary and developmental disorders. As described in the individual research
summaries, CABM researchers are collaborating with clinical investigators at The Cancer Institute
of New Jersey to elicit new targets and to develop therapies for non-Hodgkins lymphomas and
metastatic breast cancers as well as to design novel proteins for therapeutic use in cancer and other
devastating diseases. Several CABM groups have gained new insights and found clever approaches
to answer the health challenges of infections by antibiotic resistant bacteria, HIV/AIDS, hepatitis
and influenza viruses. Other groups have used model systems to define a temperature dependent
molecular mechanism for regulating biological clocks, uncover an autism susceptibility gene and
decipher the differentiation cascade of retinal cells essential for vision. Another CABM laboratory
has discovered the molecular basis of Batten Disease, a lethal childhood hereditary disorder that
may become reversible and even curable based on this finding and developing technology licensed
to a biotechnology company.
Fostering the Growth of Structural Biology
Another stellar event in 2011 has been the completion by Rutgers University of an impressive
Center for Integrative Proteomics Research. The new building is physically connected to CABM
and will accommodate computational research and training activities including the Biomaps
Institute, high field NMR groups, the CABM Mass Spectrometry core facility, a cryoEM laboratory
and the international Protein Data Bank (PDB). CABM had the pleasure of hosting the PDB group
this year while the proteomics building was under construction. This proved to be an enjoyable
arrangement that led to productive interactions and mutually beneficial collaborations, notably
between PDB and the Northeast Structural Genomics Consortium, a multi-institutional center led
by a CABM group and sponsored by NIH as part of the Protein Structural Initiative (PSI).
3

Teaching in the Classroom and Laboratory
All CABM faculty participate actively in the teaching of students and postdoctoral fellows both in
the lecture hall and at the laboratory bench. Trainees include undergraduates, graduate students
from many different MS and PhD programs and medical students. The NIH Biotechnology
Program has been an excellent source of training and support for PhD students from various
disciplines for more than 20 years. In recognition of its success, the training program was recently
renewed for another five years. Outreach education programs also introduce scientific research to
highly motivated high school students at local schools through SMART Team and Biolinks
programs. In addition, CABM hosts a Summer Undergraduate Research Experience (SURE) that is
now in its 8th year. In 2011 SURE students from Rutgers and several other leading universities
participated in lectures and lab projects mentored by CABM graduate students and postdoctoral
fellows—providing opportunities for both budding and committed scientists to interact. Other
outreach programs include a seminar series that brings visiting scientists to talk about their work
and to meet with trainees and the annual CABM Symposium each year on a topic of special interest.
The next Symposium, our 26 th , will be held in October, 2012.
Awards and Service
CABM faculty have received significant national honors for their scientific contributions and
service. These include elected fellowship in AAAS, the American Academy of Microbiology, the
American Academy of Arts & Sciences and the US National Academy of Sciences. Drs. Stock and
Arnold are recipients of MERIT awards from NIH, and Drs. Gelinas, Millonig and Rabson are NIH
study section members. Dr. Stock recently completed service as Chair of the Board of Scientific
Counselors for NIH-NIDCR and is completing a long-held position as HHMI investigator. After
completing service on the American Society of Biochemistry & Molecular Biology Council, she
was appointed this year to the Society’s Education & Professional Development and Finance
Committees. Dr. Montelione is advisor to the NSF Committee of Visitors. Many faculty serve on
other national committees and in journal editorial positions. At the local level, Dr. Millonig recently
joined Drs. Gelinas and Stock as Master Educators. In addition, Dr. Gelinas serves as Associate
Dean for Research, and Dr. Millonig leads the RWJMS/Rutgers/Princeton joint MD/PhD program.
This past year Dr. Rabson was appointed director of the Child Health Institute of New Jersey.
Financial Support
Advancing science through research requires strong support from many sources, administrative as
well as financial. CABM is jointly administered by the University of Medicine and Dentistry of
New Jersey-Robert Wood Johnson Medical School and Rutgers, the State University of New Jersey.
We thank the Universities, in particular for providing a wonderfully functional building for doing
science. CABM also benefits from the advice, wisdom and guidance freely given by a Scientific
Advisory Board composed of leaders from academia and industry. We acknowledge with gratitude
their help and support on many issues. Despite difficult economic times, CABM faculty were
successful again in obtaining grants and contracts—nearly $18 million in 2011. Since the founding
of CABM, a total of ~$300 million has been awarded, mostly for research but also for education
and service functions that have had positive impacts on the two universities and stimulated the NJ
economy. We are indebted to the numerous public agencies, private foundations, companies and
individuals for their generous and essential financial assistance in our pursuit of excellence at
CABM for the past 25 years. The sources of federal funding notably include the National Institutes
4

of Health, National Science Foundation, the Department of Defense and, at the state level, The NJ
Commission on Spinal Cord Research, NJ Commission on Cancer Research, and the Governor’s
Council for Medical Research and Treatment of Autism. The Howard Hughes Medical Institute has
been supportive of CABM for nearly 20 years, and the Ara Parseghian Medical Research
Foundation and Batten Disease Support and Research Association provided important help. CABM
is very grateful to numerous companies including Johnson & Johnson, Hoffmann-LaRoche, Sanofi-
Aventis, Pfizer, Takara Bio Inc., Cisco Inc., Nexomics Biosciences Inc., BioMarin Pharmaceuticals,
Amicus Therapeutics, LifeGas, CIL, GenScript, Macrogen, New England BioLabs, Taxis
Pharmaceuticals Inc., Rigaku and Genewiz. Without this combined financial help, CABM could
not have maintained its commitment to excellence in advancing basic knowledge in the life sciences
to improve human health. We are most grateful.
Aaron J. Shatkin, Professor and Director
shatkin@cabm.rutgers.edu
http://www.cabm.rutgers.edu
5

Research Programs and
Laboratories
6

Cell & Developmental Biology
Laboratory Faculty Director
Molecular Chronobiology Isaac Edery 8
Tumor Virology Céline Gélinas 11
Bacterial Physiology and Protein Engineering Masayori Inouye 15
Growth and Differentiation Control Fang Liu 19
Protein Targeting Peter Lobel 22
Developmental Neurogenetics James Millonig 25
Viral Pathogenesis Arnold Rabson 29
Molecular Virology Aaron Shatkin 32
Molecular Neurodevelopment Mengqing Xiang 35
7

Dr. Isaac Edery
CABM Resident Faculty Member
Professor
Department of Molecular Biology
and Biochemistry
Rutgers University
Dr. Rudra Dubey
Asst. Research Professor
Dr. Weihuan Cao
Research Assistant
Dr. Kwang Huei Low
Research Assistant
Evrim Yildirim
Graduate Student
Chhaya Dharia
Lab Researcher
Molecular Chronobiology Laboratory
Dr. Isaac Edery completed his doctoral studies in biochemistry as a Royal
Canadian Cancer Research Fellow under Dr. Nahum Sonenberg at McGill
University in Montreal. His Ph.D. research focused on the role of the
eukaryotic mRNA cap structure during protein synthesis and precursor
mRNA splicing. Subsequently, he was in the laboratory of Dr. Michael
Rosbash at Brandeis University where he pursued postdoctoral studies
aimed at understanding the time-keeping mechanism underlying circadian
clocks. He joined CABM in 1993, and his research is supported by NIH. Dr.
Edery is a member of the editorial board of Chronobiology International and
Journal of Biological Rhythms.
The main focus of the Edery lab is to understand the biochemical and cellular bases
underlying circadian (~24 hr) rhythms, using Drosophila as a model system. Our
strength lies in applying biochemical strategies that are integrated with genetic,
ecological and evolutionary perspectives to understand how circadian clocks
function and regulate animal physiology and behavior. Circadian rhythms are driven
by cellular clocks and enable organisms to anticipate daily and seasonal changes in
environmental conditions, ensuring activities occur at optimal times in the day and
appropriate seasonal responses are elicited. Understanding how clocks function is
highly relevant for human health and well-being. Indeed, clock malfunctions in
humans have been implicated in many diseases, including manic-depression, cancer,
sleep problems and metabolic syndromes. Our lab is investigating the core clock
mechanism, identifying novel clock proteins and how they interact to build a
biological time-keeping device that is synchronized to local time. In a second major
effort, we are determining the role of clocks in seasonal adaptation, which has led to
novel ecological and evolutionary implications. These studies have also broadened
our research scope by revealing mechanisms that regulate sleep and arousal. In
addition, we are investigating how environmental stimuli, most notably temperature,
controls global gene expression. Below is a brief summary of some of our ongoing
research and future directions
Mechanisms underlying circadian clocks: The central clock mechanism is a
dynamically changing multi-subunit biochemical oscillator based on a small set of
interacting core “clock” proteins and auxiliary factors that as a unit generates a selfperpetuating
daily transcriptional feedback loop that also drives global cyclical gene
expression, which underlies many of the daily rhythms manifested by organisms. In
addition, to the transcriptional architecture, numerous post-translational regulatory
pathways, most notably reversible phosphorylation, regulate various aspects of clock
8

protein metabolism/activity, such that the biochemical oscillator has an endogenous
period of ~24 hr. A conserved feature of animal clocks is that the key clock protein
termed PERIOD (PER) undergoes daily rhythms in phosphorylation that are central
to normal clock progression in animals.
We showed that phosphorylated PER is recognized by the F-box protein, SLIMB
(homolog of β-TrCP) and targeted to the 26S proteasome for rapid degradation (Ko et
al., 2002, Nature), a key event in stimulating the next round of daily gene expression.
We used mass spectrometry and phospho-specific antibodies to identify the critical
phosphorylation events that promote the binding of SLIMB to PER (Chiu et al., 2008,
Genes & Development). Converting key phospho-sites to Ala or Asp (phosphomimetic)
led to decreases or increases in the pace of the clock, respectively (Chiu et
al., 2008, Genes & Development). In more recent work we identified a novel clock
kinase, NEMO, and showed that different phospho-clusters have distinct functions
(Chiu et al., 2011, Cell). Ongoing work is aimed at identifying the roles of different
phospho-clusters on PER and the relevant kinases and phosphatases. We are also
applying these techniques to other clock proteins, and investigating the effects of other
post-translational modifications in clock function, such as SUMOylation and
acetylation. Moreover, PER proteins not only function as the principle biochemical
timer but also link to gene expression by acting as transcriptional repressors, whereby
they “deliver” factors such as chromatin remodeling factors to central clock
transcription factors, yielding cyclical gene expression and hence rhythmic physiology
and behavior. We are undertaking proteomic strategies to identify native clock
protein complexes and how they change throughout a daily cycle. In related work we
are investigating the roles of micro RNAs (miRNAs) in clock function.
Seasonal and thermal adaptation: Many animals exhibit a bimodal distribution of
activity, with ‘morning’ and ‘evening’ bouts of activity that are separated by a midday
dip in activity or ‘siesta’. Ambient temperature is a key environmental modality
regulating the daily distribution of activity in animals. In D. melanogaster, as
temperatures rise there is less midday activity and the two bouts of activity are
increasingly shifted into the cooler nighttime hours, almost certainly an adaptive
response that minimizes the detrimental effects of the hot midday sun (Majercak et al.,
1999, Neuron). We showed that the temperature-dependent splicing of the 3'-terminal
intron (termed dmpi8) from the D. melanogaster per RNA is a major ‘thermosensor’
that adjusts the distribution of daily wake-sleep cycles, eliciting seasonably
appropriate responses. In more recent work we showed that this mechanism does not
operate in several Drosophila species with more restricted and ancestral locations in
equatorial Africa wherein temperature and daylength do not show large seasonal
variations (Low et al., 2008, Neuron). We investigated the molecular basis for the
species-specific splicing phenotypes and found that multiple suboptimal splicing
signals on dmpi8 underlie the thermosensitivity (Low et al., 2008, Neuron).
Presumably, higher temperatures progressively destabilize interactions between the
non-consensus 5’ splice site (ss) and the U1 snRNP, the initial step in the splicing
reaction. Ongoing work is aimed at understanding how temperature regulates global
gene expression. In addition, these studies are revealing new mechanisms that
regulate sleep and arousal.
9

Publications (2010-2011):
Ko, H.W., Chiu, J., Vanselow, J.T., Kramer, A. and Edery, I. A hierarchical
phosphorylation cascade that regulates the timing of PERIOD nuclear entry reveals novel
roles for proline-directed kinases and GSK-3β/SGG in circadian clocks. J. Neurosci.
2010 30: 12664-75.
Chiu, J.C., Low, K.H., Pike, D.H., Yildirim, E. and Edery, I. Assaying locomotor activity
to study circadian rhythms and sleep parameters in Drosophila. J. Visualized Expts.
2010 43.
Sun, W.C., Jeong, E.H., Jeong, H.J., Ko, H.W., Edery, I. and Kim, E.Y. Two distinct
modes of PERIOD recruitment onto dCLOCK reveal a novel role for TIMELESS in
circadian transcription J. Neurosci. 2010 43: 14458-69.
Edery, I. Circadian rhythms. Temperatures to communicate by. Science 2010 330: 329-
30.
Chiu, J.C. Ko, H.W. and Edery, I. NEMO/NLK phosphorylates PERIOD to initiate a
time-delay phosphorylation circuit that sets circadian clock speed. Cell 2011 145: 357-
70.
Edery, I. A master CLOCK hard at work brings rhythm to the transcriptome. Genes &
Dev. 2011 25 (in press).
Edery, I. A morning induced phosphorylation-based repressor times evening gene
expression: a new way for circadian clocks to use an old trick. Mol. Cell. 2011 (in press).
10

Dr. Céline Gélinas
CABM Resident Faculty Member
Professor
Department of Biochemistry
Associate Dean for Research
UMDNJ-Robert Wood Johnson
Medical School
Dr. Sheng Ge
Research Associate
Dr. Poonam Molli
Research Associate
Dr. Sophie Richard-
Bail
Research Associate
Dr. Anitha Suram
Research Associate
Na Yang
Graduate Student
Tumor Virology Laboratory
Dr. Céline Gélinas came to CABM in September 1988 from the University of
Wisconsin, where she conducted postdoctoral studies with Nobel laureate Dr.
Howard M. Temin. She earned her Ph.D. at the Université de Sherbrooke in
her native country, Canada, and received a number of honors including the
Jean-Marie Beauregard Award for Academic and Research Excellence, the
National Cancer Institute of Canada King George V Silver Jubilee
Postdoctoral Fellowship, a Medical Research Council of Canada Postdoctoral
Fellowship and a Basil O’Connor Starter Scholar Research Award. Her
research is funded by the NIH, the Leukemia and Lymphoma Society and the
Department of Defense Breast Cancer Research Program. Dr. Gélinas served
for several years as a member of the NIH Experimental Virology Study Section
and the Virology B Study Section. In 2006, she was elected to the UMDNJ
Stuart D. Cook Master Educators Guild. Dr. Gelinas was appointed Associate
Dean for Research for RWJMS in 2008. She was elected to Fellowship in the
American Academy of Microbiology in 2010.
Our laboratory focuses on the Rel/NF-kB signaling pathway and its role in cell
survival and cancer. The Rel/NF-kB transcription factors are key to normal immune
and inflammatory responses and play critical roles in tumor cell survival,
pathogenesis and chemoresistance. They are thus important targets for therapy.
Rel/NF-kB is constitutively activated in many human cancers, and the Rel proteins
are implicated in leukemia/lymphomagenesis and in breast cancer. However, the
detailed mechanism is not fully understood. Our studies aim at understanding how
changes in NF-kB’s transcriptional activity and regulation contribute to
carcinogenesis and tumor cell resistance to anti-cancer treatment.
We published a study demonstrating that defective ubiquitin-proteasome mediated
turnover of the NF-kB-regulated apoptosis inhibitor Bfl-1 (Bcl2A1, A1) can
predispose to lymphoma (Fan et al. 2010). Ubiquitination-resistant mutants of Bfl-1
showed decreased turnover and greatly accelerated tumor formation in a mouse
model of leukemia/lymphoma. We also showed that these tumors also displayed
upregulation and activation of tyrosine kinase Lck along with activation of the IKK,
Akt and Erk signaling pathways, which are key mediators in cancer. Coexpression of
Bfl-1 and constitutively active Lck promoted tumor formation, whereas Lck
knockdown in tumor-derived cells suppressed leukemia/lymphomagenesis. Since
Bfl-1 is overexpressed in many therapy-resistant leukemia and lymphomas and is
necessary for tumor cell maintenance and chemoresistance, these data suggest that
ubiquitination is an important tumor suppression mechanism to regulate Bfl-1
function. This also raises the possibility that mutations in bfl-1 or in the signaling
pathways that control its ubiquitination may predispose to cancer. This work was
conducted together with our colleagues, Drs. Eileen White (CINJ and Rutgers
Univ.), Yacov Ron (RWJMS) and David Weissmann (RWJMS, RWJUH).
11

The findings above suggested that accelerating Bfl-1 turnover could perhaps be
used to improve tumor cell response to anti-cancer therapy. We pursued our
investigation of kinase-specific inhibitors that can accelerate Bfl-1 turnover and
showed that some of them could significantly sensitize drug-resistant human
leukemia and lymphoma cell lines to anti-cancer agents. Ongoing studies are
evaluating the effectiveness of combination treatment in vivo in mouse xenograft
models and in patient-derived specimens ex vivo together with our Drs. Roger
Strair, Daniel Medina, Lauri Goodell and Susan Goodin (CINJ).
Our efforts looking into the mechanisms that regulate Bfl-1 turnover and function
revealed that while Bfl-1 is regulated by ubiquitination, it is not a substrate for
sumoylation. This indicated that ubiquitination is the primary mode of posttranslational
regulation to control its half-life. We identified specific mutations in
putative Bfl-1 phosphorylation sites that markedly alter its turnover and have been
investigating if these are substrates for phosphorylation. We also identified a
naturally occurring gene mutation in human lymphoma cells that alters turnover
of apoptosis inhibitor Bfl-1 and chemoresistance, and have optimized conditions
to purify Bfl-1 binding partners with the ultimate goal to identify factors that
control its turnover.
Collaborative studies with the group of Dr. Gaetano Montelione (CABM)
elucidated the structure of Bfl-1∆C (residues 1-151) bound to a Noxa BH3
peptide, refined to 2.25 Å resolution. This provided additional key insights into
the structure of the helix-binding cleft of Bfl-1 and helped to understand how Bfl-
1 selectively associates with some proapoptotic Bcl-2 family members and what
dictates its affinity and specificity for Noxa compared to other Bcl-2 family
members. A manuscript is in preparation (Guan et al. In preparation).
We also pursued our studies on the role of CAPER in breast cancer and its
functional interaction with estrogen receptor and NF-kB. Constitutive Rel/NF-kB
activity is inversely correlated with expression of estrogen receptor alpha (ERα)
and is key to breast cancer cell survival, invasion and resistance to chemotherapy.
Our studies uncovered a new role for CAPER in breast cancer cell invasion. In
vivo studies using a mouse model of breast cancer metastasis are ongoing to
elucidate its role in breast cancer progression and metastasis. Since CAPER was
previously implicated both in transcriptional regulation as well as in alternative
splicing, we used Affymetrix exon arrays to probe for possible effects on global
gene expression in order to better understand the mechanisms by which it affects
invasion. Preliminary results suggest interesting effects of CAPER at both levels.
This is consistent with CAPER mutation data and with immunofluorescence data
showing co-localization of CAPER with splicing factor SC35. These experiments
are being conducted in collaboration with the group of Dr. Guna Rajagopal
(CINJ).
Collaborative work emanating from the laboratories of Drs. Daniel Medina and
Roger Strair (CINJ), together with Drs. John Glod (CINJ), Arnold Rabson
12

(CHINJ, CINJ and CABM) and Lauri Goodell (RWJUH) characterized the effects
of mesenchymal stromal cell (MSC) on the survival and drug resistance of
primary mantle cell lymphoma (MCL) cells, an aggressive subtype of non-
Hodgkin’s lymphoma. Studies revealed an important role for the canonical and
non-canonical NF-kB pathways and expression of cytokine BAFF by MSC in the
long term survival of MSC. A manuscript was submitted (Medina et al.
Submitted).
Finally, we pursued our collaborative work with Dr. Eileen White (CINJ) on the
role of autophagy in tumorigenesis and the role of NF-kB in this context. These
studies uncovered that activated Ras, commonly found in human tumors, requires
autophagy to maintain oxidative metabolism and tumorigenesis. This suggests
that therapeutic strategies to inhibit autophagy could perhaps be useful for the
treatment of cancers in which Ras is activated. This work was published (Guo et al.
2011). Ongoing studies focus on understanding how p62 modulates autophagy and
tumorigenesis and the role of NF-kB in this context, expressed and purified active
fragment was crystallized and the structure determined by X-ray crystallography.
Seven related conformational states were obtained in the crystal. Position
differences of the oligonucleotide/oligosaccharide (OB) binding fold lid domain
over the conserved GTP binding site in the seven structures provided snapshots of
the opening and closing of the active site cleft via a swivel motion. While the
GTP binding site is structurally and evolutionarily conserved, the overall GTase
mechanism in mammalian and yeast systems differs somewhat. Experiments are
underway to crystallize complexes of human GTase with CTD and RNA as well
as GTP. Protein engineering is being applied in an effort to crystallize the full
length human CE.
CAPER co-localizes
with splicing factor
SC35 in breast
cancer cells, as seen
by
immunofluorescence
and confocal
microscopy.
13

Publications:
Fan, G., Simmons, M.J., Ge, S., Dutta-Simmons, J., Kucharczak, J..F, Ron, Y.,
Weissmann, D., Chen, C.C., Mukherjee, C., White, E. and Gélinas, C. Defective
ubiquitin-mediated degradation of anti-apoptotic Bfl-1 predisposes to lymphoma.
Blood 2010 115: 3559-3569.
Guo, J.Y., Chen, H-Y, Mathew, R., Fan, J., Strohecker, A.M., Kamphorst, J.J.,
Chen, G., Lemmons, J.M.S., Karantza, V., Coller, H.A., DiPaola, R.S., Gélinas,
C., Rabinowitz, J.D. and White, E.) Activated Ras requires autophagy to maintain
oxidative metabolism and tumorigenesis. Genes & Dev. 2011 25: 460-470.
14

Dr. Masayori Inouye
CABM Resident Faculty Member
Distinguished Professor
Department of Biochemistry
UMDNJ-Robert Wood Johnson
Medical School
Dr. Sangita Phadtere
Adjunct Associate Professor
Yojiro Ishida
Research Associate
Hiroshi Kobayashi
Research Associate
Dr. Lili Mao
Research Associate
Dr. Yoshihiro
Yamaguchi
Research Associate
Dr. Kuen-Phon Wu
Postdoctoral Associate
Dr. Hisako Masuda
Postdoctoral Fellow
Yu-Jen Chen
Graduate Student
Chun-Yi Lin
Graduate Student
Bacterial Physiology and Protein Engineering Laboratory
Dr. Masayori Inouye joined CABM in October 2009. He is well-known for
his discovery of antisense-RNA in 1984, the function of the signal peptide for
secretion, biogenesis of outer membrane proteins, propeptide-mediated
protein folding and molecular biology of histidine kinases. Currently he is
working on the characterization of the toxin-antitoxin (TA) systems from E.
coli and human pathogens such as Mycobacterium tuberculosis and
Staphylococcus aureus. The discovery of a sequence (ACA)-specific
endoribonuclease from the E. coli TA systems led his laboratory to develop a
unique protein production system converting E. coli cells to a single-protein
production (SPP) bioreactor. This system allows one to label only a protein
of interest in the cells with a specific isotope(s), an amino acid(s) or a toxic
non-natural amino acid analogue(s) in a high yield. His laboratory also
does research on the mechanism of ribosome stalling during protein
synthesis. In May 2011, he received the Edward J. Ill Excellence in Medicine
Award for Outstanding Medical Research Scientist. Dr. Inouye is a member
of the American Academy of Arts & Sciences.
Toxin-antitoxin (TA) systems; their roles in bacterial physiology and the
development of novel antibiotics
Almost all bacteria including human pathogens contain suicide or toxin genes which
are induced under stress conditions leading to cell growth arrest and eventual cell
death in a way similar to apoptosis or programmed cell death in higher systems.
Escherichia coli contains at least 35 TA systems and their toxins are highly diverse,
targeting DNA, mRNA, protein and cell wall synthesis. The importance of these TA
systems in medical science has not been fully appreciated until recently. The Inouye
laboratory works to decipher the cellular targets of these toxins and the molecular
mechanisms of toxin functions.
Promoter
ATP-dependent
proteases
Antitoxin
Toxin
Cellular targets
Bacterial Toxin-Antitoxin (Apoptosis) System
Protein
DNA
15

mRNA interferases
mRNA interferases are encoded by one of the TA systems. MazF from E. coli is
the first mRNA interferase discovered in Dr. Inouye’s laboratory and functions as
a sequence-specific (ACA) endoribonuclease. Its induction in E. coli cells results
in growth arrest and eventual cell death. The Inouye group also observed that
MazF induction in mammalian cells effectively causes Bak (a pro-apoptotic
protein)-dependent programmed cell death. The application of bacterial mRNA
interferases for mammalian cell growth regulation is currently being explored to
develop an effective, novel method for cancer treatment and HIV eradication. In
addition to E. coli MazF, the laboratory has identified a large number of mRNA
interferases having different RNA cleavage specificity, including one from a
highly halophilic archaeon that cleaves a specific seven base sequence. mRNA
interference using highly sequence-specific mRNA interferases instead of
antisense RNA or RNAi may be a novel and exciting way to regulate gene
expression.
Single protein production in living cells
Expression of MazF, an ACA-specific mRNA interferase, results in nearly
complete degradation of cellular mRNAs, leading to almost complete inhibition
of protein synthesis. Intriguingly, MazF-induced cells are still fully capable of
producing a protein at a high level if the mRNA for that protein is engineered to
have no ACA sequences without altering its amino acid sequence. Therefore, it is
possible to convert E. coli cells into a bioreactor producing a single protein of
interest. This “single-protein production” (SPP) system allows NMR structural
studies of proteins without purification, which makes this system especially useful
for structural studies of membrane proteins. In addition, the SPP system provides
a unique opportunity to produce proteins in which all the residues of a specific
amino acid in a protein are replaced with toxic non-natural amino acid analogues
to create proteins of novel structures and functions.
Publications:
Awano, N., Rajagopal, V., Arbing, M., Patel, S., Hunt, J., Inouye, M., Phadtare, S.
Escherichia coli RNase R has dual activities, helicase and ribonuclease. J.
Bacteriol. 2010 192(5):1344-52.
Peng, Y.Y., Yoshizumi, A., Danon, S.J., Glattauer, V., Prokopenko, O.,
Mirochinitchenko, O., Yu, Z., Inouye, M., Werkmeister, J.A., Brodsky, B.,
Ramshaw, J.A. A Streptococcus pyogenes derived collagen-like protein as a noncytotoxic
and non-immunogenic cross-linkable biomaterial. Biomaterials 2010
31(10):2755-61.
Jung-Ho Park
Graduate Student
Narumi Tokunaga
Graduate Student
Zhuoxin Yu
Graduate Student
Dr. Qian Tan
Research Teaching Spec.
Chun Ying Xu
Research Teaching Spec.
Dr. Yoshihiro
Yamaguchi
Research Teaching Spec.
Dr. Yong Long Zhang
Research Teaching Spec.
Xushen Chen
Lab Technician
16

Xu, Z., Mirochnitchenko, O., Xu, C., Yoshizumi, A., Brodsky, B., Inouye, M.
Noncollagenous region of the streptococcal collagen-like protein is a trimerization domain
that supports refolding of adjacent homologous and heterologous collagenous domains.
Protein Sci. 2010 19(4):775-85.
Hwang, J., and Inouye, M. Interaction of an essential E. coli GTPase, Der with 50S
ribosome via the KH-like domain. J. Bacterial. 2010 192(8):2277-83.
Schneider, W.M., Tang, Y., Vaiphei, S.T., Mao, L., Maglaqui, M., Inouye, M., Roth, M.J.,
Montelione, G.T. Efficient condensed-phase production of perdeuterated soluble and
membrane proteins. J. Struct. Funct Genomics 2010 11(2):143-54.
Hwang, J. and Inouye, M. A bacterial GAP-like protein, YihI, regulating the GTPase of
Der, an essential GTP-binding protein in Escherichia coli. J. Mol. Biol. 2010 399 (5):759-
72.
Vaiphei, S. T., Mao, L., Shimazu, T., Park, J.H. and Inouye, M. The Use of Amino Acids
as Inducers for High Level Protein expression in the Single-Protein Production (SPP)
System. Appl. Environ. Microbiol. 2010 76 (18):6063-8.
Love, J., Mancia, F., Shapiro, L., Punta, M., Rost, B., Girvin, M., Wang, D.N., Zhou, M.,
Hunt, J.F., Szyperski, T., Gouaux, E., Mackinnon, R., McDermott, A., Honig, B., Inouye,
M., Montelione, G., Hendrickson, W.A. The New York Consortium on Membrane Protein
Structure (NYCOMPS): a high-throughput platform for structural genomics of integral
membrane proteins. J. Struct. Funct. Genomics. 2010 11(3):191-9.
Arbing, M.A., Handelman, S.K., Kuzin, A.P., Verdon, G., Wang, C., Su, M., Rothenbacher,
F.P., Abashidze, M., Liu, M., Hurley, J.M., Xia, R., Acton, T., Inouye, M., Montelione,
G.T., Woychik, N.A., Hung, J.F. Crystal structures of Phd-Doc, HigA, and YeeU establish
multiple evolutionary links between microbial growth-regulating toxin-antitoxin systems.
Structure. 2010 18(8):996-1010.
Tang, Y., Schneider, W.M., Shen, Y., Raman, S., Inouye, M., Baker, D., Roth, M.J.,
Montelione, G.T. Fully automated high-quality NMR structure determination of small
(2)H-enriched proteins. J. Struct. Funct. Genomics 2010 11(4):223-32.
Mao, L., Stathopulos, P.B., Ikura, M., Inouye, M. Secretion of human superoxide
dismutase in Escherichia coli using the condensed single-protein-production (cSPP)
System. Protein Sci. 2010 19 (12):2330-5.
Zhu, L., Sharp, J.D., Kobayashi, H., Woychik, N.A., Inouye, M. Noncognate
Mycobacterium tuberculosis toxin-antitoxins can physically and functionally interact. J.
Biol. Chem. 2010 285(51):39732-8.
Vaiphei, S.T., Tang, Y., Montelione, G.T., Inouye, M. The Use of the Condensed Single
Protein Production System for Isotope-Labeled Outer Membrane Proteins, OmpA
17

and OmpX in E. coli. Mol. Biotechnol. 2010 47(3):205-10.
Chono, H., Matsumoto, K., Tsuda, H., Saito, N., Lee, K., Kim, S., Shibata, H.,
Ageyama, N., Terao, K., Yasutomi, Y., Mineno, J., Kim, S., Inouye M. and Kato I.
Acquisition of HIV-1 Resistance in T Lymphocytes Using an ACA-Specific E.
coli mRNA interferase. Hum. Gene. Ther. 2011 22(1):35-43.
Tan, Q., Awano, N., Inouye, M. YeeV is an Escherichia coli Toxin that Inhibits
Cell Division by Targeting the Cytoskeleton Proteins, FtsZ and MreB. Mol. Micro.
2011 79(1):109-18.
Mao, L., Inouye, K., Tao, Y., Montelione, G.T., McDermott, A.E. and Inouye, M.
Suppression of phospholipid biosynthesis by cerulenin in the condensed Single-
Protein-Production (cSPP) system. J. Biomol. NMR. 2011 49(2):131-7.
Zhang, Y.L. and Inouye, M. RatA (YfjG), an Escherichia coli toxin, inhibits 70S
ribosome association to block translation initiation. Mol. Microbiol. 2011
79(6):1418-29.
Yu, Z., Brodsky, B., Inouye, M. Dissecting a bacterial collagen domain from
Streptococcus pyogenes: sequence and length-dependent variations in triple helix
stability and folding. J. Biol. Chem. 2011 286(21):18960-8.
Park, J.H., Yamaguchi, Y., Inouye, M. Bacillus subtilis MazF-bs (EndoA) is a
UACAU-specific mRNA interferase. FEBS Lett. 2011 585(15):2526-32.
Yamaguchi, Y. and Inouye, M. Regulation of growth and death in Escherichia
coli by toxin-antitoxin systems. Nat. Rev. Microbiol. 2011 9(11):779-90.
Yamaguchi, Y., Park, J.H. and Inouye, M. Toxin-antitoxin systems in bacteria and
archaea. Annu. Rev. Genet. 2011 45:61-79.
18

Dr. Fang Liu
CABM Resident Faculty Member
Associate Professor
Department of Chemical Biology
Ernest Mario School of Pharmacy
Susan Lehman Cullman Laboratory
for Cancer Research
Rutgers University
Growth and Differentiation Control Laboratory
Dr. Fang Liu obtained her B.S. in biochemistry from Beijing University and
Ph.D. in biochemistry from Harvard University working with Dr. Michael R.
Green. She conducted postdoctoral research with Dr. Joan Massagué at
Memorial Sloan-Kettering Cancer Center and joined CABM in 1998. Dr.
Liu has received awards from the American Association for Cancer
Research-National Foundation for Cancer Research, the Pharmaceutical
Research and Manufacturers of America Foundation, the Burroughs
Wellcome Fund, and the Sidney Kimmel Foundation for Cancer Research.
She also obtained fellowships from the K.C. Wong Education Foundation
and the Jane Coffin Childs Memorial Fund for Medical Research.
We study TGF-ß/Smad signal transduction, transcriptional regulation, cell cycle
control and their roles in cancer.
TGF-ß regulates a wide variety of biological activities. It induces potent growth
inhibitory responses in normal cells, but promotes migration and invasion of cancer
cells. Smads mediate the TGF-ß responses. TGF-ß binding to the cell surface
receptors leads to the phosphorylation of Smad2/3 in their carboxyl-terminus as well
as in the proline-rich linker region. The serine/threonine phosphorylation sites in the
linker region are followed by the proline residue. Pin1, a peptidyl-prolyl cis/trans
isomerase, recognizes phosphorylated serine/threonine-proline (pS/T-P) motifs. We
show that Smad2/3 interacts with Pin1 in a TGF-ß-dependent manner. We further
show that the phosphorylated threonine 179-proline motif in the Smad3 linker region
is the major binding site for Pin1. Although EGF also induces phosphorylation of
threonine 179 and other residues in the Smad3 linker region the same as TGF-ß,
Pin1 is unable to bind to the EGF-stimulated Smad3. Further analysis suggests that
phosphorylation of Smad3 in the carboxyl-terminus is necessary for the interaction
with Pin1. Depletion of Pin1 by shRNA does not affect significantly TGF-ß-induced
growth-inhibitory responses and a number of TGF-ß/Smad target genes analyzed. In
contrast, knockdown of Pin1 in human PC3 prostate cancer cells strongly inhibited
TGF-ß-mediated migration and invasion. Accordingly, TGF-ß induction of Ncadherin,
which plays an important role in migration and invasion, is markedly
reduced when Pin1 is depleted in PC3 cells. The catalytic activity of Pin1 is essential
for TGF-ß-induced migration and invasion (see Figure). Since Pin1 is overexpressed
in many cancers, our findings highlight the importance of Pin1 in TGF-ß-induced
migration and invasion of cancer cells.
19

Smad3 plays an important role in inhibiting cell proliferation and promoting
apoptosis. Human Smad3 is localized near a hot spot mutation area for breast
cancer and for several other types of cancers. We have found that Smad3 levels are
reduced in human primary breast cancer samples and in human breast cancer cell
lines. Importantly, Smad3 expression is high in normal breast stem cells but low in
breast cancer stem cells. In addition, our preliminary studies indicate that 7,12dimethylbenz-[a]-anthracene
(DMBA), a chemical carcinogen, induces mammary
tumor formation at a much higher frequency in Smad3 -/- or Smad3 +/- mice than in
Smad3 +/+ mice. Thus, we hypothesize that Smad3 has important tumor suppressor
function for breast cancer.
Breast cancer stem cells are CD44 + CD24 -/low . Although CD44 lacks its own
signaling domain, it associates with and co-stimulates signaling by a number of
growth factor receptors, such as Her2 and EGF receptor 1. CD44 is overexpressed
in the vast majority of breast cancers. CD44 is not just a marker for breast cancer
stem cells. It is necessary for breast tumor initiation, tumor growth, and metastasis.
Knockdown of CD44 greatly reduces tumor-initiating frequency, tumor weight,
and colony formation in soft agar assay. Disruption of tumor cell surface CD44
function induces apoptosis in metastatic mammary carcinoma cells in vivo. A
predominant function of CD44 is to promote growth and to inhibit apoptosis. The
growth-inhibitory and tumor-suppressive functions of p53 depend on its repression
of CD44 expression. Our preliminary studies have discovered that Smad3 potently
represses CD44 transcription in mammary epithelial cells. Thus, we further
hypothesize that Smad3 repression of CD44 expression is essential for its tumor
suppressor activity, and that Smad3 and p53 cooperate to inhibit breast
tumorigenesis. Our research is directed towards testing these hypotheses. Our
findings will be highly significant for preventing and treating breast cancer.
20

Publications:
Matsuura, I., Chiang, K.-N., Lai, C.-Y., He, D., Wang, G., Ramkumar, R. Uchida, T.,
Ryo, A., Lu, K. P., and Liu, F. (2010)Pin1 promotes TGF-ß-induced migration and
invasion.J. Biol. Chem. 285, 1854-1864.
Sasseville, M., Ritter, L. J., Nguyen, T., Liu, F., Mottershead, D. G., Russell, D. L., and
Gilchrist, R. B. (2010).Growth differentiation factor 9 signaling requires ERK1/2
activity in mouse granulosa and cumulus cells.J. Cell Sci. 123, 3166-3176.
Chang, X., Liu, F., Wang, X., Lin, A., Zhou, H., and Su, B. (2011) The kinases MEKK2
and MEKK3 regulate transforming growth factor-ß-mediated helper T cell
differentiation. Immunity 34, 201-212.
Liu, F. (2011) Inhibition of Smad3 activity by cyclin D-CDK4 and cyclin E-CDK2 in
breast cancer cells. Cell Cycle 10, 186.
So, J. Y., Lee, H. J., Smolarek, A. K., Paul, S., Maehr, H., Uskokovic, M., Zheng, X.,
Conney, A., Cai, L., Liu, F., and Suh, N. (2011) A novel Gemini vitamin D analog
represses the expression of a stem cell marker CD44 in breast cancer. Mol. Pharmacol.
79, 360-367.
Cohen-Solal K. A., Merrigan K. T., Chan, J. L., Goydos, J. S., Chen, W., Foran, D. J.,
Liu, F., Lasfar, A., and Reiss, M. (2011) Constitutive Smad linker phosphorylation in
melanoma: a mechanism of resistance to transforming growth factor-β-mediated growth
inhibition. Pigment Cell Melanoma Res. 24, 512-524.
Dhar-Mascareno, M., Belishov, I., Liu, F., and Mascareno, E. J. (2011) Hexim-1
modulates androgen receptor and the TGFβ signaling during the progression of prostate
cancer. The Prostate in press
21

Dr. Peter Lobel
CABM Resident Faculty Member
Professor
Department of Pharmacology
UMDNJ-Robert Wood Johnson
Medical School
Dr. David Sleat
Research Associate Professor
Dr. Haiyan Zheng
Principal Research Associate
Dr. Yu Meng
Research Associate
Dr. Istvan Sohar
Research Associate
Ling Huang
Graduate Student
Su Xu
Graduate Fellow
Mukarram El-Banna
Research Teaching Spec.
Dr. Meiqian Qian
Research Teaching Spec.
Protein Targeting Laboratory
Dr. Peter Lobel trained at Columbia University and Washington University
in St. Louis and joined CABM in 1989. He is currently conducting research
on lysosomes and associated human hereditary metabolic diseases. This
work resulted in identification of three disease genes that cause fatal
neurodegenerative disorders. He was a Searle Scholar and received the
excellence in research award from the UMDNJ Foundation. Dr. Lobel is the
director of the CABM Mass Spectrometry Core Facility.
.
Our laboratory has developed new methods for disease discovery that evolved from
our research on lysosomal enzyme targeting. Lysosomes are membrane-bound,
acidic organelles that are found in all eukaryotic cells. They contain a variety of
different proteases, glycosidases, lipases, phosphatases, nucleases and other
hydrolytic enzymes, most of which are delivered to the lysosome by the mannose 6phosphate
targeting system. In this pathway, lysosomal enzymes are recognized as
different from other glycoproteins and are selectively phosphorylated on mannose
residues. The mannose 6-phosphate serves as a recognition marker that allows the
enzymes to bind mannose 6-phosphate receptor which ferries the lysosomal enzyme
to the lysosome. In the lysosome, the enzymes function in concert to break down
complex biological macromolecules into simple components. The importance of
these enzymes is underscored by the identification of over thirty lysosomal storage
disorders (e.g., Tay Sach's disease) where loss of a single lysosomal enzyme leads to
severe health problems including neurodegeneration, progressive mental retardation
and early death.
Our approach to identify the molecular basis for unsolved lysosomal storage
disorders is based on our ability to use mannose 6-phosphate receptor derivatives to
visualize and purify mannose 6-phosphate containing lysosomal enzymes. Once we
discover the cause of a given disease, we conduct further research to understand the
underlying system and potentially to develop therapeutics. We also investigate the
basic mechanism for targeting of lysosomal proteins and the composition of the
lysosome.
22

In the prior year, we have made considerable progress investigating late infantile
neuronal ceroid lipofuscinosis (LINCL), a recessive neurodenerative disease of
childhood that is due to deficiencies in the lysosomal protease tripeptidyl-peptidase 1
(TPP1). In one study, we performed mass spectrometric analyses on storage material
and lysosomal fractions from an LINCL mouse model. This revealed several
candidates for proteins stored in brain. In depth analysis of the most prominent of
these, glial fibrillary acidic protein, revealed that this protein represented a
contaminant that adventitiously associated with storage material and lysosomes during
the isolation procedure. We also used the mouse model to explore potential
therapeutic approaches and found that intrathecal administration of recombinant
human TPP1 resulted in significant delivery of enzyme to the brain. Importantly, this
treatment prolonged lifespan and improved decreased disease symptoms. Finally, in
collaboration with scientists at the University of Missouri and BioMarin Therapeutics,
as a step towards the clinic we conducted pilot enzyme replacement studies using an
LINCL dog model.
We are also continuing our investigation of the lysosomal proteome. Following the
principles of de Duve and colleagues that lead to the discovery of the lysosome, we
analyzed rat liver subcellular fractions using mass spectrometry to identify and
determine the distribution of different proteins. This led to the identification of
numerous candidate lysosomal proteins and provided further evidence that ABCB6 is
lysosomal and that superoxide dismutase 1 has a mixed cytoplasmic-lysosomal
localization.
Percent survival
100
50
0
1.2 mg/animal
0.38 mg/animal
0.12 mg/animal
0.038 mg/animal
vehicle
0 30 60 90 120 150 180
Time (days)
Acute intrathecal administration of recombinant human TPP1 extends lifespan of a
LINCL mouse model. Animals were administered the indicated dose of TPP1 at the
age of 28-30 days and then followed for survival.
Jennifer Wiseman
Research Teaching Spec.
Caifeng Zhao
Research Teaching Spec.
23

Publications:
Della Valle, M. C., Sleat, D. E., Zheng, H., Moore, D. F., Jadot, M. and Lobel, P.
Classification of subcellular location by comparative proteomic analysis of native
and density-shifted lysosomes. Mol.Cell. Proteomics. 2011 10, M110 006403.
Qian, Y., Lee, I., Lee, W. S., Qian, M., Kudo, M., Canfield, W. M., Lobel, P. and
Kornfeld, S. Functions of the alpha, beta, and gamma subunits of UDP-
GlcNAc:lysosomal enzyme N-acetylglucosamine-1-phosphotransferase. J. Biol.
Chem. 2010 285: 3360-3370.
Vuillemenot, B. R., Katz, M. L., Coates, J. R., Kennedy, D., Tiger, P., Kanazono, S.,
Lobel, P., Sohar, I., Xu, S., Cahayag, R., Keve, S., Koren, E., Bunting, S., Tsuruda,
L. S. and O'Neill, C. A. Intrathecal tripeptidyl-peptidase 1 reduces lysosomal storage
in a canine model of late infantile neuronal ceroid lipofuscinosis. Mol. Genet. Metab.
2011 104: 325-337.
Xu, S., Sleat, D. E., Jadot, M. and Lobel, P. Glial fibrillary acidic protein is elevated
in the lysosomal storage disease classical late-infantile neuronal ceroid
lipofuscinosis, but is not a component of the storage material. Biochem. J. 2010 428:
355-362.
Xu, S., Wang, L., El-Banna, M., Sohar, I., Sleat, D. E. and Lobel, P. Large-volume
intrathecal enzyme delivery increases survival of a mouse model of late infantile
neuronal ceroid lipofuscinosis. Mol Ther. 2011 19: 1842-1848
24

Dr. James Millonig
CABM Resident Faculty Member
Associate Professor
Department of Neuroscience and
Cell Biology
UMDNJ-Robert Wood Johnson
Medical School
Adjunct Assistant Professor
Department of Genetics
Rutgers University
Dr. Paul Matteson
Research Associate
Anna Dulencin
Graduate Fellow
Myka Ababon
Graduate Student
Ji Yeon Choi
Graduate Student
Silky Kamdar
Graduate Student
Bo Li
Graduate Student
Mai Soliman
Graduate Student
Developmental Neurogenetics Laboratory
Dr. James H. Millonig came to CABM in September 1999 from the Rockefeller
University where he was a postdoctoral fellow in the laboratory of Dr. Mary
E. Hatten. His postdoctoral research combined neurobiology and mouse
genetics to characterize and clone the dreher mouse locus. He did his doctoral
research at Princeton University with Dr. Shirley M. Tilghman. Dr. Millonig
is a recipient of the March of Dimes Basil O’Connor Starter Research Award
and grants from the National Institutes of Health, Department of Defense,
National Alliance for Research on Schizophrenia and Depression, Autism
Speaks, National Alliance for Autism Research, N.J. Governor’s Council on
Autism and New Jersey Commission on Spinal Cord Research. He is director
of the RU/Princeton/RWJMS M.D./Ph.D. program.
Autism Spectrum Disorder (ASD)
Individuals diagnosed with ASD exhibit deficiencies in communication and reciprocal
social interactions that are accompanied by rigid or repetitive interests and behaviors.
ASD is considered to be a neurodevelopmental disorder that has a polygenic basis.
Increased risk for the disorder is believed to be due to multiple genes interacting with each
other as well as environmental factors.
Risk for ASD is likely due to both genetic and non-genetic environmental factors, with
epigenetic regulation of genes providing a possible interface between genetic and
environmental factors. Our previous research has focused on the homeobox transcription
factor, ENGRAILED 2 (EN2). The common alleles (underlined) of two intronic EN2 SNPs,
rs1861972 (A/G) and rs1861973 (C/T), are significantly associated with ASD (518
families, P=.00000035). Subsequent association, LD mapping, and re-sequencing
identified the associated rs1861972-rs1861973 as the most suitable candidate to test for
function.
Function was then tested in primary cultures of cerebellar granule cells since endogenous
En2 is expressed at high levels in these cells. Luciferase assays demonstrated that the A-C
haplotype results in an ~250% increase in expression. Additional analysis determined that
both associated alleles are sufficient and necessary for this activator function. EMSAs
revealed that nuclear factors specifically bind the A-C haplotype. An unbiased proteomic
screen identified two transcription factors, Cux1 and NfiB, that bind significantly better to
the A-C haplotype. Knock-down, over-expression, ChIP and EMSA supershift analysis
demonstrated that both transcription factors bind the A-C haplotype at the same time and
are required for activator function. These studies determined that the ASD-associated A-C
haplotype functions as a transcriptional activator.
25

We then investigated if EN2 levels are increased in individuals with autism. Ninety
cerebellar samples were acquired and Taqman QRTPCR measured normalized EN2
mRNA levels. A significant increase was observed in affected individuals with an A-C
haplotype compared to controls (74% increase, P=0.0005). Thus the A-C haplotype is
also correlated with increased EN2 levels in individuals with ASD.
Because ASD is a neurodevelopmental disorder, we generated transgenic mice. EN2 was
replaced with a DsRed, reporter and 25kb of evolutionarily conserved sequence was
used to drive expression of the transgene. 6 A-C and 8 G-T lines were generated.
QRTPCR measured Ds-Red levels for all the lines at 5 developmental time points (E9.5,
E12.5, E17.5, P6 and adult). At all stages the A-C haplotype results in increased
expression (P

We have mapped 5 different vl modifier loci on these different genetic
backgrounds (Modifiers of vacuolated lens, Modvl 1-5, LOD 3.7-5.0)(Matteson
et al., 2008; Korstanje et al., 2008).
To identify the genes in the Modvl 95% CIs that may contribute to these
modifying effects, transcripts co-expressed with Gpr161 during development
were identified by bioinformatic analysis. Ingenuity Pathway Analysis
indicates the Wnt and EMT pathways are over-represented (P

Publications:
Figure 1. A) Luc assays demonstrate 50% increase in A-C haplotype
after 1 day in vitro (left), and ~250% increase after 3 days in vitro in P6
mouse granule cells (right). B) Luc assays demonstrate that a 200bp
fragment encompassing both SNPs is sufficient for activator function
(left), while analysis of the rare haplotypes (A-T and G-C) determined
that both associated alleles are necessary (right) for function. C)
EMSAs with P6 mouse granule cell nuclear extract demonstrate
nuclear factors (arrow) bind better to A-C than G-T haplotype. D)
Knockdown of both Cux1 and NfIB demonstrate that both factors are
required for endogenous EN2 expression in HEK-293T cells (n=3).
Choi J, Matteson PG, Millonig JH. 2011 Cut-like homeobox1 and Nuclear factor I/B
mediate ENGRAILED2 Autism Spectrum Disorder-associated haplotype function. Human
Molecular Genetics. EPub 12/12/11
Choi J, Kamdar S, Rahman T, Matteson PG, Millonig JH. (2011). ENGRAILED 2 (EN2)
genetic and functional analysis. Autism Spectrum Disorders - From Genes to Environment,
edited by
Tim Williams
Deng Q, Andersson E, Hedlund E, Alekseenko Z, Coppola E, Panman L, Millonig JH,
Brunet J-F, Ericson J. Specific and Integrated Roles of Lmx1a, Lmx1b and Phox2a in
Ventral Midbrain. Development 2011 138:3399-408
28

Dr. Arnold Rabson
Director
Child Health Institute of New Jersey
Professor
Department of Molecular Genetics,
Microbiology and Immunology
Department of Pathology and
Laboratory Medicine
Department of Pediatrics
UMDNJ-Robert Wood Johnson
Medical School
Dr. Celine Granier
Postdoctoral Fellow
Dr. Hsin-Ching Lin
Research Scientist
Viral Pathogenesis Laboratory
Dr. Rabson’s laboratory studies the molecular basis of cancer and human
retroviral infections. His recent research activities are focused in two major
areas: 1) the mechanisms responsible for the pathogenesis of retroviral
infections, particularly infection with the human T-cell leukemia virus
(HTLV-1), and 2) the roles of cellular transcriptional regulation in
development and in human cancer.
It is estimated that over 20 million people are infected by HTLV-1, the first
identified human retrovirus, and 2-5% of them are likely to develop a serious
HTLV-1-associated disease. Dr. Rabson is studying the differential mechanisms
by which HTLV-1 causes an aggressive and fatal T cell leukemia/lymphoma
(Adult T-Cell Leukemia, ATL) in some infected individuals and a series of
immunological disorders including a neurological disease of the spinal cord
(HTLV-associated Myelopathy, HAM/TSP) in other infected people. These
disorders occur in only a minority of patients, years after initial infection. This
suggests that there are important interactions between the virus and the host that
determine its pathogenicity. Furthermore, a strong host immune response against
HTLV-1 gene products favors the establishment of latent infection in vivo.
Nonetheless, expression of HTLV-1 gene products, particularly the Tax
transactivator, is required for disease development. The Rabson laboratory has
identified and characterized the mechanisms by which the expression of HTLV-1
can be activated in infected human T-lymphocytes leading ultimately to disease
pathogenesis. They have shown that stimulation through the T-cell receptor can
potently induce HTLV-1 gene expression, including the expression of Tax,
leading to T cell immortalization. They have recently confirmed this in a mouse
model of HTLV-1 latency and gene expression. T cell receptor stimulation of
CD4+ cells in a Tax transgenic mouse leads to increased T cell proliferation and
long-lived survival (>13 months). Thus, activation of latently infected T cells in
HTLV-1-infected individuals may induce expression of Tax, ultimately leading to
proliferation of subsets of cells, based on specific T cell receptor-ligand
interactions. This could explain the progressive polyclonal to oligoclonal
proliferation to ultimately monoclonal proliferation of infected T-cells that
characterizes HTLV-1-associated diseases.
29

Another important feature of HTLV-1-infected T cells expressing the Tax
transactivator is the production of multiple cytokines. The Rabson laboratory has
shown that Tax-expressing CD4+ T cells fail to properly “bias”, i.e. fail to
differentiate into specific T helper subtypes, such as Th1, Th2, Th17 and Treg cells.
Instead, the Tax-expressing cells express cytokines characteristic of all of these
different cells, suggesting a “confused” phenotype that may in turn lead to immune
dysregulation with the potential for both opportunistic infections and autoimmunelike
diseases.
The second major area of study in Dr. Rabson’s laboratory continues to be the
roles of transcriptional regulation in the pathogenesis of human cancer. In
collaboration with Drs. Ruth Steward (Waksman Institute), Dale Schaar (CINJ),
and Hatem Sabaawy (CINJ), the Rabson lab is investigating the functions of
PDCD2, a highly conserved nuclear and cytoplasmic protein, the mutation of
which disrupts hematopoiesis in Drosophila (Drs. Steward and Minakhina). The
Rabson lab has shown high levels of expression of this enigmatic protein in very
early developing embryos and is currently performing mouse genetic experiments
and transcriptional studies to determine its function. Dr. Rabson has also
continued collaborations with Dr. Roger Strair at CINJ on the potential utility of
NF-κB inhibition in leukemia therapy. A clinical trial, examining the effects of
NF-κB inhibition, as part of induction chemotherapy, on the molecular phenotype
of Acute Myeloid Leukemia is in the late stages of development and is a follow-up
to a published trial showing the feasibility of inhibiting NF-κB in patients.
Differentiated mouse embryonic stem cells
30

Publications:
Zheng, X., Cui, X.X., Gao, Z., Zhao, Y., Lin, Y., Shi, W.J., Huang, M.T., Liu, Y.,
Rabson, A., Reddy, B., Yang, C.S., and Conney, A.H. Atorvastatin and celecoxib in
combination inhibits the progression of androgen-dependent LNCaP xenograft prostate
tumors to androgen independence. Cancer Prev. Res. 2010 3:114-24.
Rabson, A.B. Trisomy 21 leukemias: Finding the hits that matter. Oncogene 2010
29:6099-101.
Swaims, A.Y., Khani, F, Zhang, Y., Roberts, A.I., Devadas, S., Shi, Y.*, and Rabson,
A.B.* Immune activation induces immortalization of HTLV-1 LTR-Tax transgenic CD4 +
T-cells. Blood 2010 116(16):2994-3003.
Chen, Y., Rabson, A.B., and Gorski, D.H. MEOX2 regulates nuclear factor-κB activity in
vascular endothelial cells through interactions with p65 and IκBβ. Cardiovasc Res. 2010
87:723-31.
Chen, Y., Banda, M., Speyer, C.L., Smith, J.S., Rabson, A.B. and Gorski, D.H.
Regulation of the expression and activity of the antiangiogenic homeobox gene,
GAX/MEOX2, by ZEB2 and microRNA-221. Mol. Cell Biol. 2010 30:3902-13.
Fu, J., Qu, Z., Yan, P., Ishikawa, C., Mori, N., Aqeilan, R.I., Rabson, A.B. and Xiao, G.
The tumor suppressor gene WWOX links the canonical and non-canonical NF-κB
pathways in HTLV-1 Tax-mediated tumorigenesis. Blood 2011 117:1652-61.
De Lorenzo, M.S., Baljinnyam, E., Vatner, DE, Abarzua, P., Vatner S.F., and Rabson,
A.B. Caloric Restriction reduces mammary tumor growth and metastasis. Carcinogenesis
2011 32:1381-7.
31

Dr. Aaron J. Shatkin
Director of CABM
Professor
Department of Molecular
Genetics, Microbiology and
Immunology
UMDNJ-Robert Wood Johnson
Medical School
University Professor
of Molecular Biology
Rutgers University
Dr. Weihua Qiu
Research Associate
Molecular Virology Laboratory
Dr. Aaron J. Shatkin, a member of the National Academy of Sciences, has held
research positions at the National Institutes of Health, The Salk Institute, and the
Roche Institute of Molecular Biology. He has taught at Georgetown University
Medical School, Cold Spring Harbor Laboratory, The Rockefeller University,
UMDNJ-Newark Medical School, University of Puerto Rico, Princeton University and
other institutions. Shatkin was editor of the Journal of Virology from 1973-1977,
founding editor-in-chief of Molecular and Cellular Biology from 1980-1990 and is
currently editor of Advances in Virus Research. He has also served on the advisory
boards of a number of organizations. In 1989 he was recognized by New Jersey
Monthly magazine with a New Jersey Pride Award for his contributions to the State’s
economic development. In 1991 the State of N.J. awarded Shatkin the Thomas Alva
Edison Science Award, and he was selected as one of New Jersey’s top ten scientists
by N.J. Business magazine. He was elected Fellow of the American Academy of Arts
and Sciences in 1997 and the American Association for the Advancement of Science in
1999. Shatkin received the 1977 National Academy of Sciences Molecular Biology
Award, the 2003 Association of American Medical Colleges Award for Distinguished
Research in the Biomedical Sciences, the Edward J. Ill Outstanding Medical Research
Scientist Award and from Robert Wood Johnson Medical School the R.W. Schlesinger
Basic Science Mentoring Award in 2009 and the Honorary Alumnus Award in 2011.
mRNA 5'-capping
One of the earliest steps in the cascade of events necessary for mRNA formation and
function is the addition of a 5'-terminal m7GpppN "cap" to nascent RNA Polymerase
II transcripts. This structural hallmark is present on most eukaryotic cellular as well
as viral mR2NAs and is essential for viability. The presence of a cap enhances several
downstream events in cellular gene expression including RNA stability, splicing of
pre-mRNAs in the nucleus and initiation of protein synthesis in the cytoplasm. These
important effects have fostered many studies that defined the enzymatic mechanisms
of capping. We have cloned and sequenced the mouse and human capping enzymes
(CEs, ~98% identical) and mapped the human protein to 6q16, a region implicated in
tumor suppression. The 597-amino acid, 68kD mammalian polypeptides consist of
two functional domains --N-terminal RNA 5' triphosphatase (RTase) and C-terminal
guanylyltransferase (GTase). Mutational, biochemical and genetic analyses
demonstrated that the GTase active site is a lysine in the sequence 294 Lys-X-Asp-
Gly 297, one of several highly conserved motifs characteristic of a
nucleotidyltransferase superfamily of proteins that includes other cellular and viral
CEs. A haploid deletion strain of S. cerevisiae missing the guanylyltransferase
enzyme was complemented for growth by the mouse wild type cDNA clone despite
only ~25% sequence identity. However, a mouse clone containing alanine in place of
lysine in the KXDG motif did not complement. The results demonstrated the
functional conservation of CEs from yeast to mammals.
We found that mammalian capping enzyme binds via its GTase region to the
hyperphosphorylated C-terminal domain (CTD) of the largest subunit of RNA
32

polymerase II, facilitating the selective capping of pre-mRNAs. Similarly, the full
length and C-terminal domain of CE were
localized to the nucleus in transfected cells and also bound poly (U) in vitro,
suggesting that the C-terminal domain of CE can bind nascent transcript 5' termini
for capping directly. The CE N-terminal RNA 5'-triphosphatase (amino acids 1-
237) contains the sequence VHCTHGFNRTG which corresponds to the
conserved active-site motif in protein tyrosine phosphatases (PTPs). Mutational
analyses identified the Cys and Arg residues in this motif and an upstream
aspartate as required for triphosphatase activity. These and other results indicate
that removal of phosphate from RNA 5' ends and from modified tyrosine residues
in proteins occurs by a similar mechanism.
We also cloned and characterized the third essential enzyme for mRNA 5'capping,
human mRNA (guanine-7-) methyltransferase (MTase). It mapped to
18p11.22-p11.23, a region encoding brain transcripts that have been suggested as
positional candidates for susceptibility to bipolar disorder. Sequence alignment of
the 476-amino acid MTase protein within the corresponding yeast, C. elegans and
Drosophila enzymes demonstrated several required, conserved motifs including
one for binding S-adenosylmethionine. MTase bound to human CE and also
formed ternary complexes with the elongating form of RNA polymerase II. To
identify other proteins that interact with CEs, we used a yeast two-hybrid system
to screen a human fetal brain cDNA library with full length human CE and
isolated transcription elongation factor SPT5. It bound to CE and stimulated RNA
guanylylation but not the triphosphatase step of capping. Purified,
hyperphosphorylated CTD similarly stimulated RNA guanylylation in vitro, but
the effects of P-CTD and SPT5 were not additive, suggesting a common or
overlapping binding site on CE. By using two-hybrid, GST-pulldown and coimmunoprecipitation
approaches, we also found that MTase interacts with the
nuclear transporter, importin-α (Impα). MTase selectively bound and methylated
RNA containing 5'-terminal GpppG, and both activities were stimulated severalfold
by Impα. MTase/RNA/Impα complexes were dissociated by addition of
Impβ which also blocked Impα stimulation of RNA cap methylation. RanGTP but
not RanGDP prevented these effects of Impβ. The results suggested that, in
addition to a linkage between capping and transcription, mRNA biogenesis and
nucleocytoplasmic transport are functionally connected.
A general model of capping: RNA Polymerase II containing hypophosphorylated
CTD initiates transcription, produces 20-25 nucleotide 5'-triphosphorylated
transcripts and pauses with SPT5 bound as part of a large transcription complex.
Serine 5 residues in the heptad repeats that comprise the CTD and SPT5 are
phosphorylated by transcription factor TFIIH, changing the CTD conformation to
allow CE binding. The 5’ end of the ~25 nucleotide nascent transcript is capped
as it becomes exposed at the surface of the polymerase complex, stimulated by
SPT5 as well as by the hyperphosphorylated CTD (P-CTD). MTase binds to CE
(mammals) or to P-CTD (yeast). Impα stimulates MTase binding and N7 guanine
methylation. After phosphorylation of SPT5 and RNA Polymerase II on CTD
33

serine 2 residues by pTEF-b, polymerase bound complexes of factor DSIF and
negative elongation factor (NELF) dissociate and processive elongation ensues. In
an effort to decipher how the critically important human GTase works, we
determined that the minimum enzymatically active domain resides in CE residues
229-567. The
expressed and purified active fragment was crystallized and the structure
determined by X-ray crystallography. Seven related conformational states were
obtained in the crystal. Position differences of the oligonucleotide/oligosaccharide
(OB) binding fold lid domain over the conserved GTP binding site in the seven
structures provided snapshots of the opening and closing of the active site cleft
via a swivel motion. While the GTP binding site is structurally and evolutionarily
conserved, the overall GTase mechanism in mammalian and yeast systems differs
somewhat. Experiments are underway to crystallize complexes of human GTase
with CTD and RNA as well as GTP. Protein engineering is being applied in an
effort to crystallize the full length human CE.
Publications:
Structure of the GTase domain of
human CE consisting of the base,
hinge and flexible lid. The
predicted single-stranded RNA
binding track, marked by sulfate
ions incorporated from the
crystallization solution, lies in a
positively charged cleft below the
lid and close to modeled GMP with
phosphoamide linkage to K294 of
the conserved KXDG active site
sequence near the center of the
structure. Also shown is the
predicted CTD binding site
modeled based on the structure of a
mouse homolog complex (Ghosh et
al. 2011 Mol. Cell 43: 299-310).
Blue to red correlates with
increasing flexibility.
Chu, C., Das, K., Tyminski, J.R., Bauman, J.D., Guan, R., Qiu, W., Montelione,
G.T., Arnold, E., and Shatkin, A.J. Structure of the guanylyltransferase domain of
human mRNA capping enzyme. Proc. Natl. Acad. Sci. USA. 2011 108:10104-8.
Topisirovic, I., Svitkin, Y., Sonenberg, N., and Shatkin, A.J. Cap and cap-binding
proteins in the control of gene expression. Wiley Interdiscip Rev RNA. 2011
2(2):277-98.
34

Dr. Mengqing Xiang
CABM Resident Faculty Member
Professor
Department of Pediatrics
UMDNJ-Robert Wood Johnson
Medical School
Dr. Kangxin Jin
Postdoctoral Associate
Dr. Shengguo Li
Research Teaching Spec.
Dr. Huijun Luo
Research Teaching Spec.
Dr. Kamana Misra
Research Teaching Spec.
Min Zou
Graduate Student
Molecular Neurodevelopment Laboratory
Dr. Mengqing Xiang came to CABM in September 1996 from the Johns
Hopkins University School of Medicine where he conducted postdoctoral
studies with Dr. Jeremy Nathans. He earned his Ph.D. at the University of
Texas M.D. Anderson Cancer Center and has received a number of honors
including a China-U.S. Government Graduate Study Fellowship, a Howard
Hughes Medical Institute Postdoctoral Fellowship, a Basil O’Connor Starter
Scholar Research Award and a Sinsheimer Scholar Award. In 2003 he
received the Award in Auditory Science from the National Organization for
Hearing Research Foundation. His work is currently supported by NIH.
Our laboratory investigates the molecular mechanisms that govern the determination
and differentiation of the highly specialized sensory cells and neurons. We employ a
variety of molecular genetic approaches to identify and study transcription and other
regulatory factors that are required for programming development of the retina, inner
ear, spinal cord, and other CNS areas. A major focus of our work is to develop
animal models to study the roles of these regulatory genes during normal
sensorineural development, as well as to elucidate how mutations in these genes
cause sensorineural disorders such as blindness and deafness.
Generation of a transgenic line for studying V2 neuronal lineages and functions
in the spinal cord. During spinal neurogenesis, the p2 progenitor domain generates
at least three subclasses of interneurons named V2a, V2b and V2c, which are crucial
components of the locomotor central pattern generator. We have previously shown
that the winged-helix/forkhead transcription factor Foxn4 is expressed in a subset of
p2 progenitors and required for specifying V2b interneurons. To determine the cell
lineages derived from Foxn4-expressing progenitors, we generated a Foxn4-Cre
BAC transgenic mouse line that drives Cre recombinase expression, mimicking
endogenous Foxn4 expression pattern in the developing spinal cord. We used this
transgenic line to map neuronal lineages derived from Foxn4-expressing progenitors
and found that they gave rise to all neurons of the V2a, V2b as well as the newly
identified V2c lineages. These data suggest that Foxn4 may be transiently expressed
by all p2 progenitors and that the Foxn4-Cre line may serve as a useful genetic tool
not only for lineage analysis but also for functional studies of genes and neurons
involved in locomotion.
35

Diverse developmental roles of Foxn4. In our previous studies, we have shown that
Foxn4 is transiently expressed in a subset of progenitors during retinogenesis and
spinal neurogenesis. Targeted inactivation and gain-of-function analyses have
revealed an essential function of Foxn4 in the generation of amacrine and horizontal
cells during retinal development as well as in specifying the V2b interneurons during
spinal cord development. In collaboration with Drs. Stavros Malas (University of
Cyprus) and William Richardson (University College London), we have now used
genetic fate mapping and loss-of-function analysis to show that the transcription
factor Sox1 is expressed in and required for a third type of p2-derived interneuron,
which we named V2c. These are close relatives of V2b interneurons, and, in the
absence of Sox1, they switch to the V2b fate. The absence of Foxn4 results in a
complete loss of Sox1-expressing V2c neurons, indicating that Foxn4 is necessary for
specifying not only V2b but also V2c interneuron subtypes. In another collaboration
with Dr. Jeffrey Goldberg (University of Miami, Miller School of Medicine), we
observed a developmental delay in the distribution of RGC (retinal ganglion cell)
projections to the superior colliculus. Moreover, RGC axons failed to penetrate into
the retinorecipient layers in Foxn4 mutant mice. Foxn4 was not expressed by RGCs
and was undetectable in the superior colliculus itself. Thus, Foxn4 may be indirectly
required for RGC distal axon patterning. Aside from its neural expression, we have
also shown that during murine lung development Foxn4 is expressed in proximal
airways by a subpopulation of postmitotic epithelial cells which are distinct from
basal and ciliated cells. Foxn4 inactivation causes dilated alveoli, thinned alveolar
walls and reduced septa in the distal lung but no overt gross alterations in proximal
airways, suggesting that Foxn4 may have a non-cell-autonomous role critical for
alveologenesis during lung development. Together, our data suggest that Foxn4 may
play multiple cell-autonomous and non-cell-autonomous roles during epithelial cell
development.
Brn3a regulates dorsal root ganglion sensory neuron specification and axonal
projection into the spinal cord. The sensory neurons of the dorsal root ganglia
(DRG) must project accurately to their central targets to convey proprioceptive,
nociceptive and mechanoreceptive information to the spinal cord. How these different
sensory modalities and central connectivities are specified and coordinated still
remains unclear. Given the expression of the POU homeodomain transcription factors
Brn3a and Brn3b in DRG and spinal cord sensory neurons, we analyzed subtype
specification of DRG and spinal cord sensory neurons as well as DRG central
projections in Brn3a and Brn3b single and double mutant mice. Inactivation of either
or both genes causes no gross abnormalities in early spinal cord neurogenesis;
however, in Brn3a single and Brn3a;Brn3b double mutant mice, sensory afferent
axons from the DRG fail to form normal trajectories in the spinal cord. The TrkA +
cutaneous nociceptive afferents stay outside the dorsal horn and fail to extend into the
spinal cord, while the projections of TrkC + proprioceptive afferents into the ventral
horn are also impaired. Moreover, Brn3a mutant DRGs are defective in sensory
neuron specification, as marked by the excessive generation of TrkB + and TrkC +
neurons as well as TrkA + /TrkB + and TrkA + /TrkC + double positive cells at early
embryonic stages. At later stages in the mutant, TrkB + , TrkC + and parvalbumin +
36

neurons diminish while there is a significant increase of GRP + and c-ret + neurons.
In addition, Brn3a mutant DRGs display a dramatic down-regulation of Runx1
expression, suggesting that the regulation of DRG sensory neuron specification by
Brn3a is mediated in part by Runx1. Our data together demonstrate a critical role for
Brn3a in generating DRG sensory neuron diversity and regulating sensory afferent
projections to the central targets.
Altered TrkA + and TrkC + central afferent projection patterns in Brn3a mutant
spinal cords at E12.5. The bundles of TrkA + and TrkC + afferent fibers are detected
by immunostaining from lateral to medial regions of the dorsal horn edge in Brn3a +/-
spinal cords at E12.5. In Brn3a -/- spinal cords, TrkA + and TrkC + fibers are narrowly
located in a much smaller region, and extensively overlap with each other.
Publications:
Jin, K., Jiang, H., Mo, Z., and Xiang, M. Early B-cell factors are required for specifying
multiple retinal cell types and subtypes from postmitotic precursors. J. Neurosci. 2010
30:11902-11916.
Panayi, H., Orford, M., Panayiotou, E., Genethliou, N., Mean, R., Lapathitis, G., Li, S.,
Xiang, M., Kessaris, N., Richardson, W., and Malas, S. SOX1 is required for the
specification of a novel p2-derived interneuron subtype in the mouse ventral spinal cord. J.
Neurosci. 2010 30:12274-12280.
Li, S., Misra, K., and Xiang, M. A Cre transgenic line for studying V2 neuronal lineages
and functions in the spinal cord. Genesis 2010 48:667–672.
Li, S. and Xiang, M. Foxn4 influences alveologenesis during lung development. Dev.
Dyn. 2011 240:1512-1517.
37

Kunzevitzky, N. J., Almeida, M. V., Duan, Y., Li, S., Xiang, M., and Goldberg, J. L.
Foxn4 is required for retinal ganglion cell distal axon patterning. Mol. Cell. Neurosci.
2011 46:731-741.
Jin, K. and Xiang, M. Ebf1 deficiency causes increase of Müller cells in the retina and
abnormal topographic projection at the optic chiasm. Biochem. Biophys. Res. Commun.
2011 414:539-544.
Xiang, M., Jiang, H., Jin, K., and Qiu, F. Molecular control of retinal ganglion cell
specification and differentiation. In Glaucoma - Basic and Clinical Concepts (R. Shimon,
ed.),2011 pp. 65-84, InTech, Rijeka.
Jin, K. and Xiang, M. In vitro explant culture and related protocols for the study of
mouse retinal development. In Methods in Molecular Biology. Springer, New York, NY.
2011 (in press).
Pöschl, J., Lorenz, A., von Bueren, A.O., Peraud, A., Li, S., Tonn, J.-C., Herms, J.,
Xiang, M., Rutkowski, S., Kretzschmar, H.A., and Schüller, U. Expression of BARHL1
in medulloblastoma is associated with prolonged survival in mice and humans.
Oncogene 2011(in press).
Ding, Q., Joshi. P. S., Xie, Z.-H., Xiang, M., and Gan, L. BARHL2 regulates the
ipsilateral/contralateral subtype divergence in postmitotic dI1 neurons of the developing
spinal cord. Proc. Natl. Acad. Sci. USA 2011 (in press).
38

Laboratory Faculty Director
Structural Biology
Protein Engineering Stephen Anderson 40
Biomolecular Crystallography Edward Arnold 42
Structural Biology and Bioinformatics Helen Berman 47
Structural Microbiology Joseph Marcotrigiano 51
Structural Bioinformatics Gaetano Montelione 54
Protein Design and Evolution Vikas Nanda 62
Protein Crystallography Ann Stock 65
39

Dr. Stephen Anderson
CABM Resident Faculty Member
Associate Professor
Department of Molecular Biology
and Biochemistry
Rutgers University
Yi-Wen Chiang
Lab Researcher
Protein Engineering Laboratory
Dr. Stephen Anderson conducted his postdoctoral research under Nobel
laureate Dr. Frederick Sanger at the MRC Laboratory of Molecular Biology
in Cambridge, England. That project involved the sequencing of human and
bovine mitochondrial genomes. He went on to a position at the Californiabased
biotechnology start-up company Genentech. Anderson has held
research or teaching positions at Harvard University, the MRC Laboratory
of Molecular Biology, Genentech, Inc., University of California, San
Francisco, and Rutgers University. While at Genentech he was responsible
for all specialty chemical projects and second generation tissue plasminogen
activator research.
In 2011 the lab embarked on a three-year $2.8M NIH-funded project to express a
representative set of antigens derived from human transcription factors. The
collaborators and co-PIs on this project are Profs. Gaetano T. Montelione and Joseph
Marcotrigiano, both of CABM and Rutgers, and Prof. Cheryl Arrowsmith of the
Ontario Cancer Research Center and the University of Toronto. Late in 2011, NIH
identified two “affinity capture reagent” consortia for our antigen production group
to partner with: one, headed by Prof. Anthony Kossiakoff at the University of
Chicago and including groups at UCSF and University of Toronto, that will be
making Fabs and antibodies using high throughput phage display technology; and
one based at Johns Hopkins University, headed by Prof. Jef Boike, that has invented
a low-cost, high throughput method of isolating and screening traditional
monoclonal antibodies.
NIH’s overarching goal is to eventually produce renewable cognate affinity capture
reagents (including antibodies) directed against every human protein, an effort that
has been unofficially dubbed the “Human Anti-Proteome Project”. NIH wants to
make such reagents available to the research community as powerful tools for
studying human biology. A description of this initiative is at
http://commonfund.nih.gov/proteincapture/index.aspx. The effort that we are
undertaking, namely producing human transcription factor antigens for affinity
capture reagent production, is a pilot project designed to kick-start this overall effort.
The first envisioned application for the anti-TF antibodies is to enable chromatin
immunoprecipitation (ChIP) studies aimed at obtaining a complete map of potential
transcription start sites in the human genome – much of this work is being carried
out by the NIH-funded ENCODE Consortium.
40

Human transcription factors are typically complex, multidomain proteins, and in
terms of numbers of unique genes represent roughly 10% of the entire human
proteome. Our goal is to express native, folded, individual domains from these
different transcription factors with the hope that optimal specificity and affinity may
be obtained by raising affinity capture reagents agains 3D epitopes. In the first year
the Rutgers group has designed single-domain expression constructs using advanced
“domain parsing” software developed by Dr. Janet Huang and Prof. Gaetano T.
Montelione (see figure below). Together with Dr. Thomas Acton and Prof.
Montelione, we have also developed a new series of high-efficiency E. coli vectors
using “transcript optimized expression-enhancement technology” (“TOEET” – patent
applied for). These vectors enable unprecedented levels of expression and solubility
to be achieved. In 2011 the group cloned domains from nearly 1400 separate human
transcription factors in >2700 distinct constructs and expression-tested approximately
80% of these at small scale. We are now moving on to scale-up and production of
multi-milligram quantities of purified antigen for our affinity capture reagent partners.
In December, 2011, we shipped our first batch of purified antigens.
Fig. 1. Example of a portion of the output of the DisMeta server and how it can
be used to analyze transcription factor sequences for structural information.
Shown schematically is a portion of the sequence of a human transiption factor, IF –
16 (γ-interferon-inducible protein 16), analyzed by the DisMeta server.
In this segment of the sequence the server predicts two regions that
appear to have a complex, folded, tertiary structure separated by a
region of polypeptide chain that is predicted to be relatively disordered.
Three-dimentional structures for domains represented by the two
ordered regions shown were determined by the NESG. The leftmost
structure (PDB ID 2oq0) is a HIN-200/IF120x domain (InterPro ID
IPR004021), and the rightmost structure (PDB ID 3b6y) is a pyrin
domain (InterPro ID IPR004020) (Liao et al, unpulished). This example
illustrates how the DisMeta server can be used to scan TF protein
sequences to find the regions encoding domains that are likely to have
3D epitopes.
41

Dr. Eddy Arnold
CABM Resident Faculty Member
Board of Governors Professor
Department of Chemistry and
Chemical Biology
Rutgers University
Adjunct Professor
Department of Molecular Genetics
Microbiology and Immunology
UMDNJ-RWJMS
Dr. Kalyan Das
Research Professor
Dr. Joseph Bauman
Assistant Research Professor
Dr. Daniel Himmel
Research Associate
Dr. Sergio Martinez
Research Associate
Dr. Matthew Miller
Research Associate
Dr. Steven Tuske
Research Associate
Dr. Mary Ho
Postdoctoral Associate
Dr. William Ho
Postdoctoral Associate
Biomolecular Crystallography Laboratory
Dr. Eddy Arnold obtained his Ph.D. in organic chemistry with Professor Jon Clardy
at Cornell University in 1982. From 1982 to 1987, he was a postdoctoral researcher
with Professor Michael G. Rossmann at Purdue University and was a central member
of the team that solved the structure of a human common cold virus by X-ray
crystallography. Among the awards and fellowships Arnold has received are a
National Science Foundation Predoctoral Fellowship, Damon Runyon–Walter
Winchell and National Institutes of Health Postdoctoral Fellowships, an Alfred P.
Sloan Research Fellowship, a Johnson and Johnson Focused Giving Award, and a
Board of Trustees Award for Excellence in Research at Rutgers. He received an NIH
MERIT Award in 1999 and a second consecutive one again in 2009. He was elected a
Fellow of the American Association for the Advancement of Science in 2001 and a
Fellow of the American Academy of Microbiology in 2006. In 2010 Dr. Arnold was
named a Board of Governors Professor at Rutgers University. His laboratory is
supported by grants from NIH and industrial collaborators, and by research
fellowships. Dr. Arnold is involved in numerous international collaborations aimed
at developing drugs for treatment and prevention of global infectious diseases,
including HIV/AIDS, flu, and tuberculosis. His team has contributed to the discovery
of two drugs used to treat HIV infection.
Many of the underlying biological and chemical processes of life are being detailed at the
molecular level, providing unprecedented opportunities for the development of novel
approaches to the treatment, cure and prevention of human disease. A broad base of
advances in chemistry, biology, and medicine has led to an exciting era in which
knowledge of the intricate structure of life’s machinery can help to accelerate the
development of new small molecule drugs and biomaterials such as engineered viral
vaccines. Drs. Eddy Arnold and his colleagues are working to understand molecular
mechanisms of drug resistance and apply structure-based drug design for the treatment of
serious human diseases. In pursuit of these goals, the laboratory uses research tools from
diverse fields, including X-ray crystallography, molecular biology, virology, protein
biochemistry, and macromolecular engineering. Eddy’s team of very experienced and
gifted coworkers, many of whom have been in the lab 10 years or longer, is the driving
force behind the continuing progress.
Since its establishment at CABM in 1987, our laboratory has studied the structure and
function of reverse transcriptase (RT), an essential component of the AIDS virus and the
target of most widely used anti-AIDS drugs. Using the powerful techniques of X-ray
crystallography, we have solved the three-dimensional structures of HIV-1 RT in complex
with a variety of antiviral drugs and model segments of the HIV genome. These studies
have revealed the workings of an intricate and fascinating biological machine in
42

atomic detail and have yielded numerous novel insights into polymerase structure-function
relationships, detailed mechanisms of drug inhibition and resistance, and structure-based
design of RT inhibitors. The team has solved a variety of crystal structures representing
multiple functional states of HIV-1 RT. These structures include HIV-1 RT in complex with a
double-stranded DNA template-primer, HIV-1 RT complexes with RNA:DNA templateprimers,
structures of RT with AZTMP-terminated primer representing pre-translocation and
post-translocation complexes, and ternary complexes of wild-type and drug-resistant RT with
DNA, and AZT-triphosphate/tenofovir-diphosphate. We have also determined the structures
of numerous non-nucleoside inhibitors with wild-type and drug resistant HIV-1 RT, and the
structural information was used in the design of two recently approved non-nucleoside drugs.
Also, we have obtained structures of RT:RNase H inhibitor and RT:DNA:AZTppppA (an
ATP-mediated AZT excision product) complexes (Tu et al., 2010).
Drug development against and structural studies of a molecule as complex as HIV RT require
immense and highly coordinated resources. The Arnold group has been fortunate to have
successful long-term collaborations with the groups of Stephen Hughes (NIH NCI-Frederick),
Roger Jones (Rutgers), Michael Parniak (U. of Pittsburgh), and Ronald Levy (Rutgers). The
group also benefits from generous access to synchrotron X-radiation sources (CHESS, APS,
and BNLS). Hughes and his coworkers have contributed expertise in protein engineering,
production, and biochemistry at every stage of the RT project since its inception.
Through collaboration with the late Dr. Paul Janssen we participated in a structure-based drug
design effort that resulted in the discovery and development of non-nucleoside inhibitors
(diarylpyrimidine, or DAPY analogs) with high potency against all known drug-resistant
variants of HIV-1 RT. Crystallographic work from the Arnold and Hughes laboratories
allowed precise visualization of how potential anti-HIV drug candidates latch onto RT, their
molecular target. Janssen and colleagues at the Center for Molecular Design successfully
used this structural information to guide the design and synthesis of new molecules with
improved potency against wild-type and drug-resistant HIV-1 strains. Scientists at Tibotec, a
subsidiary of Johnson & Johnson, tested the compounds for antiviral activity against wild-type
and resistant HIV-1, and have led the clinical trials.
The DAPY compounds are simple, inexpensive to make and have near ideal pharmacological
properties. Etravirine (TMC125/Intelence) was approved for treatment of HIV infection by
the FDA in 2008, and rilpivirine (TMC278) was approved as Edurant in May 2011. In what
may be unprecedented for a new best-in-class drug, Johnson & Johnson is permitting
rilpivirine to be available in generic form immediately in developing nations; this will make
the drug available to millions of people. The prototypical DAPY compound,
TMC120/dapivirine, is now being developed as a microbicide for blocking sexual
transmission of HIV-1. A broader outcome of this study is a drug design concept for
overcoming drug resistance; the strategic flexibility that permits the DAPY compounds to
“wiggle” and “jiggle” in a binding pocket to accommodate mutations apparently accounts for
their potency against a wide range of drug-resistant variants. Through a systematic protein
engineering effort we obtained high-resolution crystals of HIV-1 RT and demonstrated that
strategic flexibility of rilpivirine was responsible for its resilience against drug-resistant RT
variants. Recent efforts include using the high-
Dr. Ramaswamy
S. Vijayan
Postdoctoral Associate
Dr. Angela
McKoy
Postdoctoral Fellow
Dabyaben Patel
Graduate Student
Joseph Thomas
Eck
Graduate Fellow
Arthur Clark
Laboratory Researcher
43

esolution HIV-1 RT crystals for drug-like fragment screening. A number of novel
allosteric sites for inhibition of both polymerase and RNase H activity have been
identified from the fragment screening effort.
In addition to working to study HIV-1 RT and to develop chemotherapeutic agents, the
laboratory aims to gain greater insights into the basic molecular processes of living systems.
Other projects currently being pursued in the lab include structural studies of: 1) bacterial
RNA polymerase holoenzyme complexes with inhibitors and substrates in collaboration
with Dr. Richard Ebright at Rutgers University; 2) the human mRNA capping enzyme and
its associated factors with Dr. Aaron Shatkin at CABM, and 3) influenza virus proteins
including the polymerase from 2009 H1N1 pandemic strain.
Figure from Das et al., 2012 showing nevirapine bound in the presence of DNA. The study
confirms that nonnucleoside drugs displace the primer terminus from the polymerase active
site. This structure, which had been elusive for decades, represents one of the key missing
pieces in the HIV-1 RT structure/function puzzle.
44

Figure from Das et al., 2011 showing how the nonnucleoside inhibitor TSAO has a
shape that resembles a dragon when bound to HIV-1 RT.
Publications:
Das, K. J.M. Aramini, L.-C. Ma, R.M. Krug, and E. Arnold. Recent advances in structural
studies of influenza A proteins: insights into antiviral drug targets. Nat. Struct. Mol. Biol.
2010 17:530-538.
Lapelosa, M., E. Gallicchio, G.F. Arnold, E. Arnold, and R.M. Levy. Antigenic
characteristics of rhinovirus chimeras designed in silico for enhanced presentation of HIV-
1 gp41 epitopes. J. Mol. Biol. 2010 397:752-766.
Tu, X., K. Das, Q. Han, J.D. Bauman, A.D. Clark, Jr., X. Hou, Y.V. Frenkel, B.L. Gaffney,
R.A. Jones, P.L. Boyer, S.H. Hughes, S.G. Sarafianos, and E. Arnold. Structural basis of
HIV-1 resistance to AZT. Nat. Struct. Mol. Biol. 2010 17:1202-1209. (This publication
was the focus of a commentary by Scott, W.A. 2011. Structures of Reverse Transcriptase
Pre- and Post-Excision Complexes Shed New Light on HIV-1 AZT Resistance. Viruses
3:20-25.)
Das, K., J.D. Bauman, A.S. Rim, C. Dharia, A.D. Clark, Jr., M.J. Camarasa, J. Balzarini,
and E. Arnold. Crystal structure of tert-butyldimethylsilyl-spiroaminooxathioledioxidethymine
(TSAO-T) in complex with HIV-1 reverse transcriptase (RT) redefines the elastic
limits of the non-nucleoside inhibitor-binding pocket. J. Med. Chem. 2011 54:2727-2737.
Chu, C., Das, K., J.R. Tyminski, J.D. Bauman, R. Guan, W. Qiu, G.T. Montelione, E.
Arnold, and A.J. Shatkin. Structure of the guanylyltransferase domain of human capping
enzyme. Proc. Natl. Acad. Sci. 2011 108:10104-10108.
45

Chung, S., D.M. Himmel, J.K. Jiang, K. Wojtak, J.D. Bauman, J.W. Rausch, J.A. Wilson,
J.A. Beutler, C.J. Thomas, E. Arnold, and S.F. Le Grice. Synthesis, activity, and structural
analysis of novel a-hydroxytropolone inhibitors of human immunodeficiency virus reverse
transcriptase-associated ribonuclease H. J. Med. Chem. 2011 54:4462-4473.
Felts AK, K. Labarge K, J.D. Bauman, D.V. Patel, D.M. Himmel, E. Arnold, M.A. Parniak,
R.M. Levy. Identification of alternative binding sites for inhibitors of HIV-1 ribonuclease H
through comparative analysis of virtual enrichment studies. J Chem Inf Model. 2011
51:1986-1998.
Arnold, E., D.M. Himmel, and M.G. Rossmann. Co-editors of "International Tables for X-
Ray Crystallography, Volume F: Crystallography of Biological Macromolecules, Second
Edition.” 2011 Kluwer Academic Publisher, Dordrecht, xxix + 886 pages.
Arnold, E., D.M. Himmel, and M.G. Rossmann. Overview of this volume. In "International
Tables for X-Ray Crystallography, Volume F: Crystallography of Biological
Macromolecules, Second Edition" E. Arnold, D.M. Himmel, and M.G. Rossmann, editors.
2011 Kluwer Academic Publisher, Dordrecht.
Arnold, E. Gazing into the crystal ball: perspectives for the future. In "International Tables
for X-Ray Crystallography, Volume F: Crystallography of Biological Macromolecules,
Second Edition" E. Arnold, D.M. Himmel, and M.G. Rossmann, editors. 2011 Kluwer
Academic Publisher, Dordrecht.
Arnold, E. and M. G. Rossmann. Noncrystallographic symmetry averaging of electron
density for molecular-replacement phase refinement and extension. In "International Tables
for X-Ray Crystallography, Volume F: Crystallography of Biological Macromolecules,
Second Edition" E. Arnold, D.M. Himmel, and M.G. Rossmann, editors. 2011 Kluwer
Academic Publisher, Dordrecht.
Bauman, J.D., D. Patel, E. Arnold. Fragment screening and HIV therapeutics. Top. Curr.
Chem. Oct 5. 2011 [Epub ahead of print]
Das, K., S.E. Martinez, J.D. Bauman, E. Arnold. HIV 1 reverse transcriptase complex with
DNA and nevirapine reveals nonnucleoside inhibition mechanism. Nat. Struct. Mol. Biol.,
2012 in press.
46

Dr. Helen M. Berman
Board of Governors Professor
Department of Chemistry and
Chemical Biology
Interim Director
Biological, Mathematical, and
Physical Sciences Interfaces
(BioMaPS),
Director
RCSB Protein Data Bank
Director
PSI Structural Biology
Knowledgebase
Rutgers University
Dr. Martha Quesada
Research Professor
Dr. John Westbrook
Research Professor
Dr. Feng Zukang
Research Professor
Dr. Catherine Lawson
Associate Research Professor
Dr. Shuchismita Dutta
Assistant Research Professor
Dr. Monica Sekharan
Assistant Research Professor
Dr. Jasmine Young
Assistant Research Professor
Structural Biology and Bioinformatics
Dr. Berman's research area is structural biology and bioinformatics, with a
special focus on protein-nucleic acid interactions. She is the founder of the
Nucleic Acid Database, a repository of information about the structures of
nucleic acid-containing molecules; and is the co-founder and Director of the
Protein Data Bank, the international repository of the structures of biological
macromolecules. Professor Berman also leads the Protein Structure Initiative
Structural Biology Knowledgebase. She is a Fellow of the American
Association for the Advancement of Science and of the Biophysical Society,
from which she received the Distinguished Service Award in 2000. A past
president of the American Crystallographic Association, she is a recipient of
the Buerger Award (2006) and a member of the inaugural class of ACA
Fellows (2011). Dr. Berman received her A.B. in 1964 from Barnard College
and a Ph.D. in 1967 from the University of Pittsburgh. She received the
Department of Chemistry Alumni Award from the University of Pittsburgh in
2010.
The Protein Data Bank
The Research Collaboratory for Structural Bioinformatics (RCSB) Protein Data Bank
(PDB) supports scientific research and education worldwide by providing an essential
resource of information about biomolecular structures.
The PDB archive is the single repository of information about the 3D structures of
large biological molecules, primarily proteins and nucleic acids. Scientists from
around the world submit their data about their experiments to the PDB, which is then
processed and made freely available in the PDB archive. The RCSB PDB, which is
based at Rutgers and the University of California, San Diego, manages the PDB
archive as a member of the Worldwide PDB (wwPDB).
The wwPDB organization (www.wwpdb.org) was formed to ensure that the PDB
archive is and will be freely and publicly available to the global community. The
wwPDB members (RCSB PDB, Protein Data Bank in Europe (PDBe), Protein Data
Bank Japan (PDBj), and the BioMagResBank (BMRB)) host deposition, processing,
and distribution centers for PDB data and collaborate on a variety of projects and
outreach efforts. As 'archive keeper' for the wwPDB, the RCSB PDB maintains the
central repository of the PDB archive.
The central activity of the wwPDB is the collection, validation, archiving and
distribution of high quality structural data to the scientific community on a timely
basis. The systems developed by the RCSB PDB are reliable and stable to meet the
challenges of high data rates and complex structures. As of November 8, 2011, the
PDB archive contains more than 77,000 entries.
47

In 2011, the wwPDB commemorated the PDB’s 40 th anniversary with a special
symposium. The meeting was attended by 19 distinguished speakers,
approximately 250 participants, and 93 poster presentations. 34 travel awards for
early career scientists were made using funds raised by the wwPDB. More
information about the meeting is available at
http://meetings.cshl.edu/meetings/pdb40.shtml.
The RCSB PDB’s website at www.pdb.org provides access to the PDB FTP
archive as well as tools that help users search, analyze and visualize PDB
structural data. In 2010, the RCSB PDB website had more than 5.6 million visits
by users in 218 countries. On average, the website has more than 196,000 unique
visitors each month. Additionally, 160,713,233 data files were downloaded from
the FTP server in 2010.
The website provides access to a relational database that integrates PDB data with
related information from external sources (such as journal abstracts, functional
descriptors, sequence annotations, structure annotations, and taxonomy). Users
can search for structures using simple searches (PDB ID, keyword, sequence, or
author) and complex queries.
PDB-101 is a unique view of the RCSB PDB that packages together the resources
of interest to teachers, students, and the general public. Major topics include
Molecule of the Month columns, a top-down exploration from high-level
functional categories to PDB structures called Structural View of Biology, and
related Educational Resources and materials.
The RCSB PDB group at Rutgers is involved with undergraduate and graduate
education, and supports local K12 education with programs such as the protein
modeling event at the New Jersey Science Olympiad, and K12 education
throughout the world with online resources.
Structural Genomics and the PSI Structural Biology Knowledgebase
With the overarching goal of creating new knowledge about the interrelationships
of sequence, structure, and function, the Protein Structure Initiative Structural
Biology Knowledgebase (PSI SBKB, sbkb.org) is a free online resource that
captures and highlights the structural and technical advances made by the PSI
structural genomics efforts for use by the broader biological community. This
information is integrated with publicly available biological information so that it
can enable a better understanding of living systems and disease. Created in
collaboration with the Nature Publishing Group, the Structural Biology
Knowledgebase also provides a research library, highlights focused on new
research advances and technical tips, the latest science news, and an events
calendar to present a broader view of structural genomics and structural biology.
Searches of the SBKB by sequence or PDB ID will yield a list of related protein
structures from the Protein Data Bank, theoretical 3D models, associated
Li Chen
Research Associate
Dr. Buvna
Coimbatore-
Narayanan
Research Associate
Dr. Luigi DiCostanzo
Research Associate
Dr. Margaret
Gabanyi
Research Associate
Guanghua Gao
Research Associate
Saheli Ghosh
Research Associate
Dr. Sutapa Ghosh
Research Associate
Vladimir Guranovic
Research Associate
Dr. Brian Hudson
Research Associate
Aamir Jadoon
Research Associate
David Micallef
Research Associate
Dr. Ezra Peisach
Research Associate
Dr. Irina Persikova
Research Associate
Nomi Rom
Research Associate
Raul Sala
Research Associate
Raship Shah
Research Associate
48

Dr. Chenghua Shao
Research Associate
Dr. Lihua Tan
Research Associate
Dr. Yi-Ping Tao
Research Associate
Dr. Huanwang
Yang
Research Associate
Christine Zardecki
Research Associate
Dr. Marina
Zhuravleva
Research Associate
Kar Lun Chun
Research Assistant
Maria Voigt
Research Assistant
descriptions (annotations) from biological databases, as well as structural
genomics protein target information, experimental protocols, and the ability to
order available DNA clones. Text searches will find technology reports and
publications that were created by the PSI’s high-throughput research efforts, as
well as the monthly features and highlights from the website. Web tools that aid
in bench top research, such as protein construct design, are also available. This
information can enable scientists by providing everything that is known about a
protein sequence, including any experimental successes or failures, thus
streamlining their own research efforts.
The SBKB group also developed two entirely new resources for the Structural
Genomics community. First, a new experimental data tracking resource,
TargetTrack (sbkb.org/tt/), was created that merged two existing (and mostly
redundant) and expanding to support new types of high-throughput and
biological research. Second, a “Metrics” resource was created to track the
progress of the whole PSI program.
The Unified Data Resource for Cryo Electron Microscopy
The PDB archives large biological assemblies determined by cryo-electron
microscopy (cryoEM), a maturing methodology in structural biology that
bridges the gap between cell biology and the experimental techniques of X-ray
crystallography and NMR. In addition to 3D density maps, cryoEM experiments
often yield fitted coordinate models. Through an NIH/NIGMS-funded
collaboration, a joint EM map and model deposition tool has been developed.
The unified resource for deposition and retrieval network for cryoEM map,
model, and associated metadata is available at EMDataBank.org. This work
has been carried out in collaboration with the RCSB PDB at Rutgers, PDBe, and
the National Center for Macromolecular Imaging at Baylor College of Medicine.
Publications:
Dutta, S., Zardecki, C., Goodsell, D.S., and Berman, H.M. Promoting a
Structural View of Biology for Varied Audiences: An Overview of RCSB PDB
Resources and Experiences. Journal of Applied Crystallography. 2010 43:
1224-1229.
Lawson, C.L., Baker, M.L., Best, C., Bi, C., Dougherty, M., Feng, P., van
Ginkel, G., Devkota, B., Lagerstedt, I., Ludtke, S.J., Newman, R.H., Oldfield,
T.J., Rees, I., Sahni, G., Sala, R., Velankar, S., Warren, J., Westbrook, J.D.,
Henrick, K., Kleywegt, G.J., Berman, H.M., Chiu, W. EMDataBank.org:
unified data resource for CryoEM. Nucleic Acids Res. 2011 39: D456-D464.
49

Rose, P.W., Beran, B., Bi, C., Bluhm, W.F., Dimitropoulos, D., Goodsell, D.S.,
Prlić, A., Quesada, M., Quinn, G.B., Westbrook, J.D., Young, J., Yukich, B.,
Zardecki, C., Berman, H.M., Bourne, P.E., The RCSB Protein Data Bank:
redesigned web site and web services. Nucleic Acids Res. 2011 39: D392-D401.
Bluhm, W.F., Beran, B., Bi, C., Dimitropoulos, D., Prlić, A., Quinn, G.B., Rose,
P.W., Shah, C., Yukich, B., Berman, H.M., Bourne, P.E., Quality Assurance for
the Query and Distribution Systems of the RCSB Protein Data Bank. Database.
2011.
Rose, P.W., Bluhm, W.F., Beran, B., Bi, C., Dimitropoulos, D., Goodsell, D.S.,
Prlić, A., Quinn, G.B., Yukich, B., Berman, H.M., Bourne, P.E. The RCSB
Protein Data Bank: site functionality and bioinformatics use cases. NCI-Nature
Pathway Interaction Database Bioinformatics Primer. 2011.
Gabanyi, M.J., Adams, P.D., Arnold, K., Bordoli, L., Carter, L.G., Flippen-
Anderson, J., Gifford, L., Haas, J., Kouranov, A., McLaughlin, W.A., Micallef,
D.I., Minor, W., Shah, R., Schwede, T., Tao,YP.W., Westbrook, J.D.,
Zimmerman, M., Berman, H.M. The Structural Biology Knowledgebase: A portal
to protein structures, sequences, functions, and methods. Journal of Structural and
Functional Genomics 2011 12:45-54.
Beran, B., Bi, C., Bluhm, W.F., Dimitropoulos, D., Feng, Z., Goodsell, D.S., Prlic,
A., Quinn, G., Rose, P., Westbrook, J., Yukich, B., Young, J., Zardecki, C.,
Berman, H.M. The Evolution of the RCSB Protein Data Bank Website. WIREs
Computational Molecular Science. 2011.
Berman, H.M. The Protein Data Bank: Evolution of a key resource in biology.
Leadership in Science and Technology: A Reference Handbook (William Sims
Bainbridge, editor) SAGE Publications, Inc., 2011.
Kryshtafovych, A., Bartual, S., Bazan, J.F., Berman, H.M., Casteel, D.,
Christodoulou, E., Everett, J., Hausmann, J., Heidebrecht, T., Hills, T., Hui, R.,
Hunt, J., Jayaramanand, S., Joachimiak, A., Kennedy, M., Kim, C., Lingel, A.,
Michalska, K., Montelione, G., Otero, J., Perrakis, O., Pizarro,J., vanRaaij,
M.J., Ramelot, T., Rousseau, F., Wernimont, A., Young, J., Schwede, T. Target
Highlights in CASP9: Experimental Target Structures for the Critical Assessment
of Techniques for Protein Structure Prediction. PROTEINS: Structure, Function,
and Bioinformatics, 2011 79: 6–20.
50

Dr. Joseph Marcotrigiano
CABM Resident Faculty Member
Assistant Professor
Department of Chemistry and
Chemical Biology
Rutgers University
Dr. Abdul Khan
Postdoctoral Assoc.
Ankita Basant
Graduate Student
Fuguo Jiang
Graduate Student
Jillian Whidby
Graduate Student
Samantha Yost
Graduate Student
Structural Microbiology Laboratory
Dr. Joseph Marcotrigiano obtained his B.A. from Rutgers with highest
honors for research on the structure of HIV-1 RT and intergrase as a Henry
Rutgers Undergraduate Scholar. He received the National Starch Award
and the Bruce Garth Award for highest standing in the chemistry program
and was selected for a graduate fellowship at Rockefeller University. He
completed Ph.D. studies with Dr. Stephen Burley in 2000 and was awarded
the inaugural David Rockefeller Jr. Alumni Fellowship. He conducted
postdoctoral research as a Merck Fellow of the Life Sciences Research
Foundation in the Center for the Study of Hepatitis C with Dr. Charles Rice
at Rockefeller University. Dr. Marcotrigiano joined CABM in 2007.
.
Hepatitis C virus (HCV) continues to be a major public health problem. In most
cases, HCV infection becomes chronic and can persist for decades, leading to
cirrhosis, end-stage liver disease and hepatocellular carcinoma. Currently, 2% of the
human population – approximately 123 million people – is infected with HCV. In
fact, there are 3-4 times more individuals infected with HCV than HIV, making virus
transmission a major public health concern. In the United States, HCV infection is
the most common cause of liver transplantation and results in 10,000 to 20,000
deaths a year. There is no vaccine, and current HCV therapy, pegylated interferonalpha
in combination with ribavirin, leads to a sustained response in only 50% of
genotype 1-infected patients, the prevalent genotype in the United States. The
current HCV treatment stimulates the patient’s immune system to clear the virus, but
numerous side effects cause many patients to prematurely stop treatment. Given the
high prevalence of infection and poor response rate, inhibitors that specifically target
HCV proteins with fewer side effects are desperately needed. In addition, an
effective vaccine would greatly reduce the spread of the virus.
Our laboratory studies how HCV enters a host cell and avoids the cellular innate
immune response to infection. To elucidate these processes we employ a variety of
structural, biophysical, biochemical and virological techniques. HCV is a member
of the family Flaviviridae, which also includes Pestiviruses and Flaviviruses.
51

The HCV virion consists of an enveloped nucleocapsid containing the viral genome, a
single-stranded, positive sense RNA that encodes a single open reading frame. Once
the virus penetrates a permissive cell, the HCV genome is released into the cytosol
where the viral RNA is translated in a cap-independent manner by an internal
ribosome entry site (IRES) located within the 5’ nontranslated region (NTR).
Translation generates a viral polyprotein that is proteolytically processed by cellular
and viral encoded proteases into ten proteins. HCV is an enveloped virus with two
glycoproteins (E1 and E2) that form the outermost shell of the virion. These two
proteins are thought to be involved in cell receptor binding, entry, membrane fusion
and immune evasion. Both E1 and E2 are type I transmembrane proteins with an
amino-terminal ectodomain and a carboxy-terminal membrane-associating region.
The transmembrane regions are involved in ER retention and the formation of
noncovalent E1/E2 heterodimers. Since HCV is thought to bud into the ER, retention
of the glycoproteins at the ER membrane ensures their placement on the virion
particles. The E1 and E2 ectodomains are heavily glycosylated and contain several
intramolecular disulfide bonds. E1 and E2 contain 4 and 11 predicted N-linked
glycosylation sites, respectively, and many highly conserved cysteines.
Intracellular double-stranded RNA (dsRNA) is an important signal of virus replication.
The host has developed mechanisms to detect viral dsRNA and initiate antiviral
responses. Pathogen Recognition Receptors (PRR) are cellular proteins that sense the
presence of pathogen associated molecular patterns (PAMPs) to induce an antiviral
state. Retinoic acid inducible gene I (RIG-I) is one member of a family of PRR that
resides within the cytoplasm of a cell and senses the presence of 5’ triphosphorylated
dsRNA, an intermediate of virus replication. RIG-I encodes two caspase recruitment
domains (CARD), a DExD/H box RNA helicase, and a repressor domain (RD). The
RD blocks signaling by the CARD domains under normal growth conditions. To
investigate the contributions of the individual domains of RIG-I to RNA binding, we
determined the equilibrium dissociation constants (Kd) of the protein–RNA
complexes. The tightest RNA affinity was observed with helicase-RD, whereas the
full-length RIG-I, helicase domain and RD bind dsRNA with a 24-fold, 8,600-fold
and 50-fold weaker affinity, respectively. Crystals of RIG-I helicase-RD in complex
with ADP-BeF3 and 14 base-pair palindromic dsRNA were obtained and the structure
was determined to 2.9Å resolution. RIG-I helicase-RD organizes into a ring around
dsRNA, capping one end, while contacting both strands using previously
uncharacterized motifs to recognize dsRNA. Small-angle X-ray scattering, limited
proteolysis and differential scanning fluorimetry indicate that RIG-I is in an extended
and flexible conformation that compacts upon binding RNA. These results provide a
detailed view of the role of helicase in dsRNA recognition, the synergy between the
RD and the helicase for RNA binding and the organization of full-length RIG-I bound
to dsRNA. The results provide evidence of a conformational change upon RNA
binding.
52

The long-term goals of our studies are to provide a structural and mechanistic
understanding for how the HCV glycoproteins (E1 and E2) interact with each other
and with cellular receptors. Also we are focused on how HCV evades the host
antiviral response and how RIG-I discriminates viral from cellular RNAs.
Publications:
Structure of RIG-I helicase-
RD bound to dsRNA and
ADP-BeF
Jiang, F., Ramanathan, A., Miller, M.T., Tang, G.Q., Gale, M. Jr., Patel, S.S.,
Marcotrigiano, J. Structural basis of RNA recognition and activation by innate
immune receptor RIG-I. Nature 2011 479(7373):423-7
Whidby, J., Mateu, G., Scarborough, H., Demeler, B., Grakoui, A. and
Marcotrigiano, J.
Blocking hepatitis C virus infection with recombinant form of envelope protein 2
ectodomain. J. Virol. 2009 83(21):11078-89.
Saito, T., Owen, D.M., Jiang, F., Marcotrigiano, J., Gale, M. Jr. Innate immunity
induced by composition-dependent RIG-I recognition of hepatitis C virus RNA.
Nature 2008 454(7203):523-7
53

Dr. Gaetano Montelione
CABM Resident Faculty Member
Jerome and Lorraine Aresty Chair in
Cancer Biology Research
Professor II
Department of Molecular Biology and
Biochemistry
Rutgers University
Adjunct Professor
Department of Biochemistry
UMDNJ-RWJMS
Director
Northeast Structural Genomics
Consortium
Dr. Swapna Gurla
Associate Research Professor
Dr. Yuanpeng Huang
Associate Research Professor
Dr. Roberto Tejero
Visiting Professor
Dr. Thomas Acton
Assistant Research Professor
Dr. James Aramini
Assistant Research Professor
Dr. John Everett
Assistant Research Professor
Dr. Rongjin Guan
Assistant Research Professor
Dr. Gregory Kornhaber
Assistant Research Professor
Structural Bioinformatics Laboratory
Dr. Gaetano Montelione did graduate studies in protein physical chemistry with
Professor Harold Scheraga at Cornell University. He learned nuclear magnetic
resonance spectroscopy at the Swiss Federal Technical Institute in Zürich where he
worked with Nobel laureate Dr. Kürt Wüthrich, the first researcher to solve a protein
structure with this technique in 1985. Two years later, Dr. Montelione solved the
structure of epidermal growth factor. He has developed new NMR techniques for
refining 3D structures of proteins and triple resonance experiments for making 1 H,
13 C, and 15 N resonance assignments in intermediate-sized proteins. He has served as
a member of the NSF Molecular Biophysics Study Section, NSF Committee of Visitors,
NSF Advisory Committee for Biological Sciences (BIO AC) and advisor to the World
Wide Protein Data Bank (WW_PDB). Dr. Montelione has received the Searle
Scholar Award, the Dreyfus Teacher-Scholar Award, a Johnson and Johnson
Research Discovery Award, the American Cyanamid Award in Physical Chemistry,
the NSF Young Investigator Award, and the Michael and Kate Bárány Award of the
Biophysical Society. He is an elected Fellow of the American Association for the
Advancement of Science.
As director of the NIH-funded Northeast Structural Genomics Consortium of the
NIGMS Protein Structure Initiative, Dr. Montelione leads an inter-institutional pilot
project in large-scale structural proteomics and bioinformatics. Goals of our work
involve developing high-throughput technologies suitable for determining many new
protein structures from the human genome project using nuclear magnetic resonance
spectroscopy (NMR) and X-ray crystallography. These structures provide important
insights into the functions of novel gene products identified by genomic and/or
bioinformatic analysis. The resulting knowledge of structure and biochemical function
provides the basis for collaborations with academic laboratories and pharmaceutical
companies to develop drugs useful in treating human diseases that are targeted to these
newly discovered functions. The approach we are taking is opportunistic in the sense
that only proteins which express well in certain expression systems are screened for
their abilities to provide high quality NMR spectra or well-diffracting protein crystals.
Those that provide good NMR or X-ray diffraction data are subjected to automated
analysis methods for structure determination. The success of our approach relies on our
abilities to identify, clone, express and analyze several hundred biologically interesting
proteins per year; only a fraction of the initial sequences chosen for cloning and
analysis result in high-resolution 3D structures. However, this “funnel” process is
yielding three-dimensional structures and new functions for some 200 proteins per year,
and can thus have tremendous scientific impact. Research areas include networks of
proteins associated with human cancer biology, protein complexes involved in
influenza virus infection, innate immune response, and ubiquitination pathways.
54

s
Publications:
Singarapu, K.K., Mills, J., Xiao, R., Acton, T., Punta, M., Fischer, M., Honig, B., Rost, B.,
Montelione, G.T., Szyperski, T. Solution NMR structures of proteins VPA0419 from
Vibrio parahaemolyticus and yiiS from Shigelle flexneri provide structural coverage from
protein domain family PFAM 04175. PROTEINS: Struc. Funct. Bioinformatics 2010 78:
779 - 784.
Mao, L., Vaiphei. S.T., Shimazu, T., Schneider, W.M., Tang, Y., Mani, R., Roth, M.J.,
Montelione, G.T., Inouye, M. The E. coli single protein production (cSPP) system for
production and structural analysis of membrane proteins. J. Struct. Funct. Genomics 2010
11: 81-84.
Rossi, P., Swapna, G.V.T., Huang, Y.J., Aramini, J.M., Anklin, C., Conover, K., Hamilton,
K., Xiao, R., Acton, T.B., Ertekin, A., Everett, J.K., Montelione, G.T. A microscale protein
NMR sample screening pipeline. J. Biomol. NMR 2010 46: 11 - 22.
Raman, S., Huang, Y.J., Rossi, P., Aramini, J.M., Liu, G., Mao, B., Montelione, G.T.,
Baker, D. Accurate automated protein NMR structure determination using unassigned
NOESY data. J. Am. Chem. Soc. 2010 132: 202 - 207.
Raman, S., Lange, O.F., Rossi, P., Tyka, M., Wang, X., Aramini, J., Liu, G., Ramelot, T.,
Eletsky, A., Szyperski, T., Kennedy, M., Prestegard, J., Montelione, G.T., Baker, D. NMR
structure determination for larger proteins using backbone-only data. Science 2010 327:
1014 - 1018.
Dr. Gaohua Liu
Assistant Research Professor
Dr. Li-Chung Ma
Assistant Research Professor
Dr. Paolo Rossi
Assistant Research Professor
Dr. Rong Xiao
Assistant Research Professor
Dr. Yuefeng Tang
Research Associate
Dr. Asli Ertekin
Postdoctoral Associate
Binchen Mao
Graduate Student
Philip Kostenbader
System Administrator
Saichiu Tong
Research Programmer
Dongyan Wang
Research Teaching Spec.
Hoi Wun Au
Laboratory Researcher
Colleen Ciccosanti
Laboratory Researcher
Kenith Conover
Laboratory Researcher
Keith Hamilton
Laboratory Researcher
Haleema Janjua
Laboratory Researcher
Eitan Kohan
Laboratory Researcher
Dong Yup Lee
Laboratory Researcher
55

Melissa Maglaqui
Laboratory Researcher
Lei Mao
Laboratory Researcher
Dayaben Patel
Laboratory Researcher
Seema Sahdev
Laboratory Researcher
Ritu Shastry
Laboratory Researcher
Huang Wang
Laboratory Researcher
Ari Sapin
Technician
Liu, G., Xiao, R., Wang, D., Huang, Y.J., Acton, T.B., Montelione, G.T. NMR structure Factin
binding domain of Arg/Ab12 from Homo sapiens. PROTEINS: Struct. Funct.
Bioinformatics 2010 78: 1326 - 1330.
Montelione, G.T., Szyperski, T. Advances in protein NMR impacting drug discovery
provided by the NIGMS Protein Structure Initiative. Curr. Opin. Drug Discovery 2010 13:
335 - 349.
Arragain, S., Garcia-Serres, R., Blondin, G., Douki, T., Clemancey, M., Latour, J-M.;
Forouhar, F., Neely, H., Montelione, G.T., Hunt, J.F., Mulliez, E., Fontecave, M., Atta, M.
Post-translational modification of ribosomal proteins: Structural and functional
characterization of RimO from Thermotoga maritima, a radical S-adenosylmethionine
methylthiotransferase. J. Biol. Chem. 2010 285: 5792 - 5801.
Aramini, J.M., Tubbs, J.L., Kanugula, S., Rossi, P., Belote, R.L., Ciccosanti, C.T., Jiang, M.,
Xiao, R., Soong, T., Rost, B., Acton, T.B., Everett, J.K., Pegg, A.E., Tainer, J.A.,
Montelione, G.T. Structural basis of O6-alkylguanine recognition by a bacterial
alkyltransferase-like DNA repair protein. J. Biol. Chem. 2010 285: 13736 - 13741.
Arbing, M.A., Handelman, S.K., Kuzin, A.P., Verdon, G., Wang, C., Su, M., Rothenbacher,
F.P., Abashidze, M., Liu, M., Hurley, J.M., Xiao, R., Acton, T., Inouye, M., Montelione,
G.T., Woychik, N.A., Hunt, J.F. Crystal structures of Phd-Doc, HigA, and YeeU establish
multiple evolutionary links between microbial growth-regulating toxin-antitoxin systems.
Structure 2010 18: 996 - 1010.
Price, W.N., Handelman, S.K., Everett, J., Tong, S.N., Bracic, A., Luff, J.D., Naumov, V.,
Acton, T., Manor, P., Xiao, R., Rost, B., Montelione, G.T., Hunt, J.F. Large-scale
experimental studies show unexpected amino acid effects on protein expression and
solubility in vivo in E. Coli. Microbial Informatics and Experimentation 2011 1: 6 - 26.
Nie, Y., Xiao, R., Xu, Y., Montelione, G.T. Novel anti-prelog stereospecific carbonyl
reductases from Candida parapsilosis for asymmetric reduction of prochiral ketones. Org.
Biomol. Chem. 2011 9: 4070 - 4078.
Schneider, W.M., Tang, Y., Vaiphei, S.T., Mao, L., Maglaqui, M., Inouye, M., Roth, M.J.,
Montelione, G.T. Efficient condensed-phase production of perdeuterated soluble and
membrane proteins. J. Struct. Funct. Genomics 2010 11: 143 - 154.
Liu, G., Huang, Y.J., Xiao, R., Wang, D., Acton, T.B., Montelione, G.T. Solution NMR
structure of the ARID domain of human AT-rich interactive domain-containing protein 3A:
A human cancer protein interaction network target. PROTEINS: Struct Funct
Bioinformatics 2010 78: 2170 - 2175.
56

Zhao, L., Zhao, K., Hurst, R., Slater, M., Acton, T.B., Swapna, G.V.T., Shastry, R.,
Kornhaber, G.J., Montelione, G.T. Engineering of a wheat germ expression system to
provide compatibility with a high throughput pET-based cloning platform. J. Struct. Funct.
Genomics 2010 11: 210 - 209.
Lee, H-W., Wylie, G., Bonsal, S., Wang, X., Barb, A.W., Macnaughtan, M.A., Ertekin, A.,
Montelione, G.T., Prestegard, J.H. Three-dimensional structures of the weakly associated
protein homodimer SeR13 using RDCs and paramagnetic surface mapping. Protein Science
2010 19: 1673 - 1685.
Stark, J.L., Mercier, K.A., Mueller, G.A., Acton, T.B., Xiao, R., Montelione, G.T., Powers, R.
Solution structure and function of YndB, an AHSA1 protein from Bacillus subtilis.
PROTEINS: Struc. Funct. Bioinformatics 2010 78: 3328 - 3340.
Tang, Y., Xiao, R.; Ciccosanti, C., Janjua, H., Lee, Y.L., Everett, J., Swapna, G.V.T., Acton,
T.B., Rost, B., Montelione, G.T. Solution NMR structure of Lin0431 protein from Listeria
innocua reveals high structural similarity with domain II of bacterial transcription
antitermination protein NusG. PROTEINS: Struc. Funct. Bioinformatics 2010 78: 2563 -
2568.
Xiao, R., Anderson, S., Aramini, J.M., Belote, R., Buchwald, W., Ciccosanti, C., Conover, K.,
Everett, J.K., Hamilton, K., Huang, Y.J., Janjua, H., Jiang, M., Kornhaber, G.J., Lee, D.Y.,
Locke, J.Y., Ma, L.-C., Maglaqui, M., Mao, L., Mitra, S., Patel, D., Rossi, P., Sahdev, S.,
Sharma, S., Shastry, R., Swapna, G.V.T., Tong, S.N., Wang, D., Wang, H., Zhao, L.,
Montelione, G.T., Acton, T.B. The high-throughput protein sample production platform of
the Northeast Structural Genomics Consortium. J. Struct. Biol. 2010 172: 21 - 33.
Tang, Y., Schneider, W.M., Shen, Y., Raman, S., Inouye, M., Baker, D., Roth, M.J.,
Montelione, G.T. Fully automated high quality NMR structure determination of small 2Henriched
proteins. J. Struct. Funct. Genomics 2010 11: 223 - 232.
Yang, Y., Ramelot, T.A., Cort, J.R., Wang, D., Ciccosanti, C., Hamilton, K., Nair, R., Rost,
B., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T., Kennedy, M. Solution NMR
structure of photosystem II reaction center protein Psb28 from Synechocystis sp. strain PCC
6803. PROTEINS: Struc. Funct. Bioinformatics 2011 79: 340 - 344.
Yang, Y., Ramelot, T.A., McCarrick, R., Ni, S., Feldmann, E., Cort, J.R., Wang, D.,
Ciccosanti, C., Jiang, M., Janjua, H., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T.,
Kennedy, M. Combining NMR and EPR methods for homo-dimer protein structure
determination. J. Am. Chem. Soc. 2010 132: 11910 - 11913.
Love, J., Mancia, F., Shapiro, L., Punta, M., Rost, B., Girvin, M., Wang, D-N., Zhou, M.,
Hunt, J.F., Szyperski, T., Gouaux, E., MacKinnon, R., McDermott, A., Honig, B., Inouye, M.,
Montelione, G.T., Hendrickson, W.A. The New York Consortium on Membrane Structure
(NYCOMPS): A high-throughput platform for structural genomics of integral membrane
proteins. J. Struct. Funct. Genomics 2010 11: 191 - 199.
57

Mani, R., Vorobiev, S., Swapna, G.V.T., Neely, H., Janjua, H., Ciccosanti, C., Xiao, R.,
Acton, T.B., Everett, J.K., Hunt, J.F., Montelione, G.T. Solution NMR and X-ray crystal
structures of membrane-associated lipoprotein-17 domain reveal a novel fold. J. Struct.
Funct. Genomics 2011 12: 27 - 32.
Zhang, H., Constantine, R., Vorobiev, S., Chen, Y., Seetharaman, J., Huang, Y.J., Xiao, R.,
Montelione, G.T., Gerstner, C.D., Davis, M.W., Inana, G., Whitby, F.G., Jorgensen, E.M.,
Hill, C.P., Tong, L., Baehr, W. UNC119 is required for G protein trafficking in sensory
neurons. Nature Neuroscience 2011 14: 874 - 880.
Aramini, J.M., Rossi, P., Cort, J., Ma, L-C., Xiao, R., Acton, T.B., Montelione, G.T.
Solution NMR structure of the plasmid-encoded fimbriae regulatory protein PefI from
Salmonella enterica serovar Typhimurium. PROTEINS: Struc. Funct. Bioinformatics 2011
79: 335 - 339.
Forouhar, F., Lew, S., Seetharaman, J., Xiao, R., Acton, T.B., Montelione, G.T., Tong, L.
Crystal structures of bacterial biosynthetic arginine decarboxylases. Acta Cryst. F. 2010
F66: 1562 – 1566.
Montelione, G.T., Szyperski, T. IOS Press, Editors A.J. Dingley and S.M. Pascal.
Advances in NMR-based structural genomics spectroscopy. Advances in BioNMR
Spectroscopy 2010
Vaiphei, S.T., Tang, Y., Montelione, G.T., Inouye, M. The use of the condensed single
protein production (cSPP) system for isotope-labeled outer membrane proteins, OmpA and
OmpX in E. coli. Molecular Biotechnology 2011 47: 205 – 210.
You, L., Cho, E.J., Leavitt, J., Ma, L-C., Montelione, G.T., Anslyn, E.V., Krug, R.M.,
Ellington, A., Robertus, J.D. Synthesis and evaluation of quinoxaline derivatives as
potential NS1A protein inhibitors. Bioorg. Med. Chem. Lett. 2011 21: 3007 - 3011.
Schauder, C., Ma, L-C., Krug, R.M., Montelione, G.T., Guan, R. Crystal structure of iSH2
domain of human phosphoinositide3-kinase p85β subunit reveals conformational plasticity
in the interhelical turn region. Acta Cryst. F. 2010 F66: 1567 - 1571.
Vorobiev, S.M., Huang, Y.J., Seetharaman, J., Xiao, R., Acton, T.B., Montelione, G.T.,
Tong, L. Structure and function of human retinoblastoma binding protein 9 (RBBP9).
Protein Peptide Letts 2011 (e-pub ahead of print)
58

Acton, T.B., Xiao, R., Anderson, S., Aramini, J.M., Buchwald, W., Ciccosanti, C., Conover,
K., Everett, J.K., Hamilton, K., Huang, Y.J., Janjua, H., Kornhaber, G.J., Lau, J., Lee, D.Y.,
Liu, G., Maglaqui, M., Ma, L-C., Mao, L., Patel, D., Rossi, P., Sahdev, S., Sharma, S., Shastry,
R., Swapna, G.V.T., Tang, Y., Tong, S.N., Wang, D., Wang, H., Zhao, L., Montelione, G.T.
Preparation of protein samples for NMR structure, function, and Small Molecule screening
studies. Meth. Enzymology 2011 493: 21 - 60.
Mao, L., Inoue, K., Tao, Y., Montelione, G.T., McDermott, A.E., Inouye, M. J. Suppression of
phospholipid biosynthesis by cerulenin in the condensed Single-Protein-Production (cSPP)
system. Biomol. NMR 2011 49: 131 - 137.
Ramelot, T.A., Smola, M.J., Lee, H-W., Ciccosanti, C., Hamilton, K., Acton, T.B., Xiao, R.,
Everett, J.K., Prestegard, J.H., Montelione, G.T., Kennedy, M.A. Solution NMR structure of
4’-phosphopantetheine - GmACP3 from Geobacter metallireducens: a specialized acyl carrier
protein with aty[ical structural features and a putative role in lipopolysaccharide biosynthesis.
Biochemistry 2011 50: 1442 - 1453.
Yin, C., Aramini, J.M., Ma, L-C., Cort, J.R.; Swapna, G.V.T.; Krug, R.M.; Montelione, G.T.
Backbone and Ile-δ1, Leu, Val methyl 1H, 13C and 15N NMR chemical shift assignments for
human interferon-stimulated gene 15 protein. J. Biomol. NMR Assignments 2011 5: 215 -
219.
Karanicolas, J., Corn, J.E., Chen, I., Joachimiak, L.A., Dym, O., Peck, S.H., Albeck, S., Unger,
T., Hu, W., Liu, G., Delbecq, S., Montelione, G.T., Spiegel, C.P., Liu, D.R., Baker, D. A de
novo protein binding pair by computational design and directed evolution. Molecular Cell
2011 42: 250 - 260.
Grant, T., Luft, J.R., Wolfley, J.R., Tsuruta, H., Martel, A., Montelione, G.T., Snell, E. Small
angle x-ray scattering as a complementary tool for high-throughput structural studies.
Biopolymers 2011 95: 517 - 530.
Sgourakis, N.G., Lange, O.F., DiMaio, F., André, I., Fitzkee, N.C., Rossi, P., Montelione, G.T.,
Bax, A., Baker, D. Determination of the structures of symmetric protein oligomers from NMR
chemical shifts and residual dipolar couplings. J. Am. Chem. Soc. 2011 133: 6288 - 6298.
Barb, A.W., Cort, J.R., Seetharaman, J., Lew, S., Lee, H.W., Acton, T., Xiao, R., Kennedy,
M.A., Tong, L., Montelione, G.T., Prestegard, J.H. Structures of domains I and IV from YbbR
are representative of a widely distributed protein family. Protein Science 2011 20: 396 - 405.
59

Chu, C., Das, K., Tyminski, J.R., Bauman, J.D., Guan, R., Qiu, W., Montelione, G.T.,
Arnold, E., Shatkin, A.J. Structure of the guanylyltransferase domain of human mRNA
capping enzyme. Proc. Natl. Acad. Sci. U.S.A. 2011 108: 10104 - 10108.
Mao, B., Guan, R., Montelione, G.T. Improved technologies now routinely provide
protein NMR structures useful for molecular replacement. Structure 2011 19: 757 - 766.
Aramini, J. M., Ma, L.-C., Zhou, L., Schauder, C. M., Hamilton, K., Amer, B. R., Mack, T.
R., Lee, H.-W., Ciccosanti, C.T., Zhao, L., Xiao, R., Krug, R. M., Montelione, G. T.
(2011) The dimer interface of the effector domain of non-structural protein 1 from
influenza A virus: an interface with multiple functions. J. Biol. Chem. 2011 286: 26050 -
26060.
Aramini, J.M., Rossi, P., Fischer, M., Xiao, R., Acton, T.B., Montelione, G.T. Solution
NMR structure of VF0530 from Vibrio fischeri reveals a nucleic-acid binding function.
PROTEINS: Struc. Funct. Bioinformatics 2011 79: 2988 - 2991.
Guan, R., Ma, L-C; Leonard, P.G., Amer, B.R., Sridharan, H., Zhao, C., Krug, R.M.,
Montelione, G.T. Structural basis for the sequence-specific recognition of human ISG15
by the NS1 protein of influenza B virus. Proc. Natl. Acad. Sci. U.S.A. 2011 108: 13468 -
13473.
Eletsky, A., Ruyechan, W.T., Xiao, R., Acton, T.B., Montelione, G.T., Szyperski, T.
Solution NMR structure of MED25(391-543) comprising the activator-interacting domain
(ACID) of human mediator subunit 25. J. Struct. Funct. Genomics 2011 12: 159 - 166.
Forouhar, F., Saadat, N., Hussain, M., Seetharaman, J., Lee, I., Janjua, H., Xiao, R.,
Shastry, R., Acton, T., Montelione, G.T., Tong, L. A large conformational change in the
putative ATP pyrophosphatase PF0828 induced by ATP binding. Acta Cryst. F 2011
67:1323 - 1327.
Lowery, J., Szul, T., Seetharaman, J., Xiaoying, J., Su, M., Forouhar, F., Xiao, R., Acton,
T.B., Montelione, G.T., Lin, H., Wright, J.W., Lee, E., Holloway, Z.G., Randazzo, P.A.,
Tong, L., Sztul, E. A novel C-terminal motif within the Sec7 domain of guanine
nucleotide exchange factors regulates ARF binding and activation. J. Biol. Chem. 2011
286: 36898 - 36906.
Yang, Y., Ramelot, T.A., Cort, J.R., Wang, D., Ciccosanti, C., Jiang, M., Acton, T.B.,
Xiao, R., Everett, J.K., Montelione, G.T., Kennedy, M. Solution NMR structure of
Dsy0195 homodimer from Desulfitobacterium hafniense: First structure representative of
the YapB domain family of proteins involved in spore coat assembly. J. Struct. Funct.
Genomics 2011 12: 175 - 179.
60

Kryshtafovych, A., Bartual, S.G., Bazan, J.F., Berman, H., Casteel, D.E., Christodoulou, E.,
Everett, J.K., Hausmann, J., Heidebrecht, T., Hills, T., Hui, R., Hunt, J.F., Tong, L.,
Jayaraman, S., Joachimiak, A., Kennedy, M., Kim, C., Lingel, A., Michalska, K., Montelione,
G.T., Otero, J.M., Perrakis, A., Pizarro, M.J., van Raaij, M.J., Ramelot, T.A., Rousseau, F.,
Weraimont, A.K., Young, J., Schwede, T. Target highlights in CASP9: experimental target
structures for the critical assessment of techniques from protein structure prediction.
PROTEINS: Struc. Funct. Bioinformatics 2011 (e-pub ahead of print).
Feldmann, E.A., Ramelot, T.A., Yang, Y., Xiao, R., Acton, T.B., Everett, J.K., Montelione,
G.T., Kennedy, M.A. Solution NMR structure of Asl3597 from Nostoc sp. PCC7120, the first
structure from protein domain family PF12095, adopts a novel fold. PROTEINS: Struc. Funct.
Bioinformatics 2011 (e-pub ahead of print).
Rosato, A., Aramini, J.M., Arrowsmith, C., Bagaria, A., Baker, D., Cavalli, A., Doreleijers,
J.F., Eletsky, A., Giachetti, A., Guerry, P., Gutmanas, A., Güntert, P., He, Y., Herrmann, T.,
Huang, Y.J., Jaravine, V., Jonker, H.R.A., Kennedy, M.A., Lange, O.F., Liu, G., Malliavan,
T.E., Mani, R., Mao, B., Montelione, G.T., Nilges, M., Possi, P., van der Schot, G., Schwalbe,
H., Szyperski, T.A., Vendruscolo, M., Vernon, R., Vranken, W.F., de Vries, S., Vuister, G.W.,
Wu, B., Yang, Y., Bonvin, A.M.J.J. Blind testing of routine, fully automated determination of
protein structures from NMR data. Nature Methods 2011 (in press).
Bagaria, A., Jaravine, V., Huang, Y.P., Montelione, G.T., Guntert, P. Protein structure
validation by generalized linear model root-mean-square deviation prediction Protein Science
2011 (in press).
61

Dr. Vikas Nanda
CABM Resident Faculty Member
Associate Professor
Department of Biochemistry
UMDNJ-Robert Wood Johnson
Medical School
Dr. Fei Xu
Research Associate
Dr. Agustina
Rodriguez-Granillo
Research Assistant
Dr. James Stapleton
Postdoctoral Fellow
Dr. Isaac John Khan
Postdoctoral Assoc.
Dr. Avanish Parmar
Postdoctoral Assoc.
Sumana Giddu
Research Teaching Spec.
Teresita Silva
Research Teaching Spec.
Daniel Hsieh
Graduate Student
Protein Design and Evolution Laboratory
Dr. Vikas Nanda joined CABM in September of 2005 after studying as an
NIH National Research Service Award postdoctoral fellow in the laboratory
of Dr. William DeGrado at the Department of Biochemistry and Biophysics
at the University of Pennsylvania School of Medicine. His research focused
on studying the molecular basis of transmembrane interactions among
integrins involved in regulation of platelet hemostasis. Prior to that, Dr.
Nanda received his doctorate in Biochemistry from Johns Hopkins
University. His laboratory is supported by federal grants including a recent
highly competitive NIH New Innovator Award.
.
Our group is interested in constructing new proteins for applications in biomedical
research, nanotechnology and as tools for understanding how proteins fold and
evolve. Significant progress has been made in the last decade using sophisticated
computer programs to design proteins with novel folds and functions. We maintain
and develop the software package, protCAD (protein computer aided molecular
design), which has been applied to protein design, structure prediction and docking
of protein ligand complexes.
Computational Design of an Extracellular Matrix
The extracellular matrix (ECM) is a complex network of collagens, laminins,
fibronectins and proteoglycans that provides a surface upon which cells can adhere,
differentiate and proliferate. Defects in the ECM are the underlying cause of a wide
spectrum of diseases. The ECM mediates endothelial cell polarity and under normal
conditions can suppress pre-oncogenic transitions to a neoplastic state. We are
constructing artificial, de novo collagen-based matrices using a hierarchic
computational approach. These matrices will be physically characterized in the
laboratory and used to probe the role of chemical and spatial organization in the
ECM on the tumor forming potential of adhered cells. Successfully designed
matrices will be applied to engineering safer artificial tissues.
Rational Design of Enhanced Peptide Therapeutics
Peptides are an emergent and important class of therapeutics with over forty
compounds on the market and nearly 700 more in clinical or pre-clinical trials.
During the development of peptide drugs, D-enantiomers of amino acids are
frequently incorporated to improve pharmacokinetic and pharmacodynamics
62

properties by lowering susceptibility to proteolysis. Typically, such modifications are
introduced in lead compounds by trial-and-error or combinatorial approaches.
Our laboratory is developing components in protCAD to simulate the impact of nonnatural
amino acids on structure and stability. Using fundamental principles of protein
design, we will pursue the computational, structure-based development of peptides
with variable chirality, broadly extending our capacity to create safe and potent
therapeutics.
Biochemical Basis of Food Allergies
A crucial and unanswered question in the field of food allergy research is why certain
proteins elicit an IgE mediated immune response, while others are tolerated. One
compelling model is that non-allergens are more digestible, resulting in sufficient
protein degradation in the stomach and intestine to render the remaining fragments
immunologically inert. In this project, we develop a highly defined system for
exploring the relationship between digestibility and allergenicity using engineered
variants of protein allergens from peanut and shrimp.
Natural collagens in the connective
tissue or the basement membrane
assemble in a hierarchic fashion.
Our peptides proceed from
monomer to trimer to fiber, and
finally to a hydrogel. Hydrogels are
versatile materials with applications
in drug delivery, tissue scaffolds
and enzyme immobilization. Insight
gained from this study will improve
molecular design of biomimetic
materials. TOP PICTURE: Phase
diagram of peptides CPB and CPC
combinations showing the diversity
of self-assembling structures
formed. BOTTOM PICTURE:
Electron Microscopy images of
negatively stained CPB:CPC
samples at various mixing ratios.
Mihir Joshi
Research Assistant
Kenneth
McGuinness
Research Asstistant
Yolanda Hom
Technician
63

Publications:
Rodriguez-Granillo, A., Annavarapu, S., Zhang, L., Koder, R.L., Nanda, V.
Computational Design of Thermostabilizing D-Amino Acid Substitutions. J. Am. Chem.
Soc. (in press)
Xu, F., Zahid, S., Silva, T., Nanda, V. Computational Design of a Collagen A:B:C-type
Heterotrimer. J. Am. Chem. Soc. 2011 183:15260-63.
Hsieh, D., Davis, A., Nanda, V. A Knowledge Based Potential Highlights Differences in
Membrane a-helical and b-barrel Protein Insertion and Folding. Prot. Sci. (in press)
Woronowicz, K., Sha, D., Frese, R.N., Sturgis, J.N., Nanda, V., Niederman, R.A. The
effects of protein crowding in bacterial photosynthetic membranes on the flow of quinone
redox species between the photochemical reaction center and the ubiquinol-cytochrome c2
oxidoreductase. Metallomics 2011 3(8):765-74.
Nanda, V., Zahid, S., Xu, F., Levine, D. Computational Design of Intermolecular Stability
and Specificity in Protein Self-Assembly. Methods Enzym. 2011 487:575-93.
Braun, P., Goldberg, E., Negron, C., von Jan, M., Xu, F., Nanda, V., Koder, R.L., Noy, D.
Design principles for chlorophyll-binding sites in helical proteins. Proteins. 2011
79(2):463-76.
Stapleton, J.A., Rodriguez-Granillo, A., Nanda, V. Chapter 3.2-Artificial Enzymes (in
Nanobiotechnology Handbook). Taylor & Frances Group (in press)
Rodriguez-Granillo, A., Nanda, V. Designing new enzymes with molecular simulations.
Biotechnology International 2011
Nanda, V., Koder ,R.L. Designing artificial enzymes by intuition and computation.
Nature Chemistry 2010 2(1):15-24.
Xu, F., Zhang, L., Koder, R.L., Nanda, V. De novo self-assembling collagen heterotrimers
using explicit positive and negative design. Biochemistry. 2010 49(11):2307-16.
Grzyb, J., Xu, F., Weiner, L., Reijerse, E.J., Lubizt, W., Nanda, V., Noy, D. De novo
design of a non-natural fold for an iron-sulfur protein: alpha-helical coiled coil with fouriron
four-sulfur cluster binding site in its central core. Biochim BIophys Acta 2010
1797(3):406-13.
64

Dr. Ann M. Stock
Associate Director of CABM
Investigator
Howard Hughes Medical Institute
Professor
Department of Biochemistry
UMDNJ-Robert Wood Johnson
Medical School
Dr. Rong Gao
Research Associate
Dr. Christopher
Barbieri
Postdoctoral Associate
Dr. Paul Leonard
Postdoctoral Associate
Ian Bezar
Graduate Fellow
Hua Han
Graduate Student
Ti Wu
Research Teaching Spec.
Jizong Gao
Research Specialist
Protein Crystallography Laboratory
Dr. Ann Stock performed graduate work on the biochemistry of signal transduction
proteins with Professor Daniel E. Koshland, Jr. at the University of California at
Berkeley. From 1987 to 1991 she pursued structural analysis of these proteins
while a postdoctoral fellow with Professor Clarence Schutt at Princeton University
and Professor Gregory Petsko at the Structural Biology Laboratory in the
Rosenstiel Center at Brandeis University. Stock has received National Science
Foundation Predoctoral and Damon Runyon-Walter Winchell Postdoctoral
Fellowships, a Lucille P. Markey Scholar Award in Biomedical Science, an NSF
Young Investigator Award, a Sinsheimer Scholar Award and an NIH MERIT Award
in 2002. She has received the Foundation of UMDNJ Excellence in Teaching
Award, the Molecular Biosciences Graduate Association Educator of the Year
Award and the designation of Master Educator at UMDNJ. In 2004 Stock was
selected as an Outstanding Scientist by the NJ Association for Biomedical Research.
She was elected Fellow of the American Association for the Advancement of Science
in 2006 and fellow of the American Academy for Microbiology in 2007. Stock was
an investigator of the Howard Hughes Medical Institute from 1994-2011. She
served as Chair of the Board of Scientific Counselors for the NIH-National Institute
of Dental and Craniofacial Research in 2008-2009 and currently serves as an
Editor of the Journal of Bacteriology. She served on the Council of the American
Society for Biochemistry and Molecular Biology from 2008-2011 and currently
serves as a member of the ASBMB Education & Professional Development and
Finance Committees. Stock serves as an elected member of the RWJMS Faculty
Council and the UMDNJ Faculty Senate.
The research of the Stock laboratory focuses on structure/function studies of signal
transduction proteins. Effort is concentrated on response regulator proteins that are
the core of two-component systems, the most prevalent signal transduction pathways
in bacteria. These systems are important for virulence in pathogenic organisms and
are targets for development of new antibiotics.
The Stock laboratory has continued to focus efforts on characterizing representative
members of the OmpR/PhoB transcription factor subfamily of response regulator
proteins, but now from a systems biology perspective. Studies have shifted from in
vitro analyses to in vivo analyses with the goal of being able to describe the
parameters of protein levels, phosphorylation states, and gene expression activity
during induction of the phosphate assimilation pathway, a model two-component
system in E. coli. Tools have been developed and data are being accumulated that
will hopefully allow the mathematical modeling of the mechanism of regulation in a
representative two-component system.
An additional research focus is characterization of two-component systems of
Staphylococcus aureus, a re-emerging pathogen that is currently associated with
more deaths annually in the United States than HIV1 (AIDS). New classes of drugs
are needed to combat the economic and health burden of drug-resistant S. aureus
strains (i.e. methicillin-resistant, MRSA). Several response regulators in
Staphylococcus aureus play important roles in virulence and are potential drug
targets. The Stock laboratory has focused efforts on two S. aureus transcription
factors, AgrA and VraR. In 2008, the Stock laboratory reported the structure of the
65

DNA-binding domain of AgrA, establishing a novel fold for the LytTR domain that
regulates virulence factor expression in many pathogenic bacteria. Recent studies
have focused on purification and characterization of full-length AgrA with an
emphasis on understanding the role of the extreme C terminus that is altered by a
phase-variation mechanism, inactivating AgrA at late stages of infection.
WATERGATE LOGSY NMR experiments were used to identify drug-like fragments
that bind to AgrA. All six ligands identified bind to the same site, overlapping the
surface required for binding. Three of the fragments have been shown to inhibit DNA
binding and are being pursued for inhibitor development. The Stock laboratory has
determined the structures of both inactive and activated full-length VraR, a
vancomycin-resistance-associated regulator that plays a central role in maintaining
the integrity of the cell wall peptidoglycan and in coordinating responses to cell wall
damage. These structures represent the first inactive and active pair of full-length
response regulator transcription factors. The structures establish the mechanism of
activation of VraR via dimerization and reveal an unusual deep binding pocket with
great potential for inhibitor development. Virtual docking analyses using the Zinc
database of available compounds have identified many compounds predicted to bind
to this pocket. In collaboration with Ed LaVoie (School of Pharmacy, Rutgers
University) and John Kerrigan (CINJ), these compounds have been ranked and several
have been selected as a starting point for inhibitor development.
Dimer interface of active VraR
receiver domain. The protruding
Methionine 13 from one monomer
fits into a deep binding cleft of the
other monomer, a site that is
being targeted for development of
inhibitors as leads for
development of novel antibiotics.
66

Publications:
Barbieri, C.M., Mack, T.R., Robinson, V.L., Miller, M.T. and Stock, A.M. Regulation of
response regulator autophosphorylation through interdomain contacts. J. Biol. Chem. 2010
285: 32325-32335.
Dixit, S.S., Jadot, M., Sohar, I., Sleat, D.E., Stock, A.M. and Lobel, P. Biochemical
alterations resulting from the loss of either NPC1 or NPC2 suggest that these proteins
underlie Niemann-Pick C disease function in a common lysosomal pathway. PLOS One
2011 in Press.
67

Education, Training and Technology Transfer
Lectures and Seminars 69
CABM Lecture Series 70
Annual Retreat 71
25 th Annual Symposium 73
Undergraduate Students 76
Administrative and Support Staff 77
Patents 78
Scientific Advisory Board 81
Current Members 82
Past Members 84
Fiscal Information 86
Grants and Contracts 87
68

Lectures and Seminars
69

Lecture Series 2010-2011
Lectures will be held in CABM Seminar Room 010 unless otherwise noted
October 19, 2010 – Waksman Auditorium
(Pre-Registration Required)
24th Annual CABM Symposium
“Cancer – Progress & Prospects”
Wednesday, November 17, 12:00
Robert Lamb, HHMI, Northwestern University
“Influenza Virus Budding: Who Needs an ESCRT When There Is M2 Protein”
Wednesday, December 1, 12:00
Alanna Schepartz, Yale University
“Exploring Biology with Molecules that Nature Chose not to Synthesize”
Wednesday, January 19, 2010,12:00
Evgeny Nudler, New York University, School of Medicine
“Trafficking and Cooperation in Gene Regulation and Genome Instability”
Wednesday, February 2, 12:00
Smita Patel, UMDNJ-Robert Wood Johnson Medical School
“Mechanistic studies of a ring-shaped helicase that coordinates DNA replication”
Wednesday, March 30, 12:00
Charles Rice, The Rockefeller University
“Hepatitis C virus: New insights into replication and control”
Wednesday, April 13, 12:00
Nahum Sonenberg, McGill University
“Translational Control of Cancer”
Supported by Sanofi Aventis
70

CABM RETREAT, June 30, 2011
Cook Campus Center, New Brunswick, NJ
Program
8:15 AM Registration, Poster Set-up and Continental Breakfast
8:45 AM Opening Remarks – Aaron J. Shatkin
9:00 AM Session I – Gene Expression –From Structure to Behavior and Steps In Between
Chair: Janet Huang - Structural Bioinformatics and Proteomics Lab (Guy Montelione)
Shuchismita Dutta – Protein Data Bank Lab (Helen Berman)
“Molecular Anatomy Project: Promoting a Structural View of Biology”
Lili Mao – Bacterial Physiology and Protein Engineering Lab (Masayori Inouye)
“The Single Protein Production (SPP) system in E. coli”
Hua Han – Protein Crystallography Lab (Ann Stock)
“The Kinetics of phospho regulation by PhoBR two-component system in E. coli “
Evrim Yildirim – Molecular Chronobiology Lab (Isaac Edery)
“Phosphorylation of S826/828 on PER sets the pace of circadian clock”
Weihua Qiu – Molecular Virology Lab (Aaron Shatkin)
“Structure of the Guanylyltransferase Domain of Human mRNA Capping Enzyme”
Stephen Anderson – Protein Engineering Lab (Stephen Anderson)
“Production of human transcription factor immunogens”
10:30 AM Coffee Break and Posters
11:00 AM Session II – Model Systems to Study Growth and Development
Chair: Su Xu – Protein Targeting Lab (Peter Lobel)
Kenneth McGuinness – Protein Design and Evolution Lab (Vikas Nanda)
“Designing Collagen Self-Assembly using Hydrophobic Interactions”
Céline Granier – Viral Pathogenesis Lab (Arnold Rabson)
“PDCD2, a Novel Nuclear Body-associated Protein in Embryonic Stem Cells and Mouse
Development”
Bo Li – Developmental Neurogenetics Lab (Jim Millonig)
“Vacuolated lens (vl): a multigenic mouse mutant model of Neural Tube Defects (NTDs)”
71

12:30 PM Lunch and Break
Kamana Misra – Molecular Neurodevelopment Lab (Meng Xiang)
“To be or not to be" A neuron's perspective
2:15 PM Posters and Coffee
4:30 PM Close
Session III – Understanding Disease at the Molecular Level as a Basis for Developing
Novel Therapies
Chair: Kamana Misra – Molecular Neurodevelopment Lab (Meng Xiang)
Mary Fitzgerald Ho – Biomolecular Crystallography Lab (Eddy Arnold)
“GE23077: A novel bacterial RNA polymerase inhibitor”
Joseph Marcotrigiano – Structural Virology Lab (Joe Marcotrigiano)
“The Structure of a Precursor from the Alphavirus Replication Complex sheds light on
pathogenesis and mechanisms of polyprotein processing”
Rongjin Guan – Structural Bioinformatics and Proteomics Lab (Guy Montelione)
“Structural Basis for the Sequence-Specific Recognition of Human ISG15 by the NS1 Protein
of Influenza B Virus”
Yu Meng – Protein Targeting Lab (Peter Lobel)
“Intravenous enzyme replacement therapy for late-infantile neuronal ceroid lipofuscinosis
(LINCL)”
Fang Liu – Growth and Differential Lab (Fang Liu)
“Pin1 promotes TGF-beta-induced migration and invasion”
Na Yang – Tumor Virology Lab (Céline Gélinas)
“Understanding and targeting Bfl-1 turnover to overcome chemoresistance”
72

25 th Anniversary CABM Symposium
Friday, October 21, 2011
Program
8:15 am Registration & Continental Breakfast
RWJMS Great Hall
9:00 am Welcoming Remarks
Aaron J. Shatkin, PhD
Professor and Director, CABM
Richard L. McCormick, PhD
President, Rutgers, The State University of New Jersey
Session I: Chairperson: Joanna Chiu, PhD
Assistant Professor, UC Davis
9:10 am Phillip Sharp, PhD
Institute Professor, MIT
“The Cell Biology of Small Noncoding RNAs”
9:50 am Ken Valenzano, PhD
Vice President, Amicus Therapeutics
“Pharmacological Chaperones Offer a Two-pronged Approach to Treat Lysosomal Storage
Disorders: Fabry Disease as a Case Study”
10:10 am Zhenyu Yue, PhD
Associate Professor, Mt. Sinai Medical School
“From LRRK2 Kinase to the Hope of Understanding and Treating Parkinson’s Disease”
10:30 am Coffee Break
Session II: Chairperson: Wei-xing Zong, PhD
Assistant Professor, SUNY Stony Brook
11:00 am Robert Roeder, PhD
Arnold and Mabel Beckman Professor, Rockefeller University
“Transcriptional Regulatory Mechanisms in Animal Cells”
12:00 pm Scott Banta, PhD
Associate Professor, Columbia University
“Development of the Beta Roll Motif as a Novel Biomolecular Recognition Scaffold”
74

12:20 pm Lunch Break
RWJMS Great Hall
1:00 pm Poster Session
RWJMS Great Hall
Session III: Chairperson: Jun Zhu, PhD
Director, DNA Sequencing and Computational Biology Core, NIH-NHLBI
2:00 pm Wayne Hendrickson, PhD
University Professor, Columbia University; Investigator, HHMI
“Structural Analysis of SLAC1-family Anion Channel Activity”
2:40 pm Snezana Djordjevic, PhD
Senior Lecture, University College London, UK
“Small Molecule Inhibitors of the VEFG-Neuropilin Interaction”
3:00 pm Hunter Moseley, PhD
Assistant Professor, University of Louisville
“Metabolic Modeling of Converging Metabolic Pathways: Analysis of Non-Steady State
Stable Isotope-Resolved Metabolomics Data of UDP-GlcNAc and UDP-GalNAc”
3:20 pm Coffee Break
Session IV: Chairperson: Minjung Kim, PhD
Assistant Professor, Moffitt Cancer Center, Tampa, FL
3:50 pm Joseph Marcotrigiano, PhD
CABM Resident Faculty Member; Assistant Professor, Rutgers University
“The Innate Immune Response to Viral RNA”
4:20 pm Bruce Alberts, PhD
Editor, Science; Professor Emeritus, UCSF
“Stimulating Innovation in Scientific Research”
5:00 pm Closing
5:10 pm Reception
RWJMS Great Hall
75

Edery Lab
Joseph Albistur
George Ghanim (SURE)
Yee Chen Low
Neal Mehta
Jash Vakil (SURE)
Gelinas Lab
Nikita Ekhelikar (SURE)
Inouye Lab
Yuliya Afinogenova
Shantanu Baghel
Neel Belani
Sehrish Asmal
Lobel Lab
Mohamed Albana (SURE)
Duo Hang
Sharlina Keshava
Aakash Panchal
Dhruv Patel
Dana Betts
Tapan Patel
Samantha Schlachter
Tian Sun
Central Lab Services
Monika Kapedia
Brendan Striano
Millonig Lab
Aziz Karakhanyan
Samantha Kelly
Omar Khan
Keiry Rodriguez
Sammy Taha (SURE)
Nanda Lab
Alexander Davis (SURE)
UNDERGRADUATE STUDENTS
Shatkin Lab
Frank Zong (SURE)
Stock Lab
Christopher Burns
Jose Valverde (SURE)
Xiang Lab
Benjamin Hanft (SURE)
Montelione Lab
Brendan Amer
Hoi Wun Au
Ashley Aya
Alexander Bendik
Tina Bijlani
Nicole Brunck
Katherine Carrino-Bednarski
Ya-Min Chi
Rokhsareh Eyvazkhany
Dhaval Gandhi
Emily Grasso
Sultan Khawam
Eitan Kohan
Wylie Lopez
Joseph Miller
Ari Sapin
Jaskamel Singh
Chelsea Stahl
Amy Suhotliv (SURE)
Aparna Tatineni (SURE)
Teddy Wohlbold
Liu Lab
Kavelbhai Patel
Administration
Ashley Redmond
Daniel Yoon
76

Administrative Assistants
Darlene Bondoc
Ellen Goodman
Jane Kornhaber
Janice Nappe
Barbara Shaver
Elaine Simpson
Jane Kornhaber
Business Office
Lynnette Butler
John Drudy
Madeline Frances
Sharon Pulz
Kristin Rossi
Diane Sutterlin
ADMINISTRATIVE AND SUPPORT STAFF
Central Information Technology
Shelley Waltz
Keith Williams
Central Lab Services
Ramon Dugenio
Alba LaFiandra
Sally Marshall
Harren Mercado
Minoti Sinha
Angela Sowa
77

PATENTS
P. Lobel, et al. “Methods of treating a deficiency of functional tripeptidyl peptidase I (CLN2) protein”.
United States Patent 8,029,781
P. Lobel, et al. “Human lysosomal protein and methods of its use”. United States Patent 7,745,166
J.F. Hunt, W.M. Price, T.B. Acton, and G.T. Montelione. “Methods for altering polypeptide expression and
solubility”. PCT WO 2010/151593 A1 Filed Feb 9, 2011
T. Acton, S. Anderson, Y. Huang, and G.T. Montelione. “System for high-level production of proteins and
protein domains”. PCT Filed Nov 2011
Anderson, S., Lazarus, R.A., Hurle, M., Anderson, S. and Powers, D.B. "Enzymes for the production of 2-keto-
L-gulonic acid". U. S. Patent No. 5,376,544
Anderson, S. and Ryan, R. "Inhibitors of urokinase plasminogen activator". U. S. Patent No. 5,550,213
Lazarus, R.A., Hurle, M., Anderson, S. and Powers, D.B. "Enzymes for the production of 2-keto-L-gulonic acid".
U. S. Patent No. 5,583,025
Anderson, S. "Methods for the prevention or treatment of vascular hemorrhaging and Alzheimer's disease". U. S.
Patent No. 5,589,154
Powers, D.B. and Anderson, S. "Mutants of 2,5-diketo-D-gluconic acid (2,5-DKG) reductase A". U. S. Patent No.
5,795,761
Lazarus, R.A., Hurle, M., Anderson, S. and Powers, D.B. "Enzymes for the production of 2-keto-L-gulonic acid".
U. S. Patent No. 5,912,161
Anderson, S. “Methods for identifying useful t-PA mutant derivatives for treatment of vascular hemorrhaging”.
U. S. Patent No. 6,136,548
Anderson, S. and Banta, S. “Design and production of mutant 2,5-diketo-D-gluconic acid reductase enzymes with
altered cofactor dependency”. U. S. Patent No. 6,423,518
Anderson, S. "Methods for the prevention or treatment of Alzheimer's disease". U. S. Patent No. 6,471,960
Anderson, S. “Methods for identifying useful t-PA mutant derivatives for treatment of vascular hemorrhaging” U.
S. Patent No. 6,136,548
Anderson, S. and Banta, S. “Design and production of mutant 2,5-diketo-D-gluconic acid reductase enzymes with
altered cofactor dependency”. U. S. Patent No. 6,423,518
78

Lazarus, R.A., Hurle, M., Anderson, S. and Powers, D.B. "Enzymes for the production of 2-keto-L-gulonic acid".
U. S. Patent No. 5,912,161
Arnold, E., Kenyon, G.L., Stauber, M., Maurer, K., Eargle, D., Muscate, A., Leavitt, A., Roe, D.C., Ewing, T.J.A.,
Skillman, A.G., Jr., Kuntz, I.D. and Young, M. “Naphthols useful in antiviral methods”. U.S. Patent No.
6,140,368
Arnold, E. and Ferstandig Arnold, G. "Chimeric Rhinoviruses". U.S. Patent No. 5,714,374
Krupey, J., Smith, A., Arnold, E. and Donnelly, R. "Method of Adsorbing Viruses from Fluid Compositions".
U.S. Patent No. 5,658,779
Arnold, E. and Ferstandig Arnold, G. "Chimeric Rhinoviruses". U.S. Patent No. 5,541,100
Edery, I., Altman, M. and Sonenberg, N. “Isolation of full-length cDNA clones and capped mRNA”. U.S. Patent
No. 5219989
Lobel, P. and Sleat, D. "Human lysosomal protein and methods of its use". US Patent No. 6,302,685 B1
Lobel, P. and Sleat, D., “Human lysosomal protein and methods of its use”. US Patent No. 6,638,712. Submitted
10/28/2003
Millonig, J.H., Brzustowicz, L,M. and Gharani, N. “Genes as diagnostic tools for autism”. Provisional
application submitted 7/1/03
Montelione, G.T., Anderson, S. and Huang, Y. “Linking gene sequence to gene function by 3D protein structure
determination”. EU Patent 99935746.0-2402. Issued in United Kingdom
Stein, S. and Montelione, G.T. “Site specific 13C-enriched reagents for magnetic resonance imaging”. U.S.
Patent No. 6210655
Montelione, G. T. and Krug, R. “Process for designing inhibitors of influenza virus non-structural protein 1”.
Filed November 13, 2003. PCT/US03/36292. Patent Pending.
Montelione, G.T., Krug, R., Yin, C. and Ma, L. “Novel compositions and vaccines against influenza A and
influenza B infections”. Filed November 17, 2006. Patent Pending.
Montelione, G. T, Arnold, E., Das, K., Ma, L., Xiao, R., Twu, K.Y., Rei-Lin, K. and Krug, R.M. “Influenza A
virus vaccines and inhibitors”. Filed January 23, 2007. Patent Pending.
Montelione, G.T., Das, K. and Arnold, E. “Ribosomal RNA methyltransferases RlmAI and RlmAII: Drug target
validation and process for developing an inhibitor assay”. Submitted June 26, 2004; Priority date: June 27, 2003.
PTC/US2004/020244. Patent Pending.
79

Montelione, G.T., Ma, L. and Krug, R.M. “An assay for designing small molecule inhibitors of the life cycle of
influenza (Flu) virus targeted to the viral non-structural protein 1”. Provisional Patent Application submitted
March 2007.
Suzuki, M., Schneider, W., Tang, Y., Roth, M., Inouye, M. and Montelione, G.T. “Processes using E. coli single
protein production system (SPP) for deuterium/methyl enrichment of proteins, detergent screening of membrane
proteins using NMR, and peptide bond labeling for high throughput NMR assignments”. Provisional Patent
Application submitted March 2007.
Xiao, R.; Nie, Y.; Xu, Y.; Montelione, G.T. “Three NADPH-dependant stereospecific reductase from Candida
parapsilosis and their application to chiral alcohol production.” Provisional Patent Application submitted June
2009.
Shatkin, A.J., Pillutla, R., Reinberg, D., Maldonado, E. and Yue, Z. “mRNA Capping enzymes and uses thereof.”
U.S. Patent No. 631292631.
80

Scientific Advisory Board
81

Outside Academic Members
Dr. Wayne A. Hendrickson
Investigator, Howard Hughes Medical Institute
Professor
Department of Biochemistry & Molecular Biophysics
Columbia University
Dr. Robert G. Roeder
Arnold and Mabel Beckman Professor
Head, Laboratory of Biochemistry and Molecular Biology
The Rockefeller University
Dr. Thomas Eugene Shenk
Elkins Professor
Department of Molecular Biology
Princeton University
Industry Representatives
Dr. Nader Fotouhi
Vice President, Discovery Chemistry
Roche
Michael Dean Miller, Ph.D.
Site Lead, Infectious Disease – HIV
Merck Research Laboratories
Garry Neil, M.D. (Chair)
Corporate Vice President
Corporate Office of Science & Technology
Johnson & Johnson
Dr. William S. Somers
Assistant Vice President
Global Biotherapeutic Technologies
Pfizer
Dr. Michael J. Tocci
Director, Bridgewater Functional Genomics
Sanofi
CABM Scientific Advisory Board
82

UMDNJ MEMBERS
Robert S. DiPaola, M.D.
Director, The Cancer Institute of New Jersey
Associate Dean for Oncology Programs
Professor of Medicine
UMDNJ-Robert Wood Johnson Medical School
Dr. Leroy F. Liu
Professor and Chairman
Department of Pharmacology
Arnold B. Rabson, M.D.
Professor and Director, Child Health Institute of New Jersey
Interim Senior Associate Dean for Research
UMDNJ-Robert Wood Johnson Medical School
RUTGERS MEMBERS
Dr. Kenneth J. Breslauer
Linus C. Pauling Professor
Dean of Biological Sciences
Vice President of Health Science Partnerships
Dr. Allan H. Conney
William M. And Myrle W. Garber
Professor of Cancer and Leukemia Research
Dr. Joachim W. Messing
University of Professor and Director
Waksman Institute
Martin L. Yarmush, M.D.
Paul and Mary Monroe Professor of Science and Engineering
Director, Center for Innovative Ventures of Emerging Technologies, Rutgers
Director, Center for Engineering in Medicine, Massachusetts General Hospital
83

Former CABM Scientific Advisory Board Members
Alberts, Bruce, Prof., UCSF (Pres. National Academy of Sciences), '86
Babiss, Lee, Vice President Pre-Clinical Res. & Dev. Hoffmann-La Roche Inc.'99-'06
* Baltimore, David, Dir., Whitehead Inst., (Pres. Cal. Tech.), '86-'90
Bayne, Marvin L., VP Discovery Technologies Merck, ’07-‘10
Bolen, Joseph, Vice President, Hoechst Marin Roussel, '98
Black, Ira, M.D., Prof. & Chairman, Dept. of Neurosci. & Cell Biol., RWJ/UMDNJ '91-'06, (deceased)
Blumenthal, David, M.D., Exec. Dir., Ctr. for Health Policy & Mgmt. @ Harvard, '86-'88
Burke, James, Chairman of the Board, J & J, '86-'89
Denhardt, David, Prof. & Chairman, Rutgers, Dept. Biol. Sci., '88-'91
Drews, Jürgen, M.D., Pres., Intl. R & D, Hoffmann-La Roche Inc., '93-'96
Gage, L. Patrick, Pres., Wyeth-Ayerst, '01
Gill, Davinder, Vice President and Head Global Biotherapeutic Technologies, Pfizer, Inc. ’10-‘11
Gussin, Robert, Corporate V. P., Johnson and Johnson, '01
Haber, Edgar, M.D., Pres., Bristol-Myers Squibb Pharma. Res. Inst., '90-'91(deceased)
Hait, William, M.D., Ph.D., Prof., Associate Dean & Director, CINJ, '06-'07
Harris, Edward, Jr., M.D., Prof. & Chairman, Dept. Med., RWJ/UMDNJ '86-'88 (deceased)
Inouye, Masayori, Ph.D., Prof. of Biochemistry, UMDNJ-RWJMS 1986-2010
Koblan, Kenneth V.P. and Site Head for Basic Research, Merck, '06-'10
Lerner, Irwin, Pres. & CEO, Hoffmann-La Roche Inc., '86-'93
Levine, Arnold, Prof. & Chairman, Dept. Biol. Princeton, (Pres. Rockefeller U.), '89-'93
Loh, Dennis, Vice President Preclinical Res. & Dev. Hoffmann-La Roche Inc. '98
Lowry, Stephen F., M.D., Prof and Chair Dept. of Surgery, UMDNJ-RWJMS ’07-’11 (deceased)
Luck, David, M.D., Ph.D., Prof., Rockefeller Univ., '94-'97 (deceased)
Mansour, Tareq S., C.S. Interim Head Wyeth Research, ’09-‘10
* Merrifield, Robert, Prof., Rockefeller Univ., '91-'93 (deceased)
Moliteus, Magnus, Pres., Pharmacia, '86-'88
Morris, N. Ronald, M.D., Associate Dean & Professor, Dept. of Pharma, RWJ/UMDNJ, '86-'92
* Nathans, Daniel, M.D., Sr. Invest., HHMI, Johns Hopkins Univ., (Pres., Johns Hopkins, deceased), '93-'96
Olson, Wilma, Prof., Dept. of Chemistry, Rutgers,'86-'92
Palmer, James, CSO and Pres., Bristol-Myers Squibb Company, '00-'04 (deceased)
Pickett, Cecil, Executive V.P., Schering-Plough, '00-'06
Pramer, David, Dir., Waksman Inst. '86-'88
Reynolds, Richard C., M.D., Executive Vice President, Robert Wood Johnson Foundation,'88-' 91
Rosenberg, Leon, M.D., Pres., Bristol-Myers Squibb, '91-'97
Ruddon, Raymond W., M.D., Ph.D., Corp. V.P. Johnson & Johnson, '01
Ringrose, Peter, Pres., Bristol-Myers Squibb, 2000
Sabatini, David, M.D., Ph.D., Prof. & Chair, Dept. Cell Biol. NYU School of Med., '93-' 08
Sanders, Charles, M.D., Vice Chairman, E.R. Squibb & Sons, '88-'91
Scolnick, Edward M., M.D., President, Merck & Co. Inc. , '95 - '97
Shapiro, Bennett, M.D., Executive V.P., Merck & Company, '01
84

* Sharp, Phillip, Prof. & Dir., Ctr. for Cancer Res., MIT, '90-'93
Sigal, Elliott, M.D., Ph.D., President and CSO, Bristol Myers Squibb, '05-'08
Strader, Catherine, Exec. V.P. and CSO, Schering-Plough Research Institute, '06
Tilghman, Shirley M., Prof., Princeton University (Pres. Princeton U.), '01
Torphy, Theodore John, Corp. V.P. and CSO, Corp. Office of Science and Technology J&J, '03-'07
Turner, Mervyn J., Senior V.P. Merck & Co., '01-'05
Vagelos, P. Roy, M.D., Chairman & CEO, Merck & Co., '86-'94
Walsh, Frank S., Ph.D., Senior V.P. and Head Wyeth Research, '02-'08
Wilson, Robert, Vice Chairman, Board of Directors, J & J, '91-'95
* Nobel Laureate
85

Fiscal Information
86

CENTER FOR ADVANCED BIOTECHNOLOGY AND MEDICINE
GRANTS AND CONTRACTS SUMMARY
FY 2011: JULY 1, 2010 - JUNE 30, 2011
DIRECT COSTS INDIRECT COSTS TOTAL COSTS
FEDERAL 11,356,398 4,219,231 15,575,629
FOUNDATION 931,211 234,430 1,165,641
INDUSTRY 374,064 51,380 425,444
STATE 522,723 29,327 552,050
UNIVERSITY 25,000 0 25,000
TOTAL 13,209,396 4,534,368 17,743,764

Anderson, Stephen Rutgers
CABM Grants and Contracts
FY 2011: 7/01/2010 - 6/30/2011
Total Award
Start - End
FY 2011
Direct Costs
FY 2011
Indirect Costs
FY 2011
Total Costs
Federal 1 $2,812,622
$564,435 $252,145 $816,580
NIH
Human Transcription Factor Immunogens: Generation of a
Complete Set
$2,812,622 9/23/10 8/31/13 $564,435 $252,145 $816,580
Total - Anderson, Stephen 1 $2,812,622
$564,435 $252,145 $816,580
Arnold, Edward Rutgers
Federal 3 $6,920,622
$887,573 $485,078 $1,372,651
NIH
HIV RNase H Natural Product Inhibitors: Structural and
Computational Biology (University of Pittsburgh subcontract)
Inhibitors of Bacterial RNA Polymerase: “Switch Region” (PI -
Dr. Richard Ebright)
HIV-1 Reverse Transcriptase Structure: Function, Inhibition, and
Resistance (MERIT Award)
$2,005,345 3/5/07 2/28/12 $255,526 $141,119 $396,645
$1,161,788 1/1/07 12/31/11 $142,430 $77,118 $219,548
$3,753,489 2/1/09 1/31/14 $489,617 $266,841 $756,458
Total - Arnold, Edward 3 $6,920,622
$887,573 $485,078 $1,372,651
Das, Kalyan Rutgers
Federal 1 $421,242
$126,958
$68,605 $195,563

NIH
Defining and Targeting the HIV Nucleoside-Computing RT
Inhibitor Binding Site
Total Award
Start - End
FY 2011
Direct Costs
FY 2011
Indirect Costs
FY 2011
Total Costs
$421,242 6/15/10 5/31/12 $126,958 $68,605 $195,563
Total - Das, Kalyan 1 $421,242
$126,958 $68,605 $195,563
Edery, Isaac Rutgers
Federal 2 $2,679,362
$436,224 $231,271 $667,495
NIH
Clock Mechanism Underlying Drosophila Rhythmic Behavior $1,327,486 2/15/08 1/31/12 $217,474 $113,146 $330,620
Seasonal Adaptation of a Circadian Clock $1,351,876 7/1/10 6/30/14 $218,750 $118,125 $336,875
Total - Edery, Isaac 2 $2,679,362
$436,224 $231,271 $667,495
Gélinas, Celine UMDNJ
Federal 1 $737,308
$57,404
$32,146 $89,550
NIH
Functional Analysis of BFL-1/A1 in Apoptosis and Oncogenesis $737,308 6/3/08 3/31/12 $57,404 $32,146 $89,550
Foundation 1 $600,000
$180,018
$19,982 $200,000

Leukemia & Lymphoma Society
BFL-1 as a Therapeutic Target and Prognostic Indicator in B-CLL
and AML
Total Award
Start - End
FY 2011
Direct Costs
FY 2011
Indirect Costs
FY 2011
Total Costs
$600,000 10/1/08 9/30/11 $180,018 $19,982 $200,000
Total - Gélinas, Celine 2 $1,337,308
$237,422 $52,128 $289,550
Inouye, Masayori UMDNJ
Federal 3 $3,008,717
$576,258 $284,717 $860,975
NIH
Deciphering of the Toxin-Antitoxin Systems in E. coli $1,593,094 1/1/09 12/31/12 $250,674 $140,377 $391,051
The Method for Determination of Membrane Protein Structures
without Purification
Deciphering of the Toxin-Antitoxin Systems in E. coli (ARRA
Supplement)
$1,240,223 8/1/08 7/31/12 $198,167 $110,973 $309,140
$175,400 6/18/10 11/30/11 $127,417 $33,367 $160,784
Industry 1 $5,200,000
$208,333
$41,667 $250,000
Takara Bio Inc.
Takara Bio Initiative for Innovative Biotechnology $5,200,000 10/1/05 9/30/10 $208,333 $41,667 $250,000
Total - Inouye, Masayori 4 $8,208,717
$784,591 $326,384 $1,110,975
Liu, Fang Rutgers

Total Award
Start - End
FY 2011
Direct Costs
FY 2011
Indirect Costs
FY 2011
Total Costs
University 1 $25,000
$25,000
$0 $25,000
Rutgers University
Smad3 as a Tumor Suppressor for Breast Cancer (Busch
Memorial Fund grant)
$25,000 7/1/10 5/1/12 $25,000 $0 $25,000
Total - Liu, Fang 1 $25,000
$25,000
$0 $25,000
Lobel, Peter UMDNJ
Federal 2 $2,788,578
$521,881 $292,254 $814,135
NIH
Novel Lysosomal Enzyne Deficient in Batten Disease (ARRA
Award)
$858,000 7/17/09 6/30/11 $275,000 $154,000 $429,000
Lysosomal Enzymes and Associated Human Genetic Diseases $1,930,578 4/1/08 3/31/13 $246,881 $138,254 $385,135
Foundation 2 $153,000
$113,318
$8,182 $121,500
Ara Parseghian Medical Research Foundation
Molecular Characterization of Niemann Pick C2 Disease $90,000 7/1/10 6/30/11 $81,818 $8,182 $90,000
Batten Disease Support & Research Association
Intrathecal Enzyme Replacement Therapy for LINCL (Predoctoral
Fellowship - Su Xu)
$63,000 8/1/09 7/31/11 $31,500 $0 $31,500

Total Award
Start - End
FY 2011
Direct Costs
FY 2011
Indirect Costs
FY 2011
Total Costs
Total - Lobel, Peter 4 $2,941,578
$635,199 $300,436 $935,635
Marcotrigiano, Joseph Rutgers
Federal 1 $1,523,219
$208,333 $103,500 $311,833
NIH
Mechanistic Studies of HCV E2 $1,523,219 9/15/10 8/31/14 $208,333 $103,500 $311,833
State 1 $243,900
$106,130
$11,145 $117,275
NJ Commission on Cancer Research
Defining Essential Regions of E2 for HCV Infection $243,900 12/1/09 11/30/11 $106,130 $11,145 $117,275
Total - Marcotrigiano, Joseph 2 $1,767,119
$314,463 $114,645 $429,108
Meng, Yu UMDNJ
Foundation 1 $120,000
$36,667
$0 $36,667
Batten Disease Support & Research Association
Evaluation of Peripheral Enzyme Replacement Therapy for
LINCL and Development of Inducible Transgenic TPPI Model
(Postdoctoral Fellowship)
$120,000 8/1/10 7/31/13 $36,667 $0 $36,667
Total - Meng, Yu 1 $120,000
$36,667
$0 $36,667
Millonig, James UMDNJ
Federal 3 $3,511,051
$286,527
$154,191 $440,718

NIH
Identification and Functional Assessment of Autism Susceptibility
Genes
Elucidating the Role of miRNA Dysregulation in Schizophrenia
and Bipolar Disorder (Rutgers University subcontract)
A Mouse Knock-in Model for ENGRAILED 2 Autism
Susceptibility (Phased Innovation Award - R21/R33)
Total Award
Start - End
FY 2011
Direct Costs
FY 2011
Indirect Costs
FY 2011
Total Costs
$2,147,788 9/30/05 7/31/10 $26,336 $14,205 $40,541
$830,697 4/1/08 3/31/12 $135,191 $75,707 $210,898
$532,566 5/5/08 4/30/11 $125,000 $64,279 $189,279
State 2 $1,069,550
$416,593
$18,182 $434,775
NJ Commission on Spinal Cord Research
Orphan GPCR, Gpr161, and Apithelial-Mesenchymal Transition $600,000 6/15/10 6/30/13 $181,818 $18,182 $200,000
NJ Governor’s Council for Medical Research and Treatment of Autism
Genetics and Non-genetic ENGRAILED 2 ASD Risk Factors $469,550 6/28/10 6/27/12 $234,775 $0 $234,775
Total - Millonig, James 5 $4,580,601
$703,120 $172,373 $875,493
Molli, Poonam UMDNJ
Federal 1 $351,000
$75,000
$42,000 $117,000

Department of Defense
Tumor suppressor role of CAPER alpha in ER alpha negative &
Rel NF-kB positive breast cancer (Postdoctoral Fellowship)
Total Award
Start - End
FY 2011
Direct Costs
FY 2011
Indirect Costs
FY 2011
Total Costs
$351,000 8/15/09 8/14/12 $75,000 $42,000 $117,000
Total - Molli, Poonam 1 $351,000
$75,000 $42,000 $117,000
Montelione, Gaetano Rutgers
Federal 3 $39,383,043
$6,304,310 $1,571,103 $7,875,413
NIH
Targeting the NS1 Protein for the Development of Influenza Virus
Antivirals (University of Texas subcontract)
$1,451,279 8/17/07 7/31/12 $203,244 $109,828 $313,072
Structural Genomics of Eukaryotic Domain Families $37,810,498 9/1/10 6/30/15 $6,066,300 $1,442,501 $7,508,801
Membrane Protein Production using the Yeast SPP System
(UMDNJ subcontract)
$121,266 9/30/10 7/31/14 $34,766 $18,774 $53,540
Industry 1 $80,228
$17,821
$9,713 $27,534
Nexomics Biosciences, Inc.
Protein Production and NMR Data Collection Services $80,228 7/1/08 6/30/11 $17,821 $9,713 $27,534
Total - Montelione, Gaetano 4 $39,463,271
$6,322,131 $1,580,816 $7,902,947
Nanda, Vikas UMDNJ

Total Award
Start - End
FY 2011
Direct Costs
FY 2011
Indirect Costs
FY 2011
Total Costs
Federal 4 $4,722,697
$688,625 $378,163 $1,066,788
National Science Foundation
NIH
Design of Programmable, Self-Assembling Collagen Biomaterials $404,997 9/1/09 8/31/12 $86,538 $48,461 $134,999
Computational Design of a Synthetic Extracellular Matrix $2,340,000 9/30/09 8/31/14 $304,545 $170,545 $475,090
Structure-Based Engineering of Allergens to Enhance
Digestibility
A Computational Approach to Developing Heterochiral Peptide
Therapeutics
$426,660 4/1/10 3/31/12 $130,875 $73,290 $204,165
$1,551,040 9/1/10 8/31/15 $166,667 $85,867 $252,534
Total - Nanda, Vikas 4 $4,722,697
$688,625 $378,163 $1,066,788
Phadtare, Sangita UMDNJ
Federal 1 $156,000
$45,833
$25,667 $71,500
NIH
Transcription Antitermination by OB-fold Family Proteins (ARRA
Award)
$156,000 6/1/09 5/31/11 $45,833 $25,667 $71,500
Total - Phadtare, Sangita 1 $156,000
$45,833 $25,667 $71,500
Shatkin, Aaron UMDNJ

Total Award
Start - End
FY 2011
Direct Costs
FY 2011
Indirect Costs
FY 2011
Total Costs
Industry 1 $35,000
$35,000
$0 $35,000
Pharmaceutical Companies
CABM Symposium & Lecture Series $35,000 7/1/10 6/30/11 $35,000 $0 $35,000
Total - Shatkin, Aaron 1 $35,000
$35,000
$0 $35,000
Stock, Ann UMDNJ
Federal 2 $1,919,216
$265,579 $125,390 $390,969
NIH
Structure and Function of Response Regulator Proteins (MERIT
Award)
Structure and Function of Response Regulator Proteins (ARRA
Supplement)
$1,792,012 7/1/09 6/30/14 $225,720 $114,367 $340,087
$127,204 9/30/09 12/31/10 $39,859 $11,023 $50,882
Foundation 1 $13,990,822
$601,208 $206,266 $807,474
Howard Hughes Medical Institute
Molecular Mechanisms of Signal Transduction $13,990,822 8/1/94 2/28/11 $601,208 $206,266 $807,474
Total - Stock, Ann 3 $15,910,038
$866,787 $331,656 $1,198,443
Williams, Keith Rutgers
Industry 1 $112,910
$112,910
$0 $112,910

Cisco, Inc.
Infrastructure Improvements for Extracellular Matrix Research: A
Computational Design (Equipment Grant)
Total Award
Start - End
FY 2011
Direct Costs
FY 2011
Indirect Costs
FY 2011
Total Costs
$112,910 5/31/11 6/30/11 $112,910 $0 $112,910
Total - Williams, Keith 1 $112,910
$112,910
$0 $112,910
Xiang, Mengqing UMDNJ
Federal 2 $2,669,332
$311,458 $173,001 $484,459
NIH
Transcriptional Regulation of Retinal Development $1,156,132 12/1/07 11/30/10 $103,125 $56,334 $159,459
Dll4 Gene Regulation and Function during Retinogenesis $1,513,200 9/1/10 8/31/14 $208,333 $116,667 $325,000
Total - Xiang, Mengqing 2 $2,669,332
$311,458 $173,001 $484,459
CABM TOTAL $13,209,396
$4,534,368 $17,743,764