2001 - Center for Advanced Biotechnology and Medicine - Rutgers ...

C A B M 

Center for 

Advanced Biotechnology 

and Medicine 

http://cabm.umdnj.edu 

2002 Report 

An Advanced Technology Center 

of 

The New Jersey Commission on Science and Technology 

Jointly Administered 

By 

Rutgers, The State University of New Jersey 

and by 

The University of Medicine and Dentistry of New Jersey

CONTENTS 

Director’s Overview 3 

Research Programs and Laboratories 

Cell & Developmental Biology 6 

Molecular Neurobiology Cory Abate-Shen 7 

Molecular Chronobiology Isaac Edery 9 

Tumor Virology Céline Gélinas 11 

Growth & Differentiation Control Fang Liu 13 

Protein Targeting Peter Lobel 15 

Developmental Neurogenetics James Millonig 17 

Mammalian Embryogenesis Michael Shen 19 

Viral Transformation Eileen White 21 

Molecular Neurodevelopment Mengqing Xiang 24 

Structural Biology 25 

Biomolecular Crystallography Edward Arnold 26 

Protein NMR Spectroscopy Gaetano Montelione 31 

Protein Microchemistry Stanley Stein 33 

Protein Crystallography Ann Stock 34 

Molecular Genetics 36 

Protein Engineering Stephen Anderson 37 

Viral Pathogenesis Arnold Rabson 39 

Molecular Virology Aaron Shatkin 41 

Education, Training and Technology Transfer 43 

Lectures and Seminars 44 

CABM Lecture Series 45 

Annual Retreat 46 

15 th Annual Symposium 48 

Undergraduate, Graduate Students and Postdoctoral Fellows 52 

Patents 56 

Fiscal Information 57 

Grants and Contracts 

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Center for Advanced Biotechnology and Medicine 

2

Director’s Overview 

The community of research scientists at CABM is always looking forward to new 

experimental findings that will promote our mission – advancing basic knowledge 

in the life sciences to improve human health. On this occasion, the completion of 

our 15 th year, it is appropriate and reassuring to reflect on some of our recent 

accomplishments in research, teaching and service. 

CABM in its short lifetime has already become an important contributor to the 

biosciences revolution. As described in the following pages, CABM scientists 

continued to report the results of their latest research, designed to understand 

better and ultimately prevent AIDS, cancer, neurological disorders and other lifethreatening 

diseases. During the past year nearly 100 peer-reviewed publications 

from CABM laboratories have appeared in high impact international journals 

including Development, Genes and Development, EMBO Journal, Molecular Cell, 

Molecular and Cellular Biology, Nature, Nature Structural Biology, Proceedings 

of the National Academy of Sciences and Science. 

Generous support for this important work was provided by competitive awards 

from numerous public and private sources. We are grateful to the National 

Institutes of Health (NIH), U.S. Army Medical Research & Materiel Command, 

National Science Foundation (NSF), Veterans Administration, N.J. Commission 

on Science and Technology R&D Excellence Program, N.J. Commission on 

Cancer Research and Governor’s Council on Autism; the Howard Hughes 

Medical Institute (HHMI), American Association for Cancer, American Heart 

Association, Leukemia and Lymphoma Society, March of Dimes, Kimmel 

Foundation for Cancer Research and Sinsheimer Fund; the Ara Parseghian 

Medical Research, Burroughs Wellcome, AHEPA Cancer Research, Cure for 

Lymphoma, Emerald, Janssen Research, National Ataxia, and Whitehall 

Foundations; and Janssen-Cilag, Johnson & Johnson, Roche, Genzyme, 

GeneFormatics, Human Genome Sciences, Merck, Aventis and Genencor. In 

addition to two NIH MERIT awards and two HHMI investigators, CABM is home 

to the NIH-funded Northeast Structural Genomics Consortium. 

Besides their strong commitment to classroom teaching in courses for 

undergraduate, graduate and medical students, CABM researchers trained and 

mentored many postdoctoral fellows and students in their laboratories in 

preparation for positions of scientific leadership in academia and industry. The 

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3

Director’s Overview 

Annual Retreat and CABM Lecture Series have again this year provided 

opportunities for students to present and defend their work and to hear and interact 

with exciting speakers visiting from other leading educational institutions. The 

15 th Annual CABM Symposium, “Structural Genomics in Pharmaceutical 

Design”, was sponsored by 18 organizations and enjoyed by nearly 250 

participants. The meeting fostered productive collaborations and licensing of 

intellectual property for industrial development, adding to CABM’s economic 

impact in New Jersey and across the nation. 

CABM investigators served on various advisory, faculty search, departmental and 

other committees at Rutgers University and UMDNJ-Robert Wood Johnson 

Medical School. To foster translational aspects of our mission, several also have 

appointments and leadership roles in clinical departments and in the Cancer 

Institute of New Jersey, e.g. as Associate Director for Basic Research and 

Scientific Director of the Gallo Prostate Cancer Center. At the national and 

international levels, CABM faculty participate in meetings as invited speakers, 

serve on many journal editorial boards and meeting organizational committees, 

several grant review panels of the NIH and NSF, the National Cancer Institute 

Board of Counselors, the HHMI Cell Biology Review Panel and advisory boards 

of other government agencies, professional societies, foundations and companies. 

This has been a challenging and productive year, with CABM scientists working 

at the frontiers of structural biology, molecular genetics and cell and 

developmental biology, using and creating novel systems to translate genomic 

sequences into protein function and gaining information and insights that are 

having positive impacts on human health. After 1-1/2 decades of outstanding 

progress, 2002 promises exciting, new scientific advances at CABM. 

Aaron J. Shatkin, Professor and Director 

Shatkin@cabm.rutgers.edu 

http://cabm.umdnj.edu 

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4

Research Programs and Laboratories 

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5

Cell & Developmental Biology 

Laboratory Faculty Director 

Molecular Neurobiology Cory Abate-Shen 7 

Molecular Chronobiology Isaac Edery 9 

Tumor Virology Céline Gélinas 11 

Growth & Differentiation Control Fang Liu 13 

Protein Targeting Peter Lobel 15 

Developmental Neurogenetics James Millonig 17 

Mammalian Embryogenesis Michael Shen 19 

Viral Transformation Eileen White 21 

Molecular Neurodevelopment Mengqing Xiang 24 

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6

Cory Abate-Shen, Ph.D. 

Resident Faculty Member, CABM; Professor, UMDNJ Robert Wood Johnson Medical 

School, Department of Neuroscience and Cell Biology and Department of Medicine, 

Scientific Director of the Dean and Betty Gallo Prostate Cancer Institute, Cancer 

Institute of NJ; Head, Division of Developmental Medicine and Research-Department of 

Medicine 

Molecular Neurobiology Laboratory 

Dr. Cory Abate-Shen joined CABM in August 1991 after spending three years as a postdoctoral and research fellow in Tom Curran’s laboratory 

at the Roche Institute of Molecular Biology. Her work at Roche contributed to characterization of the DNA binding and transcriptional properties 

of the regulatory proteins Fos and Jun. Dr. Abate-Shen received her Ph.D. from Cornell University Medical College where she was awarded the 

Vincent du Vigneaud Award for Excellence in Graduate Research. She is a recipient of a Sinsheimer Scholar Award and an NSF Young 

Investigator Award and received a career recognition award from The American Society for Cell Biology. Dr. Abate-Shen is a member of the 

NIH Study Section on Cell Development and Function. She was recently appointed head of a new division in the Department of Medicine. 

My long-term interests are to understand the molecular mechanisms underlying homeobox gene 

function during embryogenesis and how aberrant homeobox function contributes to oncogenesis. 

A major focus of my recent work has been the development of animal models to elucidate the 

roles of particular homeobox genes in development, oncogenesis and embryogenesis. We have 

found that homeobox genes Msx1 and Pax3 are co-expressed in migrating limb muscle 

precursors, which are committed myoblasts that do not express myogenic differentiation genes 

such as MyoD. Msx1 negatively regulates differentiation of migrating limb muscle precursor 

cells through its ability to antagonize the myogenic activity of Pax3. Forced misexpression of 

Msx1 in cell culture and in chicken embryos inhibits MyoD expression as well as muscle 

differentiation. Conversely, forced misexpression of Pax3 activates MyoD expression and 

myogenesis, while this effect is counteracted by Msx1. Moreover, the Msx1 protein product 

interacts with Pax3, thereby inhibiting the DNA binding activity of Pax3 as well as its ability to 

transcriptionally activate MyoD regulatory elements. A major focus of our current research is the 

elucidation of additional protein partners that form functional associations with Msx proteins in 

vivo. Analysis of a functional role for Msx in breast and other carcinomas, as well as the 

identification of downstream targets for Msx, represent another important focus of our current 

studies. Our Msx1 transgenic mice provide an excellent resource to pursue these studies. 

Prostate cancer is the most commonly diagnosed neoplasm, and ranks second to lung cancer as 

the leading cause of cancer death in American men. To investigate early stages of initiation and 

progressionof prostate cancer, we have developed a mouse model using the Nkx3.1 homeobox 

gene, which is expressed specifically in the developing and adult prostate, and whose targeted 

disruption results in defects of prostate differentiation and function. Notably, human NKX3.1 

maps to chromosomal region 8p21, which is deleted in ~60-80% of prostate tumors. Moreover, 

loss of 8p21 represents an early event in carcinogenesis since it is also deleted in prostatic 

intraepithelial neoplasia (PIN), the major precursor of prostate carcinoma in humans. We have 

found that Nkx3.1 mutant mice display lesions that resemble human PIN with respect to their 

histological appearance as well as the molecular changes that occur in early stages of 

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Cory Abate 

carcinogenesis, such as loss of the basal cell layer of the prostate epithelium. Based on our 

findings we have proposed that interactions between tissue-specific regulators, such as Nkx3.1, 

and broad-spectrum tumor suppressors, such as Pten, underlie the distinct phenotypes of different 

cancers. By utilizing mouse models, we are beginning to assemble a molecular pathway for 

prostate carcinogenesis that includes loss of NKX3.1 as an initiating event followed by loss of 

PTEN as a later event leading to progression. Future goals include the identification of additional 

molecular alterations that characterize early stage prostate carcinogenesis, further elucidation of 

a molecular pathway for prostate carcinogenesis through the generation of new mutant mouse 

models, and the application of these mutant mouse models for the design of new therapeutics. 

Publications: 

Bendall, A. J. and Abate-Shen, C. (2000). Roles for MSX and DLX homeoproteins in vertebrate 

development. Gene. 247:17-31. 

Abate-Shen, C. and Shen, M. M. (2000). Molecular genetics of prostate cancer. Genes Dev. 

14:2410-2434. 

Hu, G., Price, S., Shen, M.M. and Abate-Shen, C. (2001). Msx homeobox genes inhibit 

differentiation by upregulation of Cyclin D1. Development 128:2373-2384. 

Pizette, S., Abate-Shen, C. and Niswander, L. (2001). BMP mediates vertebrate limb growth and 

dorsal-ventral patterning by differential use of two homeodomain proteins. Development 

128:4463-4474. 

Hovde, S., Abate-Shen, C. and Geiger, J.H. (2001). Crystal structure of the Msx-1 

homeodomain/DNA complex. Biochemistry 40: 12013-21. 

Cunha, G. R., Donjacour, A. A., Hayward, S.W., Thomson, A. A., Marker, P. C., Abate-Shen, 

C., Shen, M. M. and Dahiya, R. (2002). Cellular and molecular biology of prostatic development. 

In: Prostate Cancer: Principles and Practice. Kantoff, P. W., Carroll, P. D'Amico, A. (eds.), 

Lippincott, Williams and Wilkins, Philadelphia, pp. 16-28. 

Kim, M., Desai, R., Cardiff, N., Bhatia-Gaur, R., Banach-Petrosky, W., Parsons, R., Shen, M. and 

Abate-Shen, C. Cooperativity of tissue-specific and broad-spectrum tumor suppressor genes in a 

mouse model of prostate carcinogenesis. PNAS. In Press. 

Stein S. and Abate-Shen C. Homeobox Genes and Cancer. In: Schwab M (ed.) Encyclopedic 

Reference of Cancer. Springer-Verlag, Berlin Heidelberg New York. In Press. 

8

Isaac Edery, Ph.D. 

Resident Faculty Member, CABM; Associate Professor, Rutgers University, Department 

of Molecular Biology and Biochemistry 

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 biological 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. 

A wide range of organisms from bacteria to humans exhibit daily or circadian rhythms in 

physiological and behavioral phenomena that are controlled by endogenous pacemakers or 

clocks. Circadian clocks are precisely synchronized to the 24-hr solar day by the daily lightdark 

and temperature cycles, enabling organisms to perform activities at advantageous times 

and manifest appropriate seasonal responses. We use the fruitfly Drosophila as our model 

system to understand the cellular and biochemical bases underlying clock function. 

The isolation of "clock genes" has provided significant insights into the molecular 

underpinnings governing circadian rhythms. A common theme in clocks from bacteria to 

humans is that at the "heart" of these pacemakers lie transcriptional-translational feedback 

loops. The best characterized animal model system for a circadian clock is Drosophila 

melanogaster, where four clock proteins termed PERIOD (PER),TIMELESS (TIM), dCLOCK 

(CLK) and CYCLE (CYC) function in a negative transcriptional autoregulatory loop. CLK and 

CYC are members of the basic-helix-loop-helix (bHLH)/PAS (PER-ARNT-SIM) superfamily 

of transcription factors and are required for the daily stimulation of per and tim expression. PER 

and TIM form a complex in the cytoplasm that enters the nucleus in a temporally gated manner 

where they bind the CLK-CYC heterodimer, blocking its DNA binding activity. In the absence 

of denovo synthesis, the concentrations of PER and TIM in the nucleus decrease below 

threshold levels, relieving autoinhibition and enabling the next round of per and tim transcript 

accumulation. Posttranscriptional mechanisms play an important role because they introduce 

"biochemical time constraints" that stretch the transcriptional feedback loop to ~24 hr and also 

allow it to respond to external stimuli. For example, light evokes the rapid degradation of TIM, 

the primary clock-specific photoresponse resetting the oscillatory mechanism. A blue-light 

photoreceptor called CRYPTOCHROME (CRY) has been implicated in transducing photic 

signals to TIM. Furthermore, the cytoplasmic phosphorylation of PER by the kinase DOUBLE- 

TIME (DBT) renders PER unstable. Cytoplasmic PER is stabilized by interacting with TIM 

which ensures that the accumulation and nuclear entry of the PER-TIM complex is a slow 

process, creating a time-window for daily increases in the levels of per and tim transcripts. 

Our studies are geared towards isolating all the components that comprise a circadian 

timekeeping device, characterizing their interactions within the various feedback loops and 

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9

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Isaac Edery 

understanding how the daily changes in visible light modulate the oscillatory mechanism. In 

addition, we recently showed that the splicing efficiency of an intron in the 3' untranslated region of 

per is thermosensitive. At lower temperatures this intron is spliced more efficiently leading to higher 

levels of per mRNA and mainly daytime activity. By regulating the splicing efficiency of this intron 

flies are active during the warmer daytime hours during autumn/winter days typical of temperate 

zones and avoid the midday sun by manifesting mainly nocturnal activity during the warmer 

spring/summer seasons. We are continuing these studies to understand how a clock helps measure 

calendar time by adapting to seasonal changes in temperature and daylength. 

Given the similarities in the circadian timing mechanisms operating in Drosophila and mammals, we 

anticipate that our findings will continue to provide important insights into disorders associated with 

clock malfunction in humans, including manic-depression, seasonal affective disorders (SAD or 

winter depression), chronic sleep problems in the elderly and symptoms associated with transmeridian 

flight ("jet-lag") and shift-work. 

Publications: 

Bae, K., Lee, C., Hardin, P.H. and Edery, I. (2000). dCLOCK is present in limiting amounts 

and likely mediates daily interactions between the dCLOCK-CYC transcription factor and the 

PER-TIM complex. J. of Neurosci. 20, 1746-1753. 

Edery, I. (2000). Circadian rhythms in a nutshell. Physiol. Genomics 3, 59-74. 

Kim, E.Y., Bae, K., Ng, F.S., Glossop, N.R.J., Hardin, P.E. and Edery, I. Drosophila CLOCK 

protein is under posttranscriptional control and influences light-induced activity. Neuron. In 

press. 

10

Céline Gélinas, Ph.D. 

Resident Faculty Member, CABM; Professor, UMDNJ-Robert Wood Johnson Medical 

School, Department of Biochemistry 

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 and the National Cancer Institute of Canada King 

George V Postdoctoral Fellowship. Her work is currently funded by the NIH and The Cure for Lymphoma Foundation. 

Our laboratory has a long-standing interest in the role of the Rel/NF-κB proteins in the onset and 

progression of hematopoietic and solid tumors. Proteins in the Rel/NF-κB-family of transcription 

factors play fundamental roles in immune and inflammatory responses, and are implicated in the 

control of cell proliferation, the inhibition of apoptosis and in oncogenesis. Experimental 

evidence linking deregulated Rel/NF-κB activity to human cancer has emerged in recent years, 

consistent with the acute oncogenicity of the Rel/NF-κB oncoprotein v-Rel in inducing fatal 

leukemia/lymphomas in animal models. Aberrant Rel/NF-κB activity is found in various human 

leukemias, lymphomas, myelomas and Hodgkin’s disease. Chromosomal amplification, 

rearrangement, overexpression and/or constitutive activation of the rel and nf-κB genes are also 

observed in breast, colon, lung, ovarian and prostate cancer. The viral and cellular Rel proteins 

offer a powerful system to study how the Rel/NF-κB factors function in normal lymphoid cells 

and to understand how their aberrant activities lead to cancer. Our research focuses on the 

transcriptional activity and regulation of the Rel/NF-κB factors, on their role in cell growth, 

apoptosis and oncogenesis, and on the cellular genes that they control. 

In prior studies, we demonstrated that the transcriptional and anti-apoptotic activities of the v-Rel 

oncoprotein were necessary for its oncogenic function. Our analyses characterizing Rel-mediated 

effects on cell survival and neoplasia have recently demonstrated the ability of a subset of 

mammalian cellular Rel/NF-κB factors to malignantly transform primary lymphoid cells. 

Detailed analyses of the determinants required for this activity are starting to provide important 

insights into the mechanisms involved in tumors associated with aberrant Rel/NF-kB function. 

Our recent experiments suggest that the specificity of target gene activation is likely to play a 

critical role in the oncogenic conversion of cellular Rel/NF-kB factors. Our ongoing functional 

characterization of the Rel/NF-kB target genes Bfl-1/A1 and TAPIR and the analysis of their 

transcriptional regulation by Rel/NF-κB offers new avenues to characterize the Rel/NF-kB 

signaling pathway and its role in cell survival. This comprehensive approach will help to clarify 

the mechanism by which Rel/NF-κB proteins function in the immune system and in oncogenesis. 

In addition, since Rel/NF-κB activity has been implicated in various disease conditions, the 

systematic analysis of Rel/NF-κB regulation and relevant Rel/NF-κB target genes may also 

provide important insights into novel approaches for therapeutic intervention. 

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11

Publications: 

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Céline Gélinas 

Luque, I., Zong, W.-X., Chen, C. and Gélinas, C. (2000). N-terminal determinants of IκBα 

necessary for the cytoplasmic regulation of c-Rel. Oncogene 19: 1239-1244. 

Chen C., Edelstein, L.C. and Gélinas, C. (2000). Rel/NF-κB directly activates expression of the 

apoptosis inhibitor Bcl-xL. Mol. Cell. Biol. 20: 2687-2695. 

Ravi, R., Bedi, G.C., Engstrom, L.W., Zeng, Q., Mookerjee, B., Gélinas, C., Fuchs, E.J. and 

Bedi, A. (2001) Regulation of death receptor expression and TRAIL/Apo2L-induced apoptosis 

by NF-κB. Nature Cell Biol. 3: 409-416. 

Shah, N., Thomas, T.J., Lewis, J.S., Klinge, C.M., Shirahata, A., Gélinas, C. and Thomas, T. 

(2001). Regulation of estrogenic and nuclear factor κB functions by polyamines and their role in 

polyamine analog-induced apoptosis of breast cancer cells. Oncogene 20: 1715-1729. 

12

Fang Liu, Ph.D. 

Resident Faculty Member, CABM; Assistant Professor, Rutgers University, Susan 

Lehman Cullman Laboratory for Cancer Research, Department of Chemical Biology, 

Ernest Mario School of Pharmacy 

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. 

Inhibition of SMAD Transcriptional Activity by Cyclin-Dependent Kinase 

Phosphorylation: TGF-ß is the most relevant physiological inhibitor of cell proliferation of a 

wide variety of cell types. During the earliest stage of tumorigenesis, the ability of TGF-ß to 

inhibit cell growth enables it to act as a potent tumor suppressor. TGF-ß inhibits cell 

proliferation by causing cell cycle arrest at the G1 phase. SMAD proteins are candidate tumor 

suppressors and can mediate the TGF-ß growth-inhibitory effects by regulating the expression of 

several cell cycle-related genes. We have recently discovered that certain SMAD proteins are 

major substrates for cyclin-dependent kinases (CDKs). We expect that our findings will have a 

major impact in the cancer research field and may be useful for therapeutic applications. 

TGF-ß-Inducible Gene Regulation: SMAD proteins can mediate transforming growth factor-ß 

(TGF-ß) inducible transcriptional responses. In an effort to search for TGF-ß/SMAD inducible 

genes, we identified Smad7, which is rapidly upregulated by TGF-ß and can antagonize TGF-ß 

signaling by binding to and inhibiting the TGF-ß receptor function. We found that TGF-ß can 

stabilize Smad7 mRNA as well as activate Smad7 transcription. The Smad7 promoter is the first 

TGF-ß responsive promoter identified in vertebrates that contains the 8 base pair palindromic 

SMAD binding element (SBE), an optimal binding site for SMAD. We are using Smad7 

promoter as a model system to elucidate the molecular mechanisms of TGF-ß-inducible gene 

regulation. We have also identified SMAD interreacting proteins that may regulate SMAD 

transcription activity and are in the process of characterizing these interacting proteins. 

Characterization of SMAD4 as a pancreatic tumor suppressor: SMAD4 is a pancreatic 

tumor suppressor. More than 50% of pancreatic cancers bear mutations in the SMAD4 locus 

(~30% homozygous deletions and ~22-25% mutations with loss of heterozygosity). The 

mechanism of how SMAD4 functions as a pancreatic tumor suppressor is not completely 

defined. Our work is directed towards addressing this important issue. 

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Publications: 

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Fang Liu 

Denissova, N. G., Pouponnot, C., Long, J., He, D. and Liu, F. (2000). Transforming growth 

factor ß-inducible independent binding of SMAD to the Smad7 promoter. 

Proc. Natl. Acad. Sci. USA, 12:6397-6402. 

Liu, F. (2001). SMAD4/DPC4 and pancreatic cancer survival. Clin Cancer Res. 7:3853-3856. 

14

Peter Lobel, Ph.D. 


School, Department of Pharmacology 

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 recently led to the identification of a disease gene that 

causes a fatal childhood neurodegenerative disorder. At CABM he was the first faculty member of UMDNJ to be named a Searle Scholar, a 

prestigious award given to newly appointed faculty members who show outstanding promise in biomedical research. 

Our laboratory has developed new methods for disease discovery and identified the molecular 

bases for three fatal neurodegenerative disorders based on 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 6phosphate 

serves as a recognition marker that allows the enzymes to bind mannose 6-phosphate 

receptor which ferry 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. For instance, we can fractionate proteins in 

normal and disease specimens by 2-dimensional gel eletecrophoresis and then, in a manner 

analogous to Western blotting, use a radiolabeled mannose 6-phosphate receptor derivative to 

selectively visualize phosphorylated lysosomal enzymes. This allows us to compare the spectrum 

of lysosomal enzymes present in normal and disease specimens. If the disease specimen lacks a 

given lysosomal protein, this may be responsible for disease. To investigate this, we purify and 

sequence the normal protein, clone the corresponding gene, and examine patients for mutations 

associated with disease. In this manner, we found that a fatal childhood neurodegenerative disease 

called LINCL (late infantile neuronal ceroid lipofuscinosis) is caused by mutations in a gene 

encoding a previously undiscovered lysosomal protease. 

After we identified the gene and determined the function of corresponding protein, we developed 

rapid biochemical and DNA-based assays for definitive pre-and postnatal diagnosis and carrier 

screening. This allows for genetic counseling to prevent further occurrence of the disease. 

However, in the absence of universal carrier testing, new cases will continue to arise so it is 

important to develop effective therapies that can halt and reverse disease progression. To this end, 

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Peter Lobel 

we have produced recombinant enzyme in a form that can be taken up by affected cells in culture 

to correct the primary defect. We are also working to develop a LINCL mouse model that should 

allow detailed studies of disease pathophysiology and evaluation of potential therapeutics 

strategies. 

Another research program in the laboratory is to identify the spectrum of lysosomal enzymes 

encoded by the human genome. This research is particularly timely given the current effort 

towards determining the complete sequence of the human genome. Our approach is to purify 

mannose 6-phosphorylated proteins and then analyze each protein by peptide mapping, mass 

spectrometry, and chemical sequencing. This information is used to search sequence databases to 

determine if a given protein corresponds to a known lysosomal enzyme or if it represents a 

previously unidentified species. We recently used this approach to determine the molecular basis 

for Niemann Pick type C2 disease, a fatal cholesterol storage disorder. In addition to their roles in 

human inherited diseases, alterations in the lysosomal system have been implicated in a variety of 

disease processes such as tumor invasion and metastasis in cancer, tissue destruction in arthritis, 

and early changes associated with Alzheimer’s disease. Once we develop the tools to visualize 

and characterize the players, our ultimate goal will be to understand the role that lysosomal 

proteins play in these widespread pathological processes. 

Publications: 

Naureckiene, S., Sleat, D.E., Lackland, H., Fensom, A., Vanier, M.T., Wattiaux, R., Jadot, M. and 

Lobel, P. (2000). Indentification of HE1 as the second gene of Niemann-Pick C disease. Science 

290:2227-2229. 

Sohar, I., Lin, L. and Lobel, P. (2000). Enzyme-based diagnosis of classical late infantile 

neuronal ceroid lipofuscinosis: comparison of tripeptidyl peptidase I and pepstatin-insensitive 

protease assays. Clin. Chem. 46:1005-1008. 

Lin, L., Sohar, I., Lackland, H. and Lobel, P. (2001). The human CLN2 protein/tripeptidylpeptidase 

I is a serine protease that autoactivates at acidic pH. J. Biol. Chem. 276: 2249-2255. 

Sleat, D.E., Sohar, I., Gin, R.M. and Lobel, P. (2001). Aminoglycoside-mediated suppression of 

nonsense mutations in late infantile neuronal ceroid lipofuscinosis. Eur. J. Paed. Neurol. 5A:45- 

50. 

Lin, L. and Lobel, P. (2001). Production and characterization of recombinant human CLN2 

protein for enzyme replacement therapy in late infantile neuronal ceroid lipofuscinosis. Biochem. 

J. 357:49-55. 

Lin, L. and P. Lobel. (2001). Expression and analysis of CLN2 variants in CHO cells: Q100r 

represents a polymorphism, and G389E and R447H represent loss-of-function mutations. Hum. 

Mutat. 18:165. 

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16

James H. Millonig, Ph.D. 

Resident Faculty Member, CABM; Assistant Professor, UMDNJ-Robert Wood Johnson 

Medical School, Department of Neuroscience and Cell Biology 

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 Whitehall Foundation, the National Ataxia Foundation and N.J. Governor’s Council on Autism. 

My laboratory studies the development of the dorsal CNS by combining mouse molecular 

genetics and neuroanatomical approaches. The dorsal CNS includes the cerebrum, hippocampus, 

cerebellum and sensory neurons of the spinal cord. These structures play an important role in 

cognition, learning, memory, motor movement and sensation. During development, millions of 

different types of neurons are generated which are involved in controlling these neural functions. 

Our ultimate goal is to understand the molecular pathways that lead to the generation of different 

types of dorsal neurons in two simple dorsal anatomical structures, the spinal cord and 

cerebellum. 

The entire dorsal CNS arises from the lateral neural plate very early in development. At this 

stage, the epidermal ectoderm is adjacent to the lateral neural plate and dorsalizes it through the 

action of secreted proteins. This results in the delamination of the neuroectoderm from the 

epidermis and the eventual folding of the neural plate into a neural tube. Failure of this to occur 

results in spina bifida, a common human disorder that has an incidence of 1:1000. 

Once the neural tube forms, another transitory signaling center called the roof plate that is situated 

on the dorsal midline is believed to instruct neighboring cells to a particular lineage again through 

the action of secreted factors. As a postdoctoral fellow at The Rockefeller University, we 

identified the first mouse mutation to lack a roof plate. It is a spontaneous mouse mutation called 

dreher (dr). Our positional cloning of the locus determined that a gene called Lmx1a is 

responsible for the loss of roof plate in dr/dr embryos (Millonig et al, 2000). 

Expression analysis of Lmx1a indicated that it was expressed just in the roof plate. Dr can then 

be used as a mouse model to determine the role of the roof plate during dorsal CNS development. 

Any perturbation to dorsal neurons in dr/dr embryos must be due to loss of roof plate signaling. 

Our phenotypic analysis has determined that the roof plate is necessary to generate the normal 

complement of dorsal neurons and is required even after their commitment for their initial steps of 

differentiation, neuronal migration and axon extension (Millonig, unpublished results). 

We are now investigating the possible cellular mechanisms that result in the decrease of dorsal 

neurons in dr/dr embryos. There are at least three possibilities: decrease in the rate of proliferation 

of progenitors, increased cell death or progenitors spend a longer time in the cell 

__________________________________________________________________________________ 


17

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James H. Millonig 

cycle. Preliminary data suggests that the last could be true, indicating that the roof plate 

coordinates the withdrawal of cells from the cell cycle (Tanya Borusk, unpublished results). 

Splotch (Sp), another mouse mutant, exhibits a similar cell cycle withdrawal phenotype, providing 

us with two mutations that together should lead to insights into the molecular mechanisms that 

control dorsal neuronal generation. 

Another spontaneous mouse mutation, vacuolated lens (vl), appears to have the opposite 

phenotype to dr, too much roof plate. Vl/vl embryos have an expanded dorsal midline and exhibit 

phenotypes consistent with too much roof plate, such as an increase in the number of dorsal 

neurons and overgrowth of the dorsal vertebrae that lie above the roof plate. In dr, this part of the 

vertebrae is missing. Vl maps near the dr locus but sequencing of Lmx1a from vl/vl embryos 

indicates that Lmx1a is not responsible for the mutation (Jigar Desai, unpublished results). We 

are now in the process of positionally cloning the locus. 

We have also been focusing on identifying genes that are downstream of roof plate signaling. To 

this end, we have identified transcription factors that are expressed in nested domains in the 

developing cerebellum that appear to be restricted to particular cellular populations (Max 

Tischfield, unpublished results). Phenotypic analysis of dr embryos and in vitro explants are 

being used to determine if roof plate signaling is necessary and sufficient for the expression of 

these dorsal markers. The function of these genes is being tested through a combination of mouse 

genetics and the forced misexpression in the cerebellum during chick embryogenesis. Through 

these different approaches the pathways involved in dorsal CNS development will be ascertained. 

Publications: 

Millonig, J.H., Millen, K.J and Hatten, M.E. (2000) The Mouse Dreher gene (Lmx1a) Controls 

Formation of the Roof Plate Formation in Vertebrate CNS. Nature. 403:764-768. 

18

Michael M. Shen, Ph.D. 

Resident Faculty Member, CABM; Associate Professor, UMDNJ-Robert Wood Johnson 

Medical School, Department of Pediatrics 

Mammalian Embryogenesis Laboratory 

Dr. Michael Shen completed his doctoral work in genetics under Dr. Jonathan Hodgkin at the MRC laboratory of Molecular Biology in 

Cambridge, England. He then performed postdoctoral work at Harvard Medical School under Dr. Philip Leder before joining CABM in 1994. 

He is a former recipient of a Leukemia Society of America Special Fellowship, a Howard Hughes Medical Institute Post-doctoral Fellowship, a 

Jane Coffin Childs Post-doctoral Fellowship, and a National Science Foundation Graduate Fellowship. Dr. Shen is a member of the NIH Study 

Section on Cell Development and Function and of the National Cancer Institute Steering Committee for the Mouse Models of Human Cancer 

Consortium. 

The research in our laboratory is directed towards understanding the molecular mechanisms 

involved in (i) formation of the embryonic anterior-posterior and left-right axes in the mouse 

embryo, (ii) signal transduction by EGF-CFC proteins and the TGF-beta-related factor Nodal, 

and (iii) prostate development and carcinogenesis. 

To address the first two areas, we are pursuing studies of the recently identified EGF-CFC gene 

family, whose members encode novel extracellular proteins. We have used gene targeting 

approaches in mice to demonstrate that EGF-CFC genes play essential roles in embryonic axis 

formation, namely that Cripto is required for correct orientation of the anterior-posterior (A-P) 

axis, while Cryptic is necessary for determination of the left-right (L-R) axis. Thus, targeted 

disruption for Cripto results in a 90 degree mis-orientation of the A-P axis, indicating that Cripto 

is essential for an axial rotation that converts a proximal-distal asymmetry into an orthogonal A- 

P axis during pre-gastrulation stages. In contrast, null mutation for Cryptic results in L-R 

laterality defects, including randomized abdominal situs, pulmonary right isomerism, and severe 

cardiac defects, as well as lack of expression of regulatory genes in the L-R pathway, suggesting 

that Cryptic is essential for a key step in L-R axis specification. Our results also support an 

interaction of EGF-CFC proteins with the TGF-beta-related factor Nodal and with activin 

receptors, which we are currently examining using biochemical and cell culture approaches. 

In another major area of interest, we are investigating prostate development and cancer (in 

collaboration with Dr. Cory Abate-Shen's lab). We are focusing on the role of the Nkx3.1 

homeobox gene, which displays restricted expression in the embryonic and adult mouse prostate. 

We have demonstrated that homozygous Nkx3.1-/- mice created by gene targeting display 

progressive defects in prostate histology with advancing age, resulting in epithelial hyperplasia 

and dysplasia. These lesions in aged mutant mice resemble human prostatic intraepithelial 

neoplasia (PIN), which is believed to represent the precursor to prostate carcinoma. These 

observations are noteworthy given the mapping of human NKX3.1 to the minimal deleted 

interval of chromosome 8p21, which is lost as an early and frequent event in human prostate 

cancer. Our findings show that Nkx3.1 plays a critical role in the normal morphogenesis and 

function of the prostate, and suggest that it may represent a prostate-specific tumor suppressor 

gene. 

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19

Publications: 

__________________________________________________________________________________ 


Michael M. Shen 

Yan, Y.-T., Stein, S. M., Ding, J., Shen, M. M. and Abate-Shen, C. (2000). A novel PF/PN 

motif inhibits nuclear localization and DNA binding activity of the ESX1 homeoprotein. Mol. 

Cell. Biol. 20:661-671. 

Mudgett, J. S., Ding, J., Guh-Siesel, L., Chartrain, N. A., Yang, L., Gopal, S. and Shen, M. M. 

(2000). Essential role for p38a mitogen-activated protein kinase in placental angiogenesis. Proc. 

Natl. Acad. Sci. USA 97:10454-10459. 

Bamford, R. N., Roessler, E., Burdine, R. D., Saplakoglu, U., de la Cruz, J., Splitt, M., 

Goodship, J. A., Towbin, J., Bowers, P., Ferrero, G. B., Marino, B., Schier, A. F., Shen, M. M., 

Muenke, M. and Casey, B. (2000) . Loss-of-function mutations in the EGF-CFC gene Cfc1 are 

associated with human left-right laterality defects. Nature Genet. 26:365-369. 

Hu, G., Lee, H., Price, S. M., Shen, M. M. and Abate-Shen, C. (2001) . Msx homeobox genes 

inhibit differentiation through up-regulation of Cyclin D1. Development 128:2373-2384. 

Kimura, C., Shen, M. M., Takeda, N., Aizawa, S. and Matsuo, I. (2001) . Complementary 

functions of Otx2 and Cripto in initial patterning of mouse epiblast. Dev. Biol. 128:2373-384. 

Review articles (peer-reviewed): 

Schier, A. F. and Shen, M. M. (2000) . Nodal signalling in vertebrate development. Nature 

403:385-389. 

Shen, M. M. and Schier, A. F. (2000). The EGF-CFC gene family in vertebrate development. 

Trends Genet. 16:303-309. 

Abate-Shen, C. and Shen, M. M. (2000). Molecular genetics of prostate cancer. Genes Dev. 

14:2410-2434. 

Book chapters/technical articles/reviews: 

Shen, M. M. (2001). Identification of differentially expressed genes in mouse development 

using differential display and in situ hybridization. Methods 24:15-27. 

Cunha, G. R., Donjacour, A. A., Hayward, S. W., Thomson, A. A., Marker, P. C., Abate-Shen, 

C., Shen, M. M. and Dahiya, R. (2002). Cellular and molecular biology of prostatic 

development. In: Prostate Cancer: Principles and Practice. Eds. Kantoff, P. W., Carroll, P., 

D'Amico, A. V. (Lippincott, Williams and Wilkins, Philadelphia), pp. 16-28. 

20

Eileen White, Ph.D. 

Associate Investigator, Howard Hughes Medical Institute; Resident Faculty Member, 

CABM; Professor, Rutgers, Department of Molecular Biology and Biochemistry 

Viral Transformation Laboratory 

Dr. Eileen White transferred her research program to CABM in July 1990 from Cold Spring Harbor Laboratory where she was a staff 

investigator. She conducted postdoctoral research at the Cold Spring Harbor laboratory as a Damon Runyon – Walter Winchell Fellow, working 

with Dr. Bruce Stillman. Her work is currently funded by a MERIT Award from NIH and Howard Hughes Medical Institute. Dr. White is a 

member of the National Cancer Institute Board of Scientific Counselors. 

The goal of our research program is to examine viral oncogenes and mechanisms of mammalian 

cell growth. Specifically, the White lab is working to determine the mechanisms by which 

oncogenes of the DNA tumor virus adenovirus stimulate cell proliferation and inhibit cell death 

which leads to malignant transformation. 

We study the mechanisms by which human DNA tumor viruses deregulate cell cycle and 

apoptosis (programmed cell death) control in the development of cancer and during 

productive viral infection. Understanding pathways that control cell proliferation and cell death 

will lead to better treatments for cancer and viral infections. 

Description of Research 

The DNA tumor virus adenovirus infects human cells, recruits them into a proliferative state, 

and borrows elements of the host cell transcription, translation, and DNA replication machinery 

to reproduce viral proteins and DNA. In rodent cells which are semipermissive for adenovirus 

infection, cell growth is deregulated but virus replication is ineffective. As the viral infection 

does not progress to completion, the deregulation of cell growth control produces transformation. 

The viral genes required for oncogenic transformation are the E1A and E1B oncogenes. 

Understanding how the products of these viral oncogenes alter cell growth control pathways is 

important for establishing how cancer develops. 

Regulation of programmed cell death (apoptosis) by E1A and E1B is necessary for sustaining a 

productive infection in human cells and is an integral part of the transformation process in rodent 

cells. The E1A proteins are responsible for initiating a proliferative response, and an indirect 

consequence of this required function of E1A is the induction of apoptosis. The E1B gene 

encodes overlapping, redundant functions to suppress apoptosis, the 19K and 55K proteins. 

Thus, E1A expression and subsequent growth deregulation can occur unimpeded by cell death in 

the presence of E1B expression. Without inhibition of apoptosis by E1B, transformation of 

rodent cells is rare, and premature death of the host cell impairs virus yield in productively 

infected human cells. The human bcl-2 proto-oncogene, which is known to inhibit apoptosis in 

other systems, will also suppress apoptosis induced by E1A expression and cooperate with E1A 

to transform primary rodent cells. Thus, inhibition of apoptosis is an important step in the 

progression of the transformed state. 

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21

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Eileen White 

There is substantial evidence that the product of the p53 tumor suppressor gene mediates the 

induction of apoptosis by E1A and that the E1B and bcl-2 gene products function by disabling 

p53. Expression of the E1B 19K or bcl-2 genes will prevent p53-dependent apoptosis by 

modifying p53 function indirectly, whereas the E1B 55K protein acts by a direct interaction with 

p53. bcl-2 may be the cellular equivalent of the E1B 19K gene, with its oncogenic and antiapoptotic 

activity, in all or in part, attributed to bypassing the function of p53. 

One of the most important, recently identified events in humans and other life forms is 

programmed cell death or apoptosis. Failure of this process can result in excessive cell growth 

as in cancer or abnormal development; inappropriate induction of programmed cell death is 

responsible for many other diseases including neurodegenerative disorders. By studying the 

oncogenes of the DNA tumor virus, adenovirus, we have determined that malignant 

transformation requires (i) stimulation of proliferation by viral E1A proteins (ii) inhibition by 

E1B proteins of the apoptosis that results from the inappropriate stimulation, (iii) inhibition by 

E1B proteins of the apoptosis that results from the inappropriate E1A induction of apoptosis is 

mediated through the cellular p53 tumor suppressor, and E1B products prevent p53-dependent 

cell death both directly (55 Kd protein) and indirectly (19 Kd protein). 

Results 

Our recent studies have demonstrated that E1B 19 Kd protein is the equivalent of the cellular 

product of the bcl-2 gene. Both have oncogenic and anti-apoptotic activity, all or in part, 

attributed to bypassing the function of the p53 tumor suppressor. We have found that the E1B 19 

Kd protein blocks apoptosis by interacting with and inhibiting the p53-inducible and death 

promoting Bax protein. An E1B 19 Kd interacting human protein called Nbk/Bik has been 

identified, shown to contain a BH3 domain, and demonstrated to induce apoptosis. 

E1A promotes apoptosis by interacting with and inhibiting negative regulators of cell cycle 

control. Binding of E1A to, and inhibition of, the transcriptional coadaptor p300 promotes 

accumulation of the p53 tumor suppressor protein which induces apoptosis. By inhibiting p300, 

E1A prevents the transcriptional activation of mdm-2, the product of which interacts with and 

promotes the degradation of p53. Thus the E1A-p300 interaction disables the negative feedback 

loop to control p53 levels, which left unrestrained, causes apoptosis rather than growth arrest. 

The E1B 19K protein functions analogously to Bcl-2 to inhibit apoptosis by E1A, p53, and 

multiple other stimuli. The E1B 19K protein functions by at least two independent mechanisms 

to inhibit apoptosis. First, the E1B 19K protein binds to the pro-apoptotic Bax protein to prevent 

loss of mitochondrial membrane potential, caspase activation, and apoptosis. Second, the E1B 

19K protein inhibits caspase interaction by interfering with the function of adaptor molecules 

such as FADD and Ced-4 that interact with and activate caspases. By inhibiting FADDdependent 

activation of the caspase FLICE, the E1B 19K protein can disable both the TNF-α 

and Fas-mediated death signaling pathways which play an important role in immune surveillance 

against virus infection and cancer. The E1B 19K protein binds to Ced-4, and presumably 

mammalian Ced-4 homologues, and thereby prevents caspase activation. Thus, the study of the 

22

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Eileen White 

mechanism of regulation of apoptosis by the adenovirus transforming proteins has revealed 

important regulatory steps in death signaling pathways. 

Our findings have been reported in several original research reports and review articles and at 

numerous international symposia. 

Future Directions 

The current aim is to determine the molecular basis by which apoptosis is regulated by E1A, p53, 

E1B and Bcl-2. Establishing how the transforming genes of DNA tumor viruses subvert p53 

function will provide insight into the cause and prevention of cancer and lead to new strategies in 

anticancer therapy. 

Publications: 

Perez, D. and White, E. (2000). TNF-α Signals apoptosis through a Bid-dependent 

conformational change in Bax which is inhibited by E1B 19K. Mol. Cell 6:53-63. 

Thomas, A., Giesler, T. and White, E. (2000). p53 mediates Bcl-2 phosphorylation and 

apoptosis via activation of the Cdc42/JNK1 pathway. Oncogene 19:5259-5269. 

Degenhardt, K., Perez, D. and White, E. (2000). Pathways used by adenovirus E1B 19K to 

inhibit apoptosis in programmed cell death in animals and plants. Editors: J. Bryant, S. Hughes, 

J. Garland; Bios Scientific Publishers LTD, 241-251. 

Sundararajan, R., Cuconati, A., Nelson, D. and White, E. (2001). Tumor Necrosis Factor-α 

induces Bax-Bak interaction and apoptosis which is inhibited by adenovirus E1B 19K. J. Biol. 

Chem. 276:45120-45127. 

White, E. (2001). Regulation of the cell cycle and apoptosis by the oncogenes of adenovirus. 

Oncogene 20:7836-7846. 

Sundararajan, R. and White, E. (2001). E1B 19K Blocks Bax oligomerization and tumor 

necrosis factor alpha-mediated apoptosis. J. Virol. 75: 7506-7516. 

Shen, Y. and White, E. (2001). p53-Dependent apoptosis pathways. Adv. Cancer Res. 82: 55- 

84. 

Henry, H., Thomas, A., Shen, Y. and White, E. (2001). Regulation of the mitochondrial 

checkpoint in p53-mediated apoptosis confers resistance to cell death. Oncogene 21:748-760. 

23

Mengqing Xiang, Ph.D. 

Resident Faculty Member, CABM; Assistant Professor, UMDNJ-Robert Wood Johnson 

Medical School, Department of Pediatrics 

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. His work is currently supported by NIH and the 

Alexandrine and Alexander L. Sinsheimer Fund. 

Our laboratory investigates the molecular mechanisms that govern the determination and 

differentiation of highly specialized sensory cells and neurons. We employ molecular genetic 

approaches to identify and study transcription factors that are required for programming 

development of the retina, inner ear, and somatosensory ganglia. A major focus of our work is to 

develop animal models to study roles of transcription factor genes in normal sensorineural 

development, as well as to elucidate how mutations in these genes cause sensorineural disorders 

such as blindness and deafness. Current projects in my laboratory are centered on studies of 

biological roles of two small families of transcription factor genes – Brn3 POU domain genes 

and Barhl homeobox genes. During the past year we made significant progress in three projects. 

First, our studies have shown that Brn3a plays a key role in the control of soma size, target field 

innervation, and axon pathfinding of inner ear sensory neurons. Second, our work has identified 

an important transcriptional cascade involved in the control of retinal ganglion cell development. 

Finally, we have generated knockout mice to demonstrate that Barhl1 is specifically required for 

the maintenance of cochlear outer hair cells. 

Publications: 

Liu, W., Khare, S. L., Liang, X., Peters, M. A., Liu, X., Cepko, C. L. and Xiang, M. (2000). All 

Brn3 genes can promote retinal ganglion cell differentiation in the chick. Development 

127:3237-3247. 

Liu, W., Mo, Z. and Xiang, M. (2001). The Ath5 proneural genes function upstream of Brn3 

POU domain transcription factor genes to promote retinal ganglion cell development. Proc. Natl. 

Acad. Sci. USA. 98:1649-1654. 

Huang, E. J., Liu, W., Fritzsch, B., Bianchi, L. M., Reichardt, L. F. and Xiang, M. (2001). 

Brn3a is a transcriptional regulator of soma size, target field innervation, and axon pathfinding of 

inner ear sensory neurons. Development 128:2421-2432. 

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24


Structural Biology 

Biomolecular Crystallography Edward Arnold 26 

Protein NMR Spectroscopy Gaetano Montelione 31 

Protein Microchemistry Stanley Stein 33 

Protein Crystallography Ann Stock 34 

__________________________________________________________________________________ 


25

Edward Arnold, Ph.D. 

Resident Faculty Member, CABM; Professor, Rutgers, Department of Chemistry and 

Chemical Biology, Adjunct Professor, UMDNJ-RWJMS, Department of Molecular 

Genetics and Microbiology 

Biomolecular Crystallography Laboratory 

Dr. Arnold obtained his Ph.D. in organic chemistry with Professor Jon Clardy at Cornell University in 1982. From 1982 to 1987, he did 

postdoctoral work 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. Dr. 

Arnold is the director of a multi-center NIH Program Project. He received an NIH MERIT Award in 1999 and was elected a Fellow of the 

American Association for the Advancement of Science in 2001. The laboratory is supported by grants from NIH and industrial collaborators, and 

by research fellowships. 

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 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 Gail Ferstandig Arnold and their 

colleagues are working to develop and apply structure-based drug and vaccine designs for the 

treatment and prevention of serious human diseases. In pursuit of these goals, their laboratory 

takes advantage of cutting-edge research tools, including X-ray crystallography, molecular 

biology, virology, protein biochemistry, and macromolecular engineering. 

The approaches being developed in the Arnold laboratory are applicable to a wide array of 

human health problems, ranging from infectious diseases to cancer and diseases caused by 

hereditary genetic defects. Much of the Arnold lab’s research effort to date has focused on the 

development of drugs and vaccines for the treatment and prevention of AIDS. Examples of the 

results of these studies include: 1) collaborative development of drugs for the treatment of AIDS, 

some of which appear to be more effective than treatments in current use; and 2) production of 

AIDS vaccine candidates that have elicited protective immune responses against HIV. 

Dr. Eddy Arnold and coworkers study the structure and function of reverse transcriptase (RT), an 

essential component of the AIDS virus and the target of many of the most widely used anti-AIDS 

drugs. Using the powerful techniques of X-ray crystallography, his team has solved the threedimensional 

structures of HIV-1 RT in complex with a variety of antiviral drugs and small 

segments of the HIV genome. These studies have revealed the workings of an intricate and 

fascinating biological machine in atomic detail and have yielded numerous novel insights into 

polymerase structure-function relationships, detailed mechanisms of drug resistance, and 

structure-based design of RT inhibitors. Synthesis of this information has led to the development 

of a number of inhibitors that show great promise as potential treatments for AIDS. 

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26

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Edward Arnold 

Drug development and structural studies of a molecule as complex as HIV RT require immense 

and highly coordinated resources. Dr. Eddy Arnold has been fortunate to have highly successful 

collaborations with the groups of Dr. Stephen Hughes (NIH NCI, Frederick, MD) and Dr. Paul 

Janssen (Center for Molecular Design, Janssen Research Foundation, Belgium), and generous 

access to synchrotron X-radiation sources (CHESS, APS, and BNLS). Hughes and his group 

have contributed expertise in protein engineering, production, and biochemistry at every stage of 

the RT project. Janssen and his coworkers (including chemists at Janssen Research Foundation, 

Springhouse, PA) have synthesized hundreds of molecules from a number of chemical families 

in search of optimal drug candidates, eventually leading to the discovery of agents effective 

against isolates of HIV containing drug-resistance mutations that can cause the currently 

available drugs to fail. Crystallographic work from the Arnold and Hughes laboratories has 

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 have used this 

structural information to guide the design and synthesis of new molecules with improved 

properties. Following further evaluation against drug-resistant variants, scientists at Tibotec- 

Virco (Mechelen, Belgium) have coordinated testing of two of the molecules with highly 

promising results in Phase II clinical trials. Some of these anti-HIV compounds are inexpensive 

to make, potently and broadly effective, non-toxic, and simple to administer. These molecules 

have the potential to be widely accessible for treating AIDS in underdeveloped nations. 

Vaccines have proven to be the most effective tools for worldwide control of infectious diseases. 

Our laboratory’s vaccine development project, jointly directed by both of us, involves 

engineering a human common cold virus, rhinovirus, to display immunogenic segments from 

more dangerous pathogens for the purpose of developing vaccines against these pathogens. This 

work involves generating “combinatorial libraries” of chimeric human rhinoviruses using a 

technique called random systematic mutagenesis. Foreign sequences are linked to the HRV 

sequences via adapters of randomized sequences and lengths, leading to a constellation of 

presentations. Large sets of such viruses presenting the foreign sequences in many 

conformations are generated and then selected with appropriate antibodies aimed at the target 

pathogen, allowing for the isolation of vaccine candidates with the most effectively reconstructed 

foreign segments. Our combinatorial approach to the vaccine problem is akin to buying many 

tickets for a lottery: the chances of winning the jackpot are increased by having more tickets. 

Chimeric rhinovirus constructs have been made that elicit antibodies (in guinea pigs) capable of 

potently neutralizing the AIDS virus in cell culture. Virus libraries incorporating immunogens 

from the HIV gp120 and gp41 envelope glycoproteins have been constructed. We are also 

working collaboratively with Professor John Taylor of the Rutgers Chemistry and Chemical 

Biology Department to probe the immunogenic determinants of an epitope from gp41 using 

synthetic peptides. In addition to looking for chimeric viruses and peptides capable of eliciting 

the most potent and broad immune responses possible, we are also interested in elucidating the 

molecular determinants of immunogenicity. Knowledge of the relationship between structure 

and function (i.e., neutralization) would give us the opportunity to develop better vaccine 

candidates. The laboratory team is also using X-ray crystallography to analyze the structures of 

27

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Edward Arnold 

some of the engineered viruses (and soon peptides), alone and in complex with anti-HIV 

antibodies. Ultimately we hope to identify three-dimensional correlates of immunogenicity, and 

use this information to develop a structural basis for design of more effective human vaccines. 

There is every reason to expect that a structure-based approach to vaccine development will 

become as important to vaccinology as has structure-based drug design to drug discovery and 

development. 

In addition to working to develop novel vaccines and 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) the human mRNA capping 

enzyme and its associated factors (with Dr. Aaron Shatkin at CABM); 2) the TNF-like cytokine 

BLyS (B lymphocyte stimulator, with Yuling Li and colleagues at Human Genome Sciences); 3) 

and hantavirus proteins (with Dr. Colleen Jonssen at University of New Mexico). The structural 

group also collaborates with Dr. Gaetano Montelione (CABM) on crystallography of proteins 

targeted by the Northeast Structural Genomics Consortium. 

Publications: 

Sarafianos, S.G., Das, K., Tantillo, C., Clark, A.D. Jr., Ding, J., Whitcomb, J., Boyer, P.L., 

Hughes, S.H. and Arnold, E. (2001). Crystal structure of HIV-1 reverse transcriptase in 

complex with a polypurine tract RNA:DNA. EMBO J. 20: 1449-1461. 

Boyer, P.L., Sarafianos, S.G., Arnold, E. and Hughes, S.H. (2001). Selective excision of AZT 

by drug-resistant human immunodeficiency virus reverse transcriptase. J. Virol. 75:4832-4842. 

Das, K, Xiong, X., Yang, H., Westland, C.E., Gibbs, C.S., Sarafianos, S.G. and Arnold, E. 

(2001). Molecular modeling and biochemical characterization reveals the mechanism of 

hepatitis B virus polymerase resistance to lamivudine (3TC) and emtricitabine (FTC). J. Virol. 

75:4771-4779. 

Hsiou, Y., Ding, J., Das, K., Clark, A.D., Jr., Boyer, P.L., Lewi, P., Janssen, P.A.J., Kleim, J.P. 

Rösner, M., Hughes, S.H. and Arnold, E. (2001). The Lys103Asn mutation of HIV-1 RT: a 

novel mechanism of drug resistance. J. Mol. Biol. 309:437-445. 

Tachedjian, G., Orlova, M., Sarafianos, S.G., Arnold, E. and Goff, S.P. (2001). Nonnucleoside 

reverse transcriptase inhibitors are chemical inducers of dimerization of the human 

immunodeficiency type 1 reverse transcriptase. Proc. Natl. Acad. Sci. USA. 98:7188-7193. 

Boyer, P.L., Gao, H.-Q., Clark, P.K., Sarafianos, S.G., Arnold, E. and Hughes, S.H. (2001). 

YADD mutants of human immunodeficiency virus type 1 and Moloney murine leukemia virus 

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Edward Arnold 

reverse transcriptase are resistant to lamivudine triphosphate (3TCTP) in vitro. J. Virol. 75:6321- 

6328. 

Rossmann, M.G. and Arnold, E. (2001). Editors of "International Tables for X-Ray 

Crystallography, Volume F: Crystallography of Biological Macromolecules.” Kluwer Academic 

Publishers, Dordrecht, 832 pages. 

Arnold, E. and Rossmann, M.G. (2001). Overview of this volume. In "International Tables for 

X-Ray Crystallography, Volume F: Crystallography of Biological Macromolecules," M.G. 

Rossmann and E. Arnold, editors. Kluwer Academic Publishers, Dordrecht, pp. 1-3. 

Arnold, E. (2001). Gazing into the crystal ball: Perspectives for the future. In "International 

Tables for X-Ray Crystallography, Volume F: Crystallography of Biological Macromolecules," 

M.G. Rossmann and E. Arnold, editors. Kluwer Academic Publishers, Dordrecht, p. 26. 

Arnold, E. and Rossmann, M.G. (2001). 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," M.G. 

Rossmann and E. Arnold, editors. Kluwer Academic Publishers, Dordrecht, pp. 279-292 

Ding, J. and Arnold, E. (2001). Survey of programs for crystal structure determination and 

analysis of macromolecules. In "International Tables for X-Ray Crystallography, Volume F: 

Crystallography of Biological Macromolecules," M.G. Rossmann and E. Arnold, editors. 

Kluwer Academic Publishers, Dordrecht, pp. 685-694. 

Rossmann, M.G. and Arnold, E. (2001). Patterson and molecular replacement techniques. In 

International Tables for Crystallography. Shmueli, U., ed. Vol. B: Reciprocal Space. Kluwer 

Academic Publishers, Dordrecht, 2 nd edition, pp. 235-263. 

Ludovici, D.W., Kukla, M.J., Grous, P.G., Krishnan, S., Andries, K., de Béthune, M.-P., Azijn, 

H., Pauwels, R., De Clercq, E., Arnold, E. and Janssen, P.A.J. (2001). Evolution of anti-HIV 

drug candidates. Part 1: From ∝-Anilinophenylacetamide (∝-APA) to imidoyl thiourea (ITU). 

Bioorg. Med. Chem. Lett. 11:2225-2228. 

Ludovici, D.W., Kavash, R.W., Kukla, M.J., Ho, C.Y., Ye, H., De Corte, B.L., Andries, K., de 

Béthune, M.P., Azijn, H., Pauwels, R., Moereels, H.E.L., Heeres, J., Koymans, L.M.H., de 

Jonge, M.R., Van Aken, K.J.A., Daeyaert, F.F.D., Lewi, P., Das, K., Arnold, E. and Janssen, 

P.A.J. (2001). Evolution of Anti-HIV Drug Candidates Part 2: Diaryltriazine (DATA) 

Analogues. Bioorg. Med. Chem. Lett. 11:2229-2234. 

Ludovici, D.W., De Corte, B.L., Kukla, M.J., Ye, H., Ho, C.Y., Lichtenstein, M.A., Kavash, 

R.W., Andries, K., de Béthune, M.-P., Azijn, H., Pauwels, R., Lewi, P.J., Heeres, J., Koymans, 

L., de Jonge, M., Van Aken, K.J.A., Daeyaert, F.F.D., Das, K., Arnold, E. and Janssen, P.A.J. 

29

__________________________________________________________________________________ 


Edward Arnold 

(2001). Evolution of anti-HIV drug candidates. Part 3: diarylpyrimidine (DAPY) analogues. 

Bioorg. Med. Chem. Lett. 11:2235-2239. 

Gao, H-Q., Sarafianos, S.G., Arnold, E. and Hughes, S.H. (2001). RNase H cleavage of the 5’ 

end of the HIV-1 genome. J. Virol. 75:11874-11880. 

Das, K., Xiao, R., Wahlberg, E., Hsu, F., Arrowsmith, C.H., Montelione, G. and Arnold, E. 

(2001). X-ray crystal structure of MTH938 from Methanobacterium thermoautotrophicum at 2.2 

Å resolution reveals a novel tertiary protein fold. Proteins: Structure, Function and Genetics 

45:486-488. 

Fitzgibbon, J.E., Dicola, M.B., Arnold, E., Das, K., Sha, B.E., Pottage, J., Nahass, R., Gaur, S. 

and John Jr., J.F. HIV-1 reverse transcriptase mutations found in a drug-experienced patient 

confer reduced susceptibility to multiple nucleoside reverse transcriptase inhibitors. Antiviral 

Therapy. In press. 

Oren, D.A., Li, Y., Volovik, Y., Morris, T.S., Dharia, C., Das, K., Galperina, O., Gentz, R. and 

Arnold, E. In the groove: structural basis of BlyS receptor recognition. Nature Structural 

Biology. In press. 

30

Gaetano Montelione, Ph.D. 

Resident Faculty Member, CABM; Professor, Rutgers, Department of Molecular Biology 

and Biochemistry; Adjunct Professor UMDNJ-RWJMS Department of Biochemistry 

Protein NMR 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 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. His laboratory has determined 3D solution structures for epidermal growth factor, 

type-α transforming growth factor, RNA-binding proteins involved in cold-shock response, and immunoglobulin-binding proteins. He is a 

member of the NSF Molecular Biophysics Study Section. 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. 

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 

collaboration with 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 bacterial 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 hundreds of 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 can yield new functions for tens of new structures 

per year and can thus have tremendous scientific impact. A New Jersey Commission on Science 

and Technology Excellence Award has been made to a research team organized jointly by 

Montelione and Steve Anderson to pursue an Initiative in Structural Bioinformatics and 

Genomics based on these ideas. Montelione is also director of the NIH-funded Northeast 

Structural Genomics Consortium, a multi-year $25 million inter-institutional pilot project in 

large scale structural proteomics. 

Publications: 

Sahasrabudhe, P.V., Xiao, R. and Montelione, G.T. (2001). Resonance assignments for 

the N terminal domain from human RNA-binding protein with multiple splicing (RBP MS) 

J. Biomol. NMR 19: 285-286. 

__________________________________________________________________________________ 


31

Gaetano T. Montelione 

Moseley, H.N.B., Monleon, D. and Montelione, G.T. ( 2001) Automatic determination of 

protein backbone resonance assignments from triple-resonance NMR data. Meth. Enzymol. 339: 

91-108. 

Bertone, P., Kluger, Y., Zheng, D.; Edwards, A.M., Arrowsmith, C.H., Montelione, 

G.T. and Gerstein, M. (2001). SPINE: An integrated tracking database and data mining 

approach for prioritizing feasible targets in high-throughput structural proteomics 

Nucleic Acids Res. 29: 2884-2898. 

Kulikowski, C. A., Muchnik, I., Yun, H. J., Dayanik, A. A., Zheng, D., Song, Y. and 

Montelione, G. T. (2001). Protein structural domain parsing by consensus reasoning 

over multiple knowledge sources and methods. MedInfo 10: 965-969. 

Greenfield, N.J., Huang, Y., Palm, T., Swapna, G.V.T., Monleon, D., Montelione, G.T. 

and Hitchcock-DeGregori, S.E. (2001). Solution NMR structure and folding dynamics 

of the N-terminus of a rat non-muscle α-tropomyosin in an engineered chimeric protein. 

J. Mol. Biol. 312: 833 – 847. 

Das, K., Xiao, R., Wahlberg, E., Hsu, F., Arrowsmith, C.A., Montelione, G.T. and 

Arnold, E. (2001). X-ray crystal structure of MTH938 from Methanobacterium 

thermoautotrophicum at 2.2 Å resolution reveals a novel tertiary protein fold. Proteins: Struct. 

Funct. Gen. 45: 486 – 488. 

Cassetti, M.C., Noah, D.L., Montelione, G.T. and Krug, R.M. (2001). Efficient translation 

of mRNAs in Influenza A virus-infected cells is independent of the viral 5’ untranslated region. 

Virology 289: 180-185. 

Montelione, G.T. (2001). Structural Genomics: An approach to the protein folding 

problem. Proc. Natl. Acad. Sci. U.S.A. 98: 13488 –13489. 

Sahasrabudhe, P.V., Chien, C.-Y. and Montelione, G.T. RNA binding motifs. Encyclopedia of 

Life Science. In press. 

Monleón, D., Colson, K., Moseley, H.N.B., Anklin, C., Oswald, R., Szyperski, T. and 

Montelione, G.T. Rapid data collection and analysis of protein resonance assignments using 

AutoProc, AutoPeak, and AutoAssign Software. J. Struct. Funct. Genomics. In press. 

Swapna, G.V.T., Shukla, K., Huang, Y.J., Ke, H.; Xia, B., Inouye, M. and Montelione, 

G.T. Resonance assignments for cold-shock protein ribosome-binding factor A (RbfA) for 

Escherichia coli. J. Biomol. NMR. In press. 

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32

Stanley Stein, Ph.D. 

Resident Faculty Member, CABM; Adjunct Professor, UMDNJ-Robert Wood Johnson 

Medical School, Department of Genetics and Microbiology and Department of 

Neuroscience and Cell Biology; Graduate Faculty Member, Rutgers University, 

Department of Chemistry 

Protein Microchemistry Laboratory 

Dr. Stanley Stein has held research positions at Hoffmann-LaRoche and Schering Corporation where he participated in the discovery and 

development of the prominent anti-viral and anti-cancer therapeutic protein, interferon. His interests in biological and analytical chemistry are 

directed toward both proteins and oligonucleotides. He has also contributed in several ways to academic-industrial technology transfer, including 

fee-for-service analyses, long-term research contracts and entrepreneurial enterprises. 

The Stein laboratory focuses on improving technologies for delivering therapeutic drugs. These 

include enhanced cell uptake of drugs against intracellular targets, preferential delivery to target 

cells such as to macrophages for treating AIDS and tuberculosis, sustained drug release over 

periods of weeks or months to overcome problems of patient noncompliance, oral delivery of 

protein/peptide drugs and oral delivery of water-insoluble small molecule drugs for cancer and 

other life-threatening diseases. 

Publications: 

Qiu, B., Brunner, M., Zhang, G., Sigal, L. and Stein, S. (2000). Selection of continuous epitope 

sequences and their incorporation into polyethylene glycol-peptide conjugates for use in 

serodiagnostic immunoassays: Application to Lyme disease. Biopolymers (Peptide Science) 55: 

319-333. 

Tung, C.-H. and Stein, S. (2000). Preparation and applications of peptide-oligonucleotide 

conjugates. Bioconjugate Chem. 11: 605-618. 

Ramanathan, S., Pooyan, S., Stein, S., Prasad, P. D., Wang, J., Leibowitz, M. J., Ganapathy, V. 

and Sinko, S. (2001). Targeting the sodium dependent multivitamin transporter (SMVT) for 

improving the oral absorption properties of a retro-inverso Tat nonapeptide. Pharmaceutical 

Res.18: 950-956. 

Ramanathan, S., Qiu, B., Pooyan, S., Zhang, G.,Leibowitz, M. J., Stein, S. and Sinko, P. 

(2001). Targeted PEG-based bioconjugates enhance the cellular 

uptake and transport of a HIV-1 TAT nonapeptide. J. Controlled Release 77: 199-213. 

__________________________________________________________________________________ 


33

Ann Stock, Ph.D. 

Associate Investigator, Howard Hughes Medical Institute; Resident Faculty Member, 

CABM; Professor, UMDNJ-Robert Wood Johnson Medical School, Department of 

Biochemistry 

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. Her CABM laboratory has solved structures of several signal transduction proteins, including receptor modification 

enzymes and members of the two-components family of signal transduction proteins. Stock has received National Science Foundation 

Predoctoral and Damon Runyon-Walter Winchell Postdoctoral Fellowships, a Lucille P. Markey Scholar Award in Biomedical Science, the NSF 

Young Investigator Award and a Sinsheimer Scholar Award. She is an associate investigator of the Howard Hughes Medical Institute. 

Research in the Stock laboratory focuses on structure/function studies of signal transduction 

proteins. Effort is concentrated on bacterial histidine protein kinases and response regulator 

proteins that mediate the majority bacterial signaling processes. These systems are important for 

virulence in pathogenic organisms and are currently targets for development of new antibiotics in 

several pharmaceutical companies. During the past year the Stock laboratory determined the 

first structure for a full-length member of the OmpR family of transcription factors, the largest 

subfamily of response regulator proteins. The structure provides insight into the mechanism of 

regulation of the protein by phosphorylation and suggests a limit to the extent of mechanistic 

similarities between proteins of similar structure and function. 

Publications: 

Schlichting, I., Berendzen, J., Chu, K., Stock, A.M., Maves, S.A., Benson, D.E., Sweet, R.M., 

Ringe, D., Petsko, G.A., and Sligar, S.G. (2000). The catalytic pathway of cytochrome P450cam 

at atomic resolution. Science 287: 1615-1622. 

Stock, A.M., Robinson, V.L. and Goudreau, P.N. (2000). Two-component signal transduction. 

Annu. Rev. Biochem. 69: 183-215. 

Buckler, D.R., Anand, G.S. and Stock, A.M. (2000). Response regulator phosphorylation and 

activation: a two-way street? Trends Microbiol. 8: 153-155. 

Anand, G.S., Goudreau, P.N., Lewis, J.K. and Stock, A.M. (2000). Evidence for 

phosphorylation-dependent conformational changes in methylesterase CheB. Protein Sci. 9: 898- 

906. 

Buckler, D.R. and Stock, A.M. (2000). Synthesis of [ 32 P]phosphoramidate for use as a low 

molecular weight phosphodonor reagent. Anal. Biochem. 283: 222-227. 

__________________________________________________________________________________ 


34

__________________________________________________________________________________ 


Ann Stock 

Robinson, V.L., Buckler, D.R. and Stock, A.M. (2000). A tale of two components: a novel 

kinase and a regulatory switch. Nature Struct. Biol. 7: 628-633. 

Hughes, C.A., Mandell, J.G., Anand, G.S., Stock, A.M. and Komives, E.A. (2001). 

Phosphorylation causes subtle changes in solvent accessibility at the interdomain interface of 

methylesterase CheB. J. Mol. Biol. 307: 967-976. 

West, A.H. and Stock, A.M. (2001). Histidine kinases and response regulator proteins in twocomponent 

signaling systems. Trends Biochem. Sci. 26: 369-376. 

Hughes, S.H. and Stock, A.M. (2001). Techniques in molecular biology and protein expression: 

Preparing recombinant proteins for X-ray crystallography. In International Tables for 

Crystallography. Vol. F Crystallography of Biological Macromolecules, M.G. Rossmann and E. 

Arnold, eds., Kluwer Academic Publishers, Dordrecht. The Netherlands. 65-80. 

Saxl, R.L., Anand, G.S. and Stock, A.M. (2001). Synthesis and biochemical characterization of a 

phosphorylated analog of the response regulator CheB. Biochemistry 40: 12896-12903. 

35

Molecular Genetics 

___________________________________________________________________________________________________________ 


Protein Engineering Stephen Anderson 37 

Viral Pathogenesis Arnold Rabson 39 

Molecular Virology Aaron Shatkin 41 

__________________________________________________________________________________ 


36

Stephen Anderson, Ph.D. 

Resident Faculty Member, CABM; Associate Professor, Rutgers University, Department 

of Molecular Biology and Biochemistry 

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 California-based 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. He is an associate editor of 

the journal SEQUENCE. Currently Dr. Anderson is on leave at GeneFormatics, Inc. 

Protein Engineering Laboratory 

Our laboratory is focusing on the study of protein folding and molecular recognition. We are 

particularly interested in the role these processes may play in the pathophysiology of 

Alzheimer’s disease. The Alzheimer’s β amyloid precursor protein (APP) is a large, membranebound 

glycoprotein that is expressed in the body from several different alternatively-spliced 

mRNAs. Contained within this precursor protein is the amyloid β peptide which has been 

strongly implicated as a causal agent in Alzheimer’s disease. Our laboratory is currently using a 

protein engineering strategy to dissect the structure and function of the APP molecule as well as 

its component domains. We are also seeking to identify and isolate other proteins in the body 

that bind to APP. We have discovered that amyloid β peptide fibrils bind and activate both 

tissue plasminogen activator and plasminogen in a manner remarkably similar to the known 

physiological cofactor, fibrin. This phenomenon may shed light on the involvement of amyloid 

peptide fibrils in cerebral amyloid angiopathy and hemorrhagic stroke. 

Recently the laboratory has been using a combination of protein expression and biophysical 

approaches to create a new structure-based functional genomics paradigm for analyzing 

“orphan” gene sequences. We have embarked on an ambitious, multidisciplinary, collaborative 

project to develop new methods for analyzing protein 3D structure and function. These methods, 

termed structural genomics, will be used to interpret the flood of novel gene sequence data being 

produced by the human genome project. The work on structural genomics, in collaboration with 

Professor Gaetano Montelione at CABM and other colleagues at Rutgers, UMDNJ-Robert Wood 

Johnson Medical School, CABM and HHMI, has picked up momentum during the last year. 

Significant progress has been made in understanding the structure and dimerization properties of 

the BRCT domain, which is found in the human breast cancer gene, BRCA1. We are also 

working on highly conserved bacterial gene products that are found in Mycobacterium 

tuberculosis and other human pathogens but not in humans themselves – understanding the 

structure and function of these may suggest strategies for developing novel antibiotics. Finally, 

we have embarked upon the scaled-up expression and biophysical characterization, in a pilotstudy 

mode, of a series of small orphan gene products from the roundworm, C. elegans. 

Our work on molecular recognition has centered on the well-characterized protease-protease 

inhibitor interaction. The specific model system we have employed is the interaction of avian 

ovomucoid third domains (OM3D) with members of the trypsin family of serine proteases. Our 

__________________________________________________________________________________ 


37

approach is the expression of recombinant turkey OM3D in E. coli and specific mutagenesis of 

reactive site residues. Mutant inhibitors are then tested for binding affinity with a panel of serine 

_____________________________________________________________ 

Stephen Anderson 

proteases. Our goal is to provide a complete, canonical set of ovomucoid third domain (OM3D) 

variants with every amino acid at the reactive site mutagenized, individually, to every other 

amino acid. This project is virtually complete, with the last mutants currently being made. The 

work is being conducted in collaboration with Dr. Michael Laskowski Jr.’s laboratory at Purdue 

University and Dr. Michael James’ laboratory at Edmonton, Alberta. The resultant database will 

represent an unparalleled resource for drug design groups and other users interested in 

rationalizing the energetics of protein-protein interactions. 

We also have a long-term effort aimed at developing improved industrial methods for 

synthesizing vitamin C. We are working on increasing the activity of a crucial enzyme in the 

pathway from glucose to 2-keto-L-gulonic acid [a precursor of vitamin C], 2,5-diketo-Dgluconic 

acid (2,5-DKG) reductase, using protein engineering techniques and extensive 

mutagenesis of the enzymes’ substrate and cofactor binding sites. 

Publications: 

Bateman, K. S., Anderson, S., Lu, W., Qasim, M. A., Laskowski Jr., M. L. and James, M. N. G. 

(2000). Deleterious effects of b-branched residues in the S1 specificity pocket of Streptomyces 

griseus proteinase B (SGPB), crystal structures of the turkey ovomucoid third domain variants 

Ile18I, Val18I, Thr18I, and Ser18I in complex with SGPB. Protein Sci., 9:83 - 94. 

Khurana, S., Powers, D. B., Anderson, S. and Blaber, M. (2000). Molecular dynamics of 2,5diketo-D-gluconic 

acid reductase A complexed with substrate. Proteins, Struct. Funct. & Genet., 

39: 68-75. 

Bateman, K.S., Huang, K., Anderson, S., Lu,W., Qasim, M.A., Laskowski, M. Jr. and James, 

M.N. (2001). Contribution of peptide bonds to inhibitor-protease binding: crystal structures of 

the turkey ovomucoid third domain backbone variants OMTKY3-Pro18I and OMTKY3psi[COO]-leu18I 

in complex with Streptomuces griseus proteinase B (SGPB) and the structure 

of the free inhibitor, OMTKY-3-psi[CH2NH2+]-Asp19I. J. Mol. Biol. 305:839-49. 

__________________________________________________________________________________ 


38

Arnold B. Rabson, M.D. 


School, Department of Molecular Genetics and Microbiology; Adjunct Professor, 

UMDNJ-RWJMS, Department of Pathology 

Viral Pathogenesis Laboratory 

Dr. Arnold Rabson joined CABM in the summer of 1990. Previously, he performed his residency in pathology at Brigham and Women’s 

Hospital in Boston. He was a medical staff fellow and a senior staff fellow in Malcolm Martin’s laboratory at the National Institute of Allergy 

and Infectious Diseases from 1981 to 1990. Dr. Rabson has served on a number of federal grant review boards, including an NIH Special Review 

Committee for AIDS. He is a member of the NIH Pathology B study section and has served as Chairman of several Special Emphasis Panels of 

the NIH Center for Scientific Review. He is on the editorial board of the Journal of Virology, Clinical Cancer Research and the Journal of 

Biomedical Science. Dr. Rabson is also the Associate Director for Basic Research of the Cancer Institute of New Jersey (CINJ) and directs the 

Transcriptional Regulation and Oncogenesis Program of CINJ. 

Dr. Rabson’s laboratory focuses on the molecular basis of cancer and human retroviruses. His 

research program encompasses studies of the viral and cellular mechanisms that regulate the 

expression of human retroviruses that cause cancer and AIDS, the human T-cell leukemia virus 

type 1 (HTLV-1) and the human immunodeficiency virus (HIV). A second aspect of the 

laboratory studies the roles of cellular transcription factors in the development and progression 

of human malignancies, including leukemia, lymphomas, and prostate cancer. 

Previous studies in Dr. Rabson's laboratory identified the frequent occurrence of molecular 

alterations in the gene encoding the NFKB2 transcription factor in the malignant cells of patients 

with cutaneous T-cell lymphoma (CTCL). Over the past year, Dr. Rabson’s laboratory has 

demonstrated that the tumor associated NF-κB-2 mutants also gain new gene regulatory 

functions. Regulated expression of these aberrant proteins can prevent T cell death and increase 

proliferation; thus the lymphoma associated rearrangements lead to both a loss of function and a 

gain of new transcriptional regulation. Dr. Rabson is now identifying the target genes of the 

tumor associated mutant proteins that may explain how this genetic alteration leads to T cell 

lymphomas. 

Dr. Rabson's laboratory has demonstrated inappropriate, constitutive, activation of NF-κB in a 

series of aggressive, tumorigenic, human prostate cancer cell lines and has shown inappropriate 

activation of NF-κB in focal areas of primary prostate cancer samples from patients with the 

disease. He has further shown that constitutive, inappropriate activation of NF-κB in the prostate 

cancer cells is due to activation of regulatory kinases such as the IkappaB kinases and the NF-κB 

kinase. He is continuing to study the consequences of NF-kB expression in prostate cancer cells. 

This work offers possible new approaches for therapy of the disease. 

__________________________________________________________________________________ 


39

Collaborative studies with Drs. Strair (CINJ) and White (CABM) are evaluating the potential 

utility of highly attenuated adenoviruses as cytotoxic agents for the therapy of different 

subsets of leukemias and lymphomas since mutated, highly attenuated adenoviruses may be 

__________________________________________________________________________________ 


Arnold B. Rabson 

useful in the therapy of this disease. In collaboration with Dr. R. Strair (CINJ) and Dr. A. 

Conney (Rutgers University), Dr. Rabson is studying the molecular mechanisms by which the 

phorbol ester, TPA, can induce differentiation of human leukemic cells. The collaborative 

studies at CABM have focused on the effects of TPA on NF-kB and on chromatin structure 

during the induction of differentiation. 

The Rabson laboratory has identified and characterized models of latent HTLV-1 infection and 

demonstrated that immune activation stimuli can potently induce HTLV-1 gene expression. This 

suggests that stimulation of particular T cell clones through their T cell receptor could lead to 

enhanced HTLV-1 gene expression, resulting in increased T cell proliferation. This could 

explain the polyclonal to oligoclonal proliferation of infected T cells that characterizes HTLV-1associated 

diseases. Over the last year, Dr. Rabson’s laboratory has demonstrated that the 

HTLV-1 Tax protein is the target of the T cell activation stimuli. These results suggest that 

inhibition of T cell signaling might alter the progression of HTLV-1 infection. 

Publications: 

Rabson, A.B. and Lin, H.-C. (2000). NF-kappaB and HIV: Linking Viral and Immune 

Activation. Adv. Pharm. 48:161-207. 

Rabson, A.B., Padarathsingh, M. and Le Beau, M. (2000). Molecular Biology and Experimental 

Models for Hematologic Malignant Diseases: Workshop of the NIH Pathology B Study Section. 

Biochim. Biophys. Acta Reviews on Cancer, B R1-R7. 

Ke S, Rabson A.B., Germino J.F., Gallo M.A. and Tian Y. (2001). Mechanism of Suppression 

of Cytochrome P-450 1A1 Expression by Tumor Necrosis Factor-alpha and Lipopolysaccharide. 

J. Biol. Chem. 276:39638-39644, 2001. 

Zheng, X., Chang, R.L., Cui, X.-X., Kelly, K.A., Strair, R., Suh, J., Han, Z.T., Rabson, A. and 

Conney, A.H. (2001). Synergistic effects of clinically achievable concentrations of 12-Otetradecanoylphorbol-13-acetate 

in combination with all-trans retinoic acid, 1α, 25dihydroxyvitamin 

D 3 and sodium butyrate on differentiation of HL-60 cells. Oncol Res. 12:419- 

27. 

40

Aaron J. Shatkin, Ph.D. 

Director, CABM; University Professor of Molecular Biology at Rutgers University and 

Professor, UMDNJ-Robert Wood Johnson Medical School, Department of Molecular 

Genetics and Microbiology 

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, among other institutions, Georgetown University Medical School, Cold 

Spring Harbor Laboratory, The Rockefeller University, UMDNJ-Newark Medical School, University of Puerto Rico, and Princeton University. 

He 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 an editor of Advances in Virus Research and a member of the editorial board of the Proceedings of the National Academy of Sciences. 

Shatkin serves on the advisory boards of a number of organizations including the Howard Hughes Medical Institute, and 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. 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. 

One of the earliest steps in the cascade of controls that regulate mRNA formation and function is 

the addition of a 5'-terminal "cap." This structural hallmark is present on all eukaryotic cellular 

mRNAs and is essential for viability. The cap enhances several downstream events in gene 

expression including splicing of pre-mRNAs, initiation of protein synthesis and mRNA stability. 

Recently we have cloned and sequenced the mouse and human capping enzymes (CE) and 

mapped the human protein to 6q16, a region implicated in tumor suppression. The mammalian 

CE are 597-aa polypeptides consisting of two functional domains, N-terminal RNA 5' 

triphosphatase (RT) and C-terminal guanylyltransferase (GT). Mutational analysis demonstrated 

that the GT active site lysine is present in one of several highly conserved motifs characteristic of 

a nucleotidyltransferase superfamily. A haploid strain of S. cerevisiae lacking GT was 

complemented for growth by the mouse wild type cDNA clone but not by a clone containing 

alanine in place of the active-site lysine. The results demonstrate the functional conservation of 

CE from yeast to mammals. 

We found that mammalian CE binds via its GT domain to the hyperphosphorylated C-terminal 

domain (P-CTD) of RNA polymerase II,accounting for the selective capping of pre-mRNAs. The 

CE N-terminal RT contains the sequenceVHCTHGFNRTG which corresponds to the conserved 

active-site motif in protein tyrosine phosphatases (PTPs). Mutational analyses indicate that 

removal of phosphate from RNA 5' ends and from protein tyrosines occurs by a similar 

mechanism. We have also cloned, mapped to 18p11.22-p11.23 and characterized the third 

essential enzyme for capping--mRNA (guanine-7-) methyltransferase (MT). Sequence alignment 

of the 476-aa human MT with the corresponding yeast, worm and fly enzymes demonstrated 

several required, conserved motifs including one for binding S-adenosylmethionine. 

Yeast two-hybrid screening with CE yielded transcription elongation factor SPT5 which 

stimulated GT, but the effects were not additive with SPT5, suggesting a common binding site 

__________________________________________________________________________________ 


41

on CE. We also found that MT interacts with the nuclear transporter, importin-alpha (Impa). MT 

selectively bound and methylated RNA containing 5'-GpppG, and both activities were stimulated 

Aaron J. Shatkin 

several-fold by Impa. MT/RNA/Impa complexes were dissociated by addition of Imp-beta 

(Impb) which also blocked Impa stimulation of RNA cap methylation. RanGTP but not RanGDP 

prevented these effects of Impb. The results suggest that, in addition to a linkage between 

capping and transcription, mRNA biogenesis and nucleocytoplasmic transport are functionally 

connected, a possibility we are exploring further. 

Publications: 

Shatkin, A.J. (2000). Reovirus translational control. Translational Control, Sonenberg, N., 

Hershey, J.W.B., Mathews, M.B., eds. Cold Spring Harbor Laboratory Press, 2nd edition, 915- 

932. 

Furuichi, Y. and Shatkin, A.J. (2000). Viral and Cellular mRNA Capping: Past and prospects. 

Adv. in Vir. Res, 55:135-184. 

Shatkin, A.J. and Manley, J.L. (2000). The ends of the affair: Capping and polyadenylation. 

Nature Structural Biology. 7:838-842. 

Wen, Y. and Shatkin, A.J. (2000). Cap methyltransferase selective binding and methylation of 

GpppG-RNA are stimulated by importin-α. Genes and Development. 14:2944-2949. 

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42

Education, Training & 

Technology Transfer 

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43

Lectures and Seminars 

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44

January 24 

James Manley, Biological Sciences, Columbia University 

“mRNA Processing and the Integration of Nuclear Events” 

February 14 

Heiner Westphal, NIH 

“How Mouse LIM Homeobox Genes Control Organogenesis” 

CABM Lecture Series 

March 29 

Rick Young, MIT 

“Lessons from Global Expression Profiling of Yeast and Human Cells” 

April 18 

Nadia Rosenthal, Harvard Medical School 

“Retinoic Acid and Heart Development” 

May 16 

Se-Jin Lee, Johns Hopkins University 

“Novel Growth and Differentiation Factors Related to TFG-β” 

September 19 

Jon Clardy, Chemistry and Chemical Biology, Cornell University 

“Natural Products and Natural Product Libraries” 

October 24 & 25 

15 th Annual CABM Symposium 

“Structural Genomics in Pharmaceutical Design” 

December 6 

Michael B. Kastan, Hematology-Oncology, St. Jude’s Children’s 

Research Hospital 

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“DNA Damage Response Pathways in the Genesis and Treatment of Cancer” 

-- The CABM Lecture Series is supported in part by Aventis -- 

ANNUAL CABM RETREAT, June 11 th , 2001 

FOREST LODGE, Warren, NJ 

Program 

8:15 AM Registration, Poster Set up and Continental Breakfast 

9:00 AM Opening Remarks – Aaron J. Shatkin 

Professor and Director, CABM 

9:10 AM Proteomics: Protein Structure, Engineering and Applications 

Chair: Hunter Moseley – Protein NMR Spectroscopy Lab (Guy Montelione) 

10:40 AM Coffee Break 

Tom Acton – Protein NMR Spectroscopy Lab (Guy Montelione) 

"The Northeast Structural Genomics Consortium, a Pilot Project Focusing on 

Eukaryotic Organisms" 

Scott Banta – Protein Engineering Lab (Stephen Anderson) 

“Alteration of the Cofactor Specificity of Corynebacterium 

2,5-diketo-D-gluconic Acid Reductase” 

Shahriar Pooyan – Protein Microchemistry Lab (Stanley Stein) 

“PEG Carrier for Drug Targeting” 

Li Lin – Protein Targeting Lab (Peter Lobel) 

“The Human CLN2 Protein/Tripeptidyl-peptidase I Is A Serine Protease” 

David Buckler – Protein Crystallography Lab (Ann Stock) 

“X-ray Crystal Structure of An OmpR Homolog from Thermotoga maritima" 

Deena Oren – Biomolecular Crystallography Lab (Eddy Arnold) 

“Determining the Structure of the Human B Lymphocyte Stimulator BlyS” 

11:00 AM Gene Expression and Cancer 

Chair: Leonard Edelstein – Tumor Virology Lab (Céline Gélinas) 

Priya Srinivasan – Molecular Virology Lab (Aaron J. Shatkin) 

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46

“Analysis of C. elegans mRNA Capping Machinery by RNA Interference” 

Annual CABM Retreat 

Wen-Feng Chen – Molecular Chronobiology Lab (Isaac Edery) 

"Analysis of Locomotor Activity and Per mRNA Splicing in Flies from Different 

Latitudes" 

Paul Lizzul – Tumor Virology Lab (Céline Gélinas) 

“TAPIR is a Novel NF-κB-inducible Gene, Distinct from IκB, Which Suppresses 

NF-κB-mediated Transactivation in Response to TNFα and IL-1β Signaling” 

Junghan Suh – Viral Pathogenesis Lab (Arnold Rabson) 

"Mechanisms of NF-kB Activation in Prostate Cancer Cells" 

Isao Matsuura – Growth and Differentiation Control Lab (Fang Liu) 

“Phosphorylation of SMAD by Cyclin-dependent Kinases” 

Kurt Degenhardt – Viral Transformation Lab (Eileen White) 

“Adenovirus Induces DNA Fragmentation through a DFF-45/ICAD Dependent 

Mechanism That Is Inhibited by E1B 19K” 

12:30-3:30 PM Lunch and Free Time 

3:30 PM Poster Presentation (odd numbers) 

5:00 PM Mammalian Development 

Chair: Yu-Ting Yan – Mammalian Embryogenesis Lab (Michael Shen) 

Jixiang Ding – Mammalian Embryogenesis Lab (Michael Shen) 

“Eyes Wide Apart - Cripto and Midline Formation” 

Hansol Lee – Molecular Neurobiology Lab (Cory Abate-Shen) 

"Searching for the Regulatory Network of Msx1 Homeobox Protein" 

Shengguo Li – Molecular Neurodevelopment Lab (Mengqing Xiang) 

“Functional Analysis of the Barhl1 Homeobox Gene during Development of the 

Mouse Nervous System" 

Ahmed Usmani – Developmental Neurogenetics Lab (James Millonig) 

“Dorsal CNS Development in the Mutant Mouse Dreher” 

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47

6:00 PM Poster Presentation (even numbers) and Buffet Reception 


Structural Genomics in Pharmaceutical Design 

Princeton Forrestal Conference Center 

Princeton, New Jersey 

October 24-25, 2001 

CABM Organizing Committee 

Edward Arnold Aaron J. Shatkin 

Gaetano Montelione Ann Stock 

Sponsors 

-Pfizer -Roche 

-Wyeth -Novartis 

-NJ Commission on Science -Bruker Biospin 

and Technology -Isotec Inc. 

-GeneFormatics, Inc. -Genentech, Inc. 

-Upstate Biotechnology -Martek 

-Merck Research Laboratories -Rigaku/MSC, Inc. 

-Structural GenomiX -Schering-Plough 

-3-Dimensional Research Institute 

Pharmaceuticals, Inc. -Bristol-Myers Squibb 

-Medarex 

Exhibitors 

-Bruker Daltonics, Inc. -ProteEx 

-GeneFormatics, Inc. -Rigaku/MSC, Inc. 

-Isotec Inc. -TKR Biotech Products 

-NJ Commission on Science -Upstate Biotechnology 

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48

and Technology -VLI Research Inc./ 

-NJ Economic Development Authority Silantes 

-Prosoft Software, Inc. 


Wednesday, October 24, 2001 

Program 

8:00 AM Registration and Continental Breakfast 

8:45 AM Opening Remarks 

Aaron Shatkin, Director, Center for Advanced Biotechnology and Medicine 

EXPERIMENTAL STRUCTURAL GENOMICS 

Chair: Edward Arnold, Rutgers University and CABM 

9:00 AM Vim Hol, University of Washington 

“Protein Structures from Tropical Parasites: A Drug Design Perspective” 

9:40 AM Gaetano Montelione, Rutgers University and CABM 

“Structural Proteomics of Eukaryotic Gene Families” 

10:20 AM Sean Buchanan, Structural GenomiX 

“New Bacterial Drug Targets from Structural Genomics” 

10:40 AM Refreshment Break 

INFORMATICS FOR STRUCTURAL GENOMICS 

Chair: Casimir Kulikowski, Rutgers University 

11:10 AM Helen Berman, Rutgers University and Protein Data Bank 

“The Protein Data Bank” 

11:50 AM Mark Gerstein, Yale University 

“Structural Genomics: Surveys of a Finite Parts List” 

PROTEIN PRODUCTION AND DRUG DESIGN 

Chair: Masayori Inouye, Robert Wood Johnson Medical School 

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49

2:00 PM David Waugh, National Cancer Institute, Frederick 

“Generic Protein Expression and Purification Strategies for Structural 

Genomics” 


2:40 PM Edward Arnold, Rutgers University and CABM 

“Optimization of Multiple Factors in Developing Potent HIV Reverse 

Transcriptase Inhibitors as Potential Anti-AIDS Drugs” 

3:40 PM Refreshment Break 

IDENTIFYING BIOCHEMICAL FUNCTIONS 

Chair: Gaetano Montelione, Rutgers University and CABM 

4:10 PM Jeffrey Skolnick, Danforth Plant Science Center 

“Prediction of Protein Structure and Function on a Genomic Scale” 

4:50 PM Ming-Ming Zhou, Mount Sinai School of Medicine 

“Structure and Function of Protein Modular Domains” 

5:30 PM F. Raymond Salemme, 3-Dimensional Pharmaceuticals 

“Protein Thermal Stability Measurements for High-Throughput Drug 

Screening and Target Decryption” 

6:15 PM Reception 

Thursday, October 25, 2001 

8:00 AM Continental Breakfast 

HIGH-THROUGHPUT STRUCTURE DETERMINATION 

Chair: Ann Stock, Robert Wood Johnson Medical School and CABM 

9:00 AM Andrzej Joachimiak, Argonne National Laboratories 

“Structural Gemonics: from Genome Sequence to Proteome Structure” 

9:40 AM Stephen Burley, Rockefeller University 

“Structural Genomics of Sterol/Isoprenoid Biosynthesis” 

10:20 AM Clemens Anklin, Bruker NMR Instruments 

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50

10:40 AM Refreshment Break 

“New Approaches to Biomolecular NMR Using Ultra High Field Systems 

and Cryoprobes” 


STRUCTURAL BIOINFORMATICS 

Chair: Donna Bassolino, Bristol-Myers Squibb Pharmaceutical Research Institute 

11:10 AM Cyrus Chothia, Cambridge University 

“Protein Repertoires in Genomes: the Immunoglobulin Superfamily in 

Humans” 

11:50 AM Ronald Levy, Rutgers University 

“Recent Developments in Protein Fold Recognition, Determination, and 

ab initio Prediction” 

12:30 PM Lunch 

NEW TARGETS FOR PHARMACEUTICAL DESIGN 

Chair: Stephen Anderson, GeneFormatics, Inc. 

2:00 PM Peter Lobel, Robert Wood Johnson Medical School and CABM 

“Lysosomal Proteomics and the Indentification of Human Disease Genes” 

2:40 PM Martin Rosenberg, GlaxoSmithKline 

“Microbial Genomics: Opportunities and Hurdles” 

3:20 PM John Chiplin, GeneFormatics, Inc. 

“Considerations for Target Selection and Drug Discovery in the 

Postgenomic Era” 

3:40 PM L. Patrick Gage, Wyeth Research 

“The Future of Molecular Medicine” 

Closing Remarks 

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51

GRADUATE, UNDERGRADUATE STUDENTS AND 

POSTDOCTORAL FELLOWS INCLUDING 

COMPETITIVE FELLOWSHIP AWARDS 

CABM faculty members also participate in UMDNJ and Rutgers University graduate student rotation programs that 

place students in CABM labs each year in order to give them education and experience in a range of research 

methods and subjects. 

Graduate Students 

-Priti Bachhawat, Protein Crystallography 

-Scott Banta, Protein Engineering 

NIH Biotech Training Grant 

-Joseph Bauman, Biomolecular Crystallography 

-Annerban Bhattacharya, Protein NMR Spectroscopy 

-Wen-Feng Chen, Molecular Chronobiology 

-Natalia Denissova, Growth & Differentiation Control 

-Jui Dutta, Tumor Virology 

-Chaosu E, Mammalian Embryogenesis 

USAMRMC 

-Leonard Edelstein, Tumor Virology 


-John Everett, Protein NMR Spectroscopy 


-Jayita Guhaniyogi, Protein Crystallography 

-Gezhi Hu, Molecular Neurobiology 

American Heart Association 

-Hyuk Wan Ko, Molecular Chronobiology 

-Gregory Kornhaber, Protein NMR Spectroscopy 

-Lynn Lagos, Tumor Virology 

-Jung Eun Lee, Molecular Chronobiology 

-Wei Liu, Molecular Neurodevelopment 

-Paul F. Lizzul, Tumor Virology 

-Denise Perez, Viral Transformation 

NIH–NCI 

-Eduardo Perez, Protein Crystallography 

NIH Biochem Training Grant 

-Shahriar Pooyan, Protein Microchemistry 

-Yan Shen, Viral Transformation 

-Matthew Simmons, Tumor Virology 

NIH Biochem Training Gran 

- David Snyder, Protein NMR Spectroscopy 


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52

-Priya Srinivasan, Molecular Virology 

-Stacey Stein, Molecular Neurobiology 

NJCCR 

-Junghan Suh, Viral Pathogenesis 

-Ramya Sundararajan, Viral Transformation 

-Alejandro Toro, Protein Crystallography 

NIH Biophysics Training Grant 

-Paola Velasco, Biomolecular Crystallography 

-Gang Xiao, Protein Targeting 

-Cuifeng Yin, Protein NMR Spectroscopy 

-Guobao Zhang, Protein Microchemistry 

-Yujie Zhao, Viral Pathogenesis 

-Deyou Zheng, Protein NMR Spectroscopy 

Postdoctoral Students 

-Dr. Andrew Bendall, Molecular Neurobiology 

-Dr. David Buckler, Protein Crystallography 

-Dr. Rajula Bhatia-Gaur, Molecular Neurobiology 

Neuroscience & Cell Biology NIH Training Grant 

UMDNJ Foundation 

-Dr. Andrea Cuconati, Viral Transformation 

Howard Hughes Medical Institute 

-Dr. Kalyan Das, Biomolecular Crystallography 

-Dr. Kurt Degenhardt, Viral Transformation 

-Dr. Jianping Ding, Biomolecular Crystallography 

-Dr. Jixiang Ding, Mammalian Embryogenesis 

-Dr. Bonnie Lynn Dixon, Protein Engineering 

& Protein NMR Spectroscopy 

-Dr. Yongjun Fan, Tumor Virology 

-Dr. Kristin Gunsalus, Protein NMR Spectroscopy 

NIH Postdoctoral Fellowship 

-Dr. Daniel Himmel, Biomolecular Crystallography 

-Dr. Holly Henry, Viral Transformation 


-Dr. Jiu-Zhen Jin, Protein Crystallography 


-Dr. Natalia Khlebtsova, Protein Crystallography 


-Dr. Eun Young Kim, Molecular Chronobiology 

-Dr. Minjung Kim, Molecular Neurobiology 

-Dr. Jerome Kucharczak, Tumor Virology 

-Dr. Hansol Lee, Molecular Neurobiology 

-Dr. Hsin-Ching Lin, Viral Pathogenesis 

Graduate and Postdoctoral Students 

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53

-Dr. Li Lin, Protein Targeting 

-Dr. Heng-Ling Liou, Protein Targeting 

-Dr. Yuanpeng Huang, Protein NMR Spectroscopy 

-Dr. Jan-Jan Liu, Mammalian Embrogenesis 

-Dr. Jianyin Long, Growth & Differential Control 

-Dr. Xuejun Ma, Biomolecular Crystallography 

-Dr. Isao Matsuura, Growth & Differential Control 

-Dr. Daniel Monleon, Protein NMR Spectroscopy 

-Dr. Hunter Moseley, Protein NMR Spectroscopy 

-Dr. Deena Oren, Biomolecular Crystallography 

-Dr. Rajan Paranji, Protein NMR Spectroscopy 

-Dr. Beatrice Rayet, Tumor Virology 

Cure for Lymphoma Foundation Fellowship and UMDNJ Foundation 

-Dr. Victoria Robinson, Protein Crystallography 


-Dr. Stefan Sarafianos, Biomolecular Crystallography 

-Dr. Anju Thomas, Viral Transformation 

-Dr. Steven Tuske, Biomolecular Crystallography 

NIH Postdoctoral Fellowship 

-Dr. Yingxia Wen, Molecular Virology 

-Dr. Yu-Ting Yan, Mammalian Embryogenesis 

Undergraduate Students 

-Alan Anschel, Viral Transformation 


-Antonious Attallah, Protein Crustallography 

-Jisook Baek, Viral Transformation 

-Angelo Banaria, Lab Management 

-Marvin Bayro, Protein NMR Spectroscopy 

-Michael Chen, Protein Crystallography 

-Helen Chow, Protein NMR Spectroscopy 

-Bonnie Cooper, Protein NMR Spectroscopy 

-Gaurev Davé, Biomolecular Crystallography 

-Michelle DeFreese, Lab Management 

-Kate Drahos, Protein NMR Spectroscopy 

-Robert Faltas, Biomolecular Crystallography 

-Manju Goyal, Protein NMR Spectroscopy 

-April Graham, Molecular Neurobiology 

Biomedical Careers Fellowship 

-Michelle Hickey, Viral Pathogenesis 

-Hui Yun Ho, Administration 

-Lydia Hsu, Viral Pathogenesis 

Graduate and Postdoctoral Students 

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54

-Hyunmi Kim, Molecular Virology 

-Rebecca Liu, Protein NMR Spectroscopy 

-Nicholas Lumia, Lab Management 

-Meera Mani, Protein Crystallography 

-Ram Mani, Protein NMR Spectroscopy 

Howard Hughes Medical Institute Fellowship 

Rutgers University Undergraduate Research Fellowship 

-Raehum Paik, Molecular Chronobiology 

-Hammad Rizvi, Mammalian Embryogenesis 

-Gurmukh Sahota, Protein NMR Spectroscopy 

-Beth Shafer, Molecular Virology 

-Rachel Siegel, Biomolecular Crystallography 

Howard Hughes Medical Institute Fellowship 

-Jennifer Staley, Administration 

-Max Tischfield, Developmental Neurogenetics 

-Melanie Vishnu, Lab Management 

-Deborah Weintraub, Protein Crystallography 

-Karlvin Wong, Molecular Neurobiology 

-Zeba Wunderlich, Protein NMR Spectroscopy 

Undergraduate Students 

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55

PATENTS 

Abate-Shen, C., Shen, M. M. and Gridley, T. “Roles for Nkx3.1 in prostate development and 

cancer”. U.S. Patent Application 09/756,151 (pending). 

Abate-Shen, C., Shen, M. M. and Kim, M. “Monoclonal antibody for NKX3.1 and method for 

detecting same”. U.S. Patent Application 09/853,121 (pending). 

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 M. Young. “Naphthols useful in 

antiviral methods.” U.S. Patent #6,140, 368. 

Edery, I., Altman, M. and N. Sonenberg. “Isolation of full-length cDNA clones and capped 

mRNA”. U.S. Patent #5219989. 

Lobel, P. and Sleat, D “Human lysosomal protein and methods of its use” U.S. 

Patent #6,302,685. 

Shatkin, A.J., Pillutla, R., Reinberg, D., Maldonado, E., and Z. Yue. “mRNA capping enzymes 

and uses thereof”. U.S. Patent # 6,312,926 B1. 

Stein, S. “Site-specific 13C-enriched reagents for diagnostic medicine by magnetic resonance 

imaging”. U.S. Patent #6,210,655. 

Stein, S., Leibowitz, M. J. and P.J. Sinko. “Carrier for in vivo delivery of a therapeutic agent”. 

U.S. Patent #6,258,774. 

Strair, R., Rabson, A.B., Medina, D. and White E. "Cytotoxic agents for the selective killing of 

lymphoma and leukemia cells and methods of use thereof" PCT Application 

PCT/US99/09793. 

White, E., Degenhardt, K., Nelson, D. and Cuconati, A. "Transformed epithelial baby mouse 

kidney cell lines (BMK) with targeted gene disruptions in Bax, Bak and Bax plus Bak”. 

Provisional Patent App. 60/323,392. 

Sabatini, P., Sherwood, A., Black, I. and White, E. "Immortalized and transformed astrocytederived 

cells for treatment and diagnosis of brain disease" Utility App filed 1996. 

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56

Thomas, A., White, E., Goyal, L. and Kasof, G. "Recombinant cell line and screening method 

for identifying agents which regulate apoptosis and tumor suppression" 2 provisionals filed and 

US Utility filed 5/6/99 Application 09/674,876. 

Fiscal Information 

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57

2001 - Center for Advanced Biotechnology and Medicine - Rutgers ...

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