Proteomics - Center for Proteomics and Bioinformatics - Case ...

Center for Proteomics
and Bioinformatics
Annual Report 2008-2009 2008 2009
Cleveland Foundation Center for Proteomic Medicine
Center for Synchrotron Biosciences
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Overview of Progress: Director’s Report
Research Highlights
Center Profile
Invention Disclosures
Funding Profile
Seminars and Workshops
Posters and Presentations by Center Members
Publications
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With $60 million in grants awarded
since 2005 and nearly $50 million
in funding currently pending, the
Center for Proteomics and
Bioinformatics continues to
grow and develop its vision as a
world-leading world leading Center for
proteomics, bioinformatics, and
systems biology.
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23-32 23 32

Director’s Report
The Center for Proteomics and Bioinformatics (CPB)
and Cleveland Foundation Center for Proteomic Medicine in
the School of Medicine continues to grow and develop its
vision as a world-leading center for proteomics,
bioinformatics, and systems biology. This vision was
dramatically altered quite recently, as the Dean of the School
of Medicine approved a plan to rename the Center and raise
the visibility of the Bioinformatics mission. As a part of this
reorganization the Center dramatically expanded its faculty
cohort by the addition of secondary faculty from Genetics,
Physiology & Biophysics, Pharmacology, Computer Science,
and the Cancer Center. Also, we made a primary appointment of Prof. John-Eudes Dazard an expert in
Biostatistics and Bioinformatics. Currently, the Center has eight primary and twelve secondary faculty
members who specialize in one or more of the three major scientific areas of the Center: Proteomics and
Genomics, Bioinformatics, or Macromolecular Structure.
The research portfolio of the faculty and staff continues to strengthen. We include selected
science highlights that showcase the best research of the CPB over the last year. The research highlights
demonstrate important clinical research progress in understanding cancer, pregnancy, diabetes, and
infectious disease. Specifically, research by the Chance group, using systems biology approaches,
defined fundamental mechanisms of metastasis using protein and gene expression data from human
colon tumor samples (published in Mol. Cell. Prot.). A study from the Moore laboratory in the Department
of Pediatrics identified fibulin as a critical protein mediating untimely rupture of fetal membranes and
likely important in pre-term birth (published in Placenta). Scientists in the Department of Biochemistry and
at the VA Hospital collaborated on the development of a novel antibiotic to combat the epidemic of
antibiotic-resistant gram-negative microorganisms (published in J. Biol. Chem.). Other highlights illustrate
novel methods to identify biomarkers of diabetes complications and demonstrate the strong structural
biology research conducted at the Center. Overall, the Center’s faculty and staff completed 40 papers
last year. They have also been quite active in presenting posters and giving talks at national meetings
and giving invited lectures around the country; nearly 60 presentations of the faculty and staff are
reported. We also report the publications of users who carried out service research within the cores of the
Center; this activity resulted in 128 papers published, in press or submitted and is primarily derived from
research at our synchrotron facilities. Overall, the record of 168 total publications indicates the depth of
the research program.
In terms of research progress the Center was awarded a number of major grants in 2008-2009.
The Cleveland Foundation made an award of $1.5 million to establish the Center for Proteomic Medicine.
These funds will be used to recruit several tenure-track faculty members over the next two to three years.
The areas of specialization will be bioinformatics and systems biology with a focus on HIV or cancer
research. The National Institute for Drug Abuse also awarded a grant of over $3.1 million to establish the
Case Proteomics Center for HIV/AIDS and Drug Abuse, which will fund several Pilot Grants with
investigators in the Departments of Medicine and in the Dental School. The current and past funding of
the Center since its inception in 2005 is shown in the report; over $60 million in total research and
training funding has been received so far.
An important goal of the CPB is to develop an infrastructure of sophisticated equipment that
facilitates and maximizes shared equipment usage, as well as to offer a wide array of proteomics
services. The Center now has eight major cores that are functioning at a high level; these include
Expression Proteomics, Interaction Proteomics, Mass Spectrometry, Biostatistics & Bioinformatics,
Systems Biology Data Analysis, Macromolecular Crystallography, X-ray Spectroscopy, and X-Ray
Footprinting. The last three cores are available to a national community of users based on Case facilities
that are operated at the National Synchrotron Light Source of Brookhaven Laboratories 1 . These cores
serve hundreds of users in Cleveland and across the world. The Major cores of the Center and its
Divisions are shown in Figure 1.
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The continued development of these cores is driving the overall research activity of the Center.
Over the course of FY 2009, 65 Cleveland based PIs and investigators utilized the Center’s facilities;
these investigators come from 31 Departments and Divisions of the University and surrounding
institutions. These users have interacted with the Center in a variety of ways, some projects have
involved simple “drop-off” service, others have included close collaboration with Center faculty and staff
in the design and execution of experiments, while a third class of interactions involve “independent use”
of Center facilities. In this case, users are trained in the use of Center instruments and conduct and
analyze their own experiments. The types of research that are carried out in the Center are summarized
on page 13.
The Center continues to be an important resource for dissemination of information on proteomics
technologies and approaches. The Center continues its Thursday seminar series. 20 seminars and
workshops were held from July 2008 through June 2009, with an average attendance of 40 people.
Speakers included Center faculty and staff, nationally recognized scientists and instrument vendors.
Updates are planned for the Center’s website 2 which include new elements of design and functionality.
The renovated site is expected to go live in the Fall of 2009.
Website Links:
1-http://casemed.case.edu/proteomics/CSB/INDEX.shtml
2-http://proteomics.case.edu
Figure 1. Major Cores and Division Structure of the Center
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Highlight #1
Discovery and Scoring of Protein Interaction Subnetworks Discriminative of Late
Stage Human Colon Cancer
We used a systems biology approach to identify and score protein interaction subnetworks whose activity
patterns are discriminative of late stage human colorectal cancer (CRC) versus control in colonic tissue.
We conducted two gel-based proteomics experiments to identify significantly changing proteins between
normal and late stage tumor tissues obtained from an adequately sized cohort of human patients. A total
of 67 proteins identified by these experiments were used to seed a search for protein-protein interaction
subnetworks. A scoring scheme based on mutual information, calculated using gene expression data as
a proxy for subnetwork activity, was developed to score the targets in the subnetworks. Based on this
scoring, the subnetwork was pruned to identify the specific protein combinations that were significantly
discriminative of late stage cancer versus control. These combinations could not be discovered using only
proteomics data or by merely clustering the gene expression data. We then analyzed the resultant pruned
subnetwork for biological relevance to human CRC. A number of the proteins in these smaller
subnetworks have been associated with the progression (CSNK2A2, PLK1, and IGFBP3) or metastatic
potential (PDGFRB) of CRC. Others have been recently identified as potential markers of CRC (IFITM1),
and the role of others is largely unknown in this disease (CCT3, CCT5, CCT7, and GNA12). The
functional interactions represented by these signatures provide new experimental hypotheses that merit
follow-on validation for biological significance in this disease. Overall the method outlines a quantitative
approach for integrating proteomics data, gene expression data, and the wealth of accumulated legacy
experimental data to discover significant protein subnetworks specific to disease.
Results from: Nibbe, R.K., Markowitz, S., Myeroff, L., Ewing, R., Chance, M.R.
Discovery and scoring of protein interaction subnetworks discriminative of late
stage human colon cancer, Mol. Cell. Proteomics, Proteomics,
8(4):827-45, 8(4):827 45, 2009.
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Figure 1. MetaCore
subnetwork. Shown is a
characteristic example of one
of four significant MetaCore
protein interaction subnetworks
returned by a search seeded
by significant proteomic
targets: subnetwork 1,
regulation of developmental
processes. Interaction effects
are positive (green), negative
(red), and unspecified (black).
Red and blue circles beside
certain objects indicate that the
protein was identified by
proteomics, either up-regulated
in cancer (red) or downregulated
in cancer (blue). Size
indicates the total number of
gene products used for scoring
by mutual information.

Highlight #2
Urinary Protein Profiles in a Rat Model for Diabetic Complications
Diabetes mellitus (DM) is estimated to affect approximately 24 million people in the US and more than
150 million people worldwide. There are numerous end organ complications of diabetes, the onset of
which can be delayed by early diagnosis and treatment. Although assays for diabetes are well founded,
tests for its complications lack sufficient specificity and sensitivity to adequately guide these treatment
options. In our study, we employed a streptozotocin (STZ) induced rat model of diabetes to determine
changes in urinary protein profiles that occur during the initial response to the attendant hyperglycemia
(e.g. the first two months) with the goal of developing a reliable and reproducible method of analyzing
multiple urine samples as well as providing
clues to early markers of disease progression.
After filtration and buffer exchange, urinary
proteins were digested with a specific protease
and the relative amounts of several thousand
peptides were compared across rat urine
samples representing various times after administration
of drug or sham control. Extensive
data analysis, including imputation of missing
values and normalization of all data was followed
by ANOVA analysis to discover peptides
that were significantly changing as a
function of time, treatment and interaction of
the two variables. The data demonstrated significant
differences in protein abundance in
urine before observable patho-physiological
changes occur in this animal model and as
function of the measured variables. These in-
Figure 1. Volcano plots of treatment effect at 1 month (A) and 2 months (B)
post STZ treatment. The t-test volcano plots arrange peptides by statistical
significance. The most significant peptides are those found by ANOVA
(highlighted in red (up) and green (down)) and distributed in the top right or
left of the plots.
Figure 2. Box plots of illustrating abundance of pro alpha (2) 1 collagen peptide
GEPGSVGAQGPPGPSGEEGK in targeted SRM analysis (A) and label free expression
analysis (B). Maximum value with a treatment group is represented by blue box, median
value for a treatment group by red box and minimum value for a treatment group by green.
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cluded decreases in relative abundance of
major urinary protein precursor and increases
in pro-alpha-collagen (2) 1 whose expression
is known to be regulated by circulating levels
of insulin and/or glucose. Peptides from these
proteins represent potential biomarkers
which can be used to
stage uro-genital complications
from diabetes. The expression
changes of a pro-alpha (2) 1 collagen
peptide was also confirmed via
selected reaction monitoring. This
analysis has demonstrated significant
differences in protein abundance
in urine before observable
patho-physiological changes occur
in this animal model. In addition,
the techniques developed have
been easily translated to human
analyses to direct additional discovery
efforts in human samples for
diabetic complications.
Results from: Schlatzer, D.M., Dazard, J-E., J E., Dharsee, M., M.,
Ewing, R.M.,
Ilchenko, S., Stewart, I., Christ, G., Chance, M.R. Urinary protein profiles in a rat
model for diabetic complications, Mol Cell Proteomics, Proteomics,
2009, [Epub ahead of print].

Highlight #3
Differential Expression of Fibulin Family Proteins in the Para-cervical Weak Zone
and Other Areas of Human Fetal Membranes
Untimely rupture of the fetal membranes (FM), the
amnion and choriodecidua, is a major cause of preterm
birth and results in significant infant mortality and morbidity.
The physiological mechanisms which normally lead the FM
to weaken and fail prior to birth are not known. Recent studies
indicate that in human, fetal membranes (FM) at term
have been shown to contain a weak zone in the region
overlying the cervix which exhibits characteristics of increased
collagen remodeling and apoptosis. It has been
hypothesized that the FM rupture initiation site is within this
weak zone. Although the FM weak zone has been partially
characterized, it is unclear what structural differences in the
extracellular matrix result in its decreased rupture strength.
In an attempt to investigate how differences between
the biomechanical properties of the FM weak zone
and that of the remaining stronger FM areas are reflected in
their extracellular matrix proteins a proteomics approach
was utilized. The initial proteomics 2D-DIGE screening
demonstrated decreases in fibulin 1 protein abundance in
the weak zone of the FM compared to the remaining areas.
As very little has been known and nothing has been reported
in amnion, we expanded our investigation to include
additional fibulin family members. Thus, a subsequent immunohistochemical
analysis revealed localization of fibulin
1, fibulin 3 and fibulin 5 but not fibulins 2 and 4 in the amnion
for the first time (Figure 1). Besides, western blot validation
analysis of the expressed fibulin 1 and additional
fibulin family members identifies the differential abundance
in the weak zone when compares with other FM regions. All
the three detected fibulins showed deceased abundance in
the amnion component of the FM weak zone (Figure 2) and
mainly produced by both amnion epithelial and mesenchymal
cells.
In summary, the fibulin family proteins have decreased
abundance in the para-cervical weak zone compared
with the other areas of the FM. Their location is coincident
with an extensive microfibrillar network that is integral
to the epithelial cell basement membrane and the amniotic
compact layer suggesting that fibulins may be integral
proteins of these very important strength maintaining, extracellular
matrix structures. Degradation or remodeling of
the microcellular network in the amnion may be a critical
element of the weakening process leading to FM rupture.
Results from: Moore, R.M., Redline, R.W., Kumar, D.,
Mercer, B.M., Mansour, J.M., Yohannes, E., Novak,
J.B., Chance. M.R., Moore, J.J. Differential expression
of fibulin family proteins in the para-cervical para cervical weak zone
and other areas of human fetal membranes, Placenta, Placenta,
30(4):335-41, 30(4):335 41, 2009.
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Figure 1. Immunohistochemical localization of fibulin
proteins in intact FM: Localization of immuno-reactive
(brown staining) fibulin family members 1–5 are shown
in representative cross-sections of fetal membranes (left
panel). Pre-treatment of sections with blocking peptides
against fibulin antibodies prior to incubation (right panel).
Abbreviations: AE, amnion epithelial layer; BM, basement
membrane; CL, compact layer; D, decidua; FL,
fibroblast layer; RL, reticular layer; T, trophoblast .
Figure 2. Fibulin protein expression in amnion from paracervical
weak zone and other FM areas: Panels indicate
fibulin 1–5 protein expression, as assessed by Western
blot analysis, of amnion from FM fragments from the paracervical
weak zone and other FM areas from three representative
patients. Actin expression is shown for comparison
of protein loading. Rupture force in Newtons (N) for
each fragment is indicated along the bottom.

The rapidly increasing number of antibiotic-resistant Gram-negative microorganisms represents a
grave threat to human health. The first-line treatments for such infections are β-lactam antibiotics, and the
most common mechanism of resistance to such agents is bacterial production of β-lactamases.
Regrettably, Enterobacteriaceae resistant to penicillins and extended-spectrum cephalosporins are
continuing to threaten the efficacy of our available β-lactam antibiotics. Of greatest concern is the
emerging number of community-acquired E. coli and Klebsiella spp. that are resistant to these
cephalosporins. This latter group presents a very significant future danger to the current use of β-lactam
antibiotics to treat common infections in the ambulatory setting.
In an effort to devise strategies for overcoming bacterial β-lactamases, we studied LN-1-255, a 6alkylidene-2'-substituted
penicillin sulfone inhibitor. By possessing a catecholic functionality that
resembles a natural bacterial siderophore,
LN-1-255 is unique among β-lactamase
inhibitors. LN-1-255 combined with
piperacillin was more potent against E. coli
DH10B strains bearing blaSHV extended-
spectrum and inhibitor-resistant
lactamases than an equivalent amount of
tazobactam and piperacillin. In addition, LN-
1-255 significantly enhanced the activity of
ceftazidime and cefpirome against extended
-spectrum
β-
cephalosporin and Sme-1
containing carbapenem-resistant clinical
strains. LN-1-255 inhibited SHV-1 and SHV-
2 β-lactamases with nM affinity (KI = 110 ±
10 and 100 ± 10 nM, respectively). When
LN-1-255 inactivated SHV β-lactamases, a
single intermediate at +488 Da was
detected by mass spectrometry (Figure 1A).
The crystal structure of LN-1-255 in complex
with SHV-1 was determined at 1.55Å
resolution (Figure 1B). Interestingly, this
novel inhibitor forms a bicyclic aromatic
intermediate with its carbonyl oxygen
pointing out of the oxyanion hole and
forming hydrogen bonds with Lys-234 and
Ser-130 in the active site. The 2'-substituted
penicillin sulfone, LN-1-255, is proving to be
an important lead compound for novel βlactamase
inhibitor design.
Highlight #4
Strategic Design of an Effective β-Lactamase Inhibitor
Figure 1. (A) Deconvoluted mass spectrum of SHV-1 and LN-1-255inactivating
SHV-1. (B) Interactions of LN-1-255 in active site of SHV-1 βlactamase.
Results from: Pattanaik, P., Bethel, C.R., Hujer, A.M., Hujer, K.M., Distler, A.M.,
Taracila, M., Anderson, V.E., Fritsche, T.R., Jones, R.N., Pagadala, S.R., van den Akker,
F., Buynak, J.D., Bonomo, R.A. Strategic Design of an Effective beta-Lactamase
beta Lactamase
Inhibitor, J. Biol. Chem., 284, 945-953, 945 953, 2009.
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Highlight #5
Conserved waters mediate structural and functional activation of family A
(rhodopsin-like) G protein-coupled receptors
G protein-coupled receptors with seven transmembrane α helices (GPCRs) are membrane
proteins that mediate signal transduction by recognizing a wide range of extracellular stimuli ranging from
photons of light, biogenic amines and odorants, to small peptides that all induce receptor activation.
Activated GPCRs signal through heterotrimeric G proteins to activate effector enzymes resulting in rapid
signal amplification. The availability of high-resolution crystal structures of five prototypical GPCRs,
bovine and squid rhodopsin, engineered A2A--adenosine, β1- and β2-adrenergic receptors, permits
comparative analysis of features common to these and likely all GPCRs. We provide a novel analysis of
the distribution of water molecules in the transmembrane region of these GPCR structures and find
conserved contacts with microdomains previously demonstrated to be involved in receptor activation. Colocalization
of water molecules associating with highly conserved and functionally important residues in
several of these GPCR crystal structures supports the notion that these waters are likely to be as
important to proper receptor function as the conserved residues. Moreover, in the absence of large
conformational changes in rhodopsin following photoactivation, we propose that ordered waters
contribute to the functional plasticity needed to transmit activation signals from the retinal-binding pocket
to the cytoplasmic face of rhodopsin and that fundamental features of the mechanism of activation,
involving these conserved waters, are shared by many if not all family A receptors.
Figure 1: A structural superpositioning diagram of high-resolution crystal structures of bovine rhodopsin (red), squid rhodopsin (wheat),
mutant β1-adrenergic receptor (light blue), mutant β2-adrenergic receptor (navy blue) and bovine opsin (grey) demonstrating a high level of
overall structural similarity. Also shown are those water molecules that co-localize in the transmembrane helices.
Results from: Angel, T., Chance, M.R., Palczewski, K. Conserved waters
mediate structural and functional activation of family A (rhodopsin-like) (rhodopsin like) G protein-
coupled receptors, Proc. Nat. Acad. Sci., 106(21):8555-60, 106(21):8555 60, 2009.
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Highlight #6
From Beamlines X3A and X29A: A Fence-like Coat for the Nuclear Pore Membrane
We recently proposed a cylindrical coat for the nuclear pore membrane in the nuclear pore
complex (NPC). This scaffold is generated by multiple copies of seven nucleoporins. Here, we report
three crystal structures of the nucleoporin pair Seh1•Nup85, which is part of the coat cylinder. The
Seh1•Nup85 assembly bears resemblance in its shape and dimensions to that of another nucleoporin
pair, Sec13•Nup145C. Furthermore, the Seh1•Nup85 structures reveal a hinge motion that may facilitate
conformational changes in the NPC during import of integral membrane proteins and/or during
nucleocytoplasmic transport. We propose that Seh1•Nup85 and Sec13•Nup145C form 16 alternating,
vertical rods that are horizontally linked by the three remaining nucleoporins of the coat cylinder. Shared
architectural and mechanistic principles with the COPII coat indicate a common evolutionary origin and
support the notion that the NPC coat represents another class of membrane coats.
Results from: Debler, E., Ma, Y., Seo, H., Hsia, K., Noriega, T., Blobel, G., Hoelz,
A. A Fence-like Fence like Coat for the Nuclear Pore Membrane, Mol. Cell, 32, 815–826, 815 826,
2008.
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Figure 1. Detailed Structural Analysis of
Nup85 and Seh1
(A) A ribbon representation of the Nup85
structure is shown in rainbow colors along the
polypeptide chain from the N to the C
terminus. The N-terminal domain invasion
motif (DIM), the α-helical solenoid domain, and
their secondary structure elements are
indicated.
(B) The structure of the Seh1•Nup85
heterodimer. The Nup85 DIM (magenta), the
Nup85 α-helical solenoid domain (blue), the
Nup85 αQ-αR connector (red), the Seh1 β
propeller (yellow), the disordered Seh1 5CD
loop (gray dots), and the Seh1 2CD loop
(orange) are indicated; a 90° rotated view is
shown on the right. Dotted lines represent
disordered regions.
(C) Schematic representation of the
Seh1•Nup85 interaction. The Seh1 2CD loop,
the Nup85 αQ-αR connector, and the DIM
region are highlighted in orange, red, and pink,
respectively.
(D) The β propeller domain of Seh1 in
complex with the Nup85 DIM . Seh1 is shown in
yellow, and the six blades are indicated. The
Nup85 DIM contributes one strand to blade 6
and three strands to blade 7, completing the β
propeller.
(E) Schematic representation of the Seh1 β
propeller and its interaction with the Nup85 DIM .

Highlight #7
From Beamlines X3A and X29A: A Family of Salmonella Virulence Factors Functions
as a Distinct Class of Autoregulated E3 Ubiquitin Ligases
Processes as diverse as receptor binding and signaling, cytoskeletal dynamics, and programmed
cell death are manipulated by mimics of host proteins encoded by pathogenic bacteria. We show here
that the Salmonella virulence factor SspH2 belongs to a growing class of bacterial effector proteins that
harness and subvert the eukaryotic ubiquitination pathway. This virulence protein possesses
ubiquitination activity that depends on a conserved cysteine residue. A crystal structure of SspH2 reveals
a canonical leucine-rich repeat (LRR) domain that interacts with a unique E3 ligase [which we have
termed NEL for Novel E3 Ligase] C-terminal fold unrelated to previously observed HECT or RING-finger
E3 ligases. Moreover, the LRR domain sequesters the catalytic cysteine residue contained in the NEL
domain, and we suggest a mechanism for activation of the ligase requiring a substantial conformational
change to release the catalytic domain for function. We also show that the N-terminal domain targets
SspH2 to the apical plasma membrane of polarized epithelial cells and propose a model whereby binding
of the LRR to proteins at the target site releases the ligase domain for site-specific function.
Figure 1. Structure of the NEL domain of SspH2. (A) Comparison of the SspH2 NEL domain with 2 bacterial E3 ligases: SopA, a HECT family
of cysteine-dependent E3 ubiquitin ligases from Salmonella (PDB ID 2QYU), and AvrPtoB, a RING finger/U-box protein (PDB ID 2FD4). The
catalytic cysteine residues are shown in a space-filling format (blue). (B) Molecular surface representation of the crystallized construct of
SspH2 with the LRR and NEL domains in orange and red, respectively. The catalytic cysteine is shown in blue. Hydrophobic residues in 2
clusters are show in green (LRR domain) and yellow (NEL domain, residues F570, F586, F587, V594, V597, M619, F620, L622, V633, and
W645). (C) Residues near the catalytic cysteine of SspH2. Hydrogen bonds are shown as yellow spheres between atoms, and atoms of
nitrogen and oxygen are shown in blue and red, respectively.
Results from: Quezada, C., Hicks, S., Galan, J., Stebbins, C. A Family of
Salmonella Virulence Factors Functions as a Distinct Class of Autoregulated E3
Ubiquitin Ligases, Proc. Nat. Acad. Sci., 106(12):4864-9, 106(12):4864 9, 2009.
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CENTER MEMBERS
Faculty
Members
Primary Faculty Members
Mark Chance, Ph.D., Director, Professor
John-Eudes Dazard, Ph.D., Assistant Professor
Rob Ewing, Ph.D., Assistant Professor
Sayan Gupta, Ph.D., Instructor *
Janna Kiselar, Ph.D., Instructor
Masaru Miyagi, Ph.D., Assistant Professor
Joan Schenkel, M.S., Instructor
Wuxian Shi, Ph.D., Assistant Professor *
Secondary Faculty Members
Mark Adams, Ph.D., Associate Professor
Robert Bonomo, M.D., Professor
Matthias Buck, Ph.D., Assistant Professor
Chris Dealwis, Ph.D., Associate Professor
Andreas Engel, Ph.D., Professor
Mehmet Koyuturk, Ph.D., Assistant Professor
Thomas LaFramboise, Ph.D., Assistant Professor
Joseph Nadeau, Ph.D., Professor
Krzysztof Palczewski, Ph.D., Professor
Jill Barnholtz-Sloan, Ph.D., Assistant Professor
Patrick Wintrode, Ph.D., Assistant Professor
Guo-Qiang Zhang, Ph.D., Professor
Research Staff
Don Abel, Research Associate *
Jen Bohon, Ph.D., Sr. Research Associate *
Giri Gokulrangan, Ph.D. Research Associate
Serguei Ilchenko, Ph.D., Research Associate
Parminder Kaur, Ph.D., Research Associate
Yu Liu, Ph.D., Research Associate
Olena Skomorovski-Prokvolit, Ph.D.,
Research Associate
Gaurav Rana, M.S., Research Associate
Daniela Schlatzer, Sr. Research Associate
Michael Sullivan, Sr. Research Associate *
John Toomey, Research Associate *
Benlian Wang, Ph.D., Sr. Research Associate
Liwen Wang, Ph.D., Research Associate
Elizabeth Yohannes, Ph.D., Sr. Research Associate
Chao Yuan, Ph.D., Sr. Research Associate
Xiaojing Zheng, Ph.D., Research Associate
Secondary
Faculty
Members
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Postdoctoral Research Fellow
Gurkan Bebek, Ph.D.
Postdoctoral Scholars
Sudipto Saha, Ph.D.
Jing Song, Ph.D.
Jacek Szymanski, Ph.D.
Research Assistants
Jennifer Burgoyne, B.S.
Rhijuta D’Mello, M.S. *
Katy Lundberg, M.S.
Hong Zhao, M.S.
Graduate Students
Dasha Hajkova Leary, M.S.
Rod Nibbe, M.S., (Ph.D. expected in
Dec. 2009)
Vishal Patel, B.S.
Administrative Support
Maita Diaz, B.S., Department Assistant
Shannon Swiatkowski, M.S.,
Department Assistant
Audrey Williams, B.S., IT Support
Student Research
Roxana Crivineau
Peter Fellowes (SOTC)
Alex Galante (RIBMS)
Rebecca Levinson
Leigh Praskac (SOTC)
Ted Roman (RIBMS)
BY THE NUMBERS...
Research
Associates
Postdoctoral
Scholars and
Fellows
Research
Assistants
* Indicates faculty and staff members
located at the Case Center for Synchrotron
Biosciences at the National Synchrotron
Light Source, Brookhaven National
Laboratory in Upton, NY.
Administrative
Support
Graduate
Students
Undergraduate
Student
Researchers
8 12 16 4 4 3 3 6 56
Totals

Center Research
Collaborative
Research
Research that is conducted and charged to grants where a
Center for Proteomics and Bioinformatics faculty member is
the PI.
Research conducted in collaboration with other departments
or centers. Research is considered collaborative when:
there is an agreement to submit a collaborative grant
a collaborative staff member has been identified
a fraction of staff member’s salary is paid by grant or
pending grant
co-authorship on publications is expected
the grant will provide on-going financial support to
Center
the collaborative grants pays for use of center facilities
Service Research Research conducted by Center according to specifications
on the Sample Submission Form. PI pays for this service.
Independent
Research
Research conducted by non-center staff using Case
Center for Proteomics facilities.
Chance and Schlatzer - 11/18/2008
Protein and peptide biomarkers of renal and
cardiovascular complications of Type 1 and Type 2
diabetes detected in urine.
Chance, Cooke, Schlatzer - 05/01/2009
Diagnostic biomarkers and molecular targets to
guide treatment of ididopathic pneumonia
syndrome: proteomics methods development and
human studies of bone marrow transplant patients.
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Invention
Disclosures and
Patent
Applications in
FY 2009

Center for Proteomics
and Bioinformatics Funding Profile
Active Projects
Principal
Investigator
Type of Grant Agency Title Total Cost Start Date End Date
Chance, Mark CF
Chance, Mark U54 GM-74945 NIH
Cleveland Foundation Faculty
Recruitment
New York Structural Genomics
Research Consortium
14
$3,000,000 8/1/2005 3/31/2012
$1,384,396 7/1/2005 6/30/2010
Chance, Mark P41 EB-01979 NIH Center for Synchrotron Biosciences $5,175,000 9/1/2005 8/31/2009
Chance, Mark OH Board of Regents Action Fund $125,000 9/1/2009 8/31/2010
Chance, Mark R01 AA-016210 NIH
Chance, Mark P30 CA-043703 NIH
Chance, Mark UL1 RR-024989 NIH
Chance, Mark P20 DA-026133 NIH
Chance, Mark P20 DA-026133S NIH
Alagramam, Kumar R21 DC-007866 NIH
Chang, Jinsook U54 CA-116867 NIH
Chang, Jinsook R21 DK- 079594 NIH
Cho, Michael P01 AI-74286 NIH
Cho, Michael R21 AI-076083 NIH
Identification and Validation of
Alcohol Biomarkers
Comprehensive Cancer Center-
Proteomics Core
CTSA: Translational Technology
Core
Case Proteomics Center for HIV/
AIDS and Drug Abuse
Case Proteomics Center for HIV/
AIDS and Drug Abuse Summer
Supplement
Proteome and Transcriptome of
Defined Cell Types in the Ear
Following Noise Exposure
Role of Genetic Susceptibility to
Obesity and Tumorigenesis
Vsca1 Biomarker Vascular
Complications
Development of a Subunit Envelope
Vaccine Against- HIV1
Targeting gp41 to Elicit Neutralizing
Antibodies Agains HIV-1
$602,000 5/1/2006 4/30/2011
$726,000 7/1/2007 6/30/2012
$3,862,500 9/1/2007 8/31/2012
$3,007,946 4/15/2009 3/31/2012
$21,666 5/25/2009 10/10/2009
$436,000 3/1/2007 2/28/2010
$154,500 7/1/2007 8/31/2009
$118,500 7/1/2007 6/30/2009
$6,001,000 5/1/2008 4/30/2013
$410,000 5/1/2008 4/30/2010
Cooper, Kevin P50 AR-055508 NIH Cort in Psorias: Genomics Core $655,000 9/24/2007 8/31/2012
Ghannoum,
Mahmoud
R01 DE-017486 NIH
Liedtke, Carole R01 HL-058598 NIH
Maguire, Mike R01 GM-039447 NIH
Miyagi, Masaru R01 CA-095851 CCF
Identification of Early Phase C.
albicans Biofilm Proteins
Differential Regulation of NKCC1-
Cotransplant
Magnesium Homeostatis in
Microrganisms
Activators and Repressors of
NFkappaBand IRF3/7 Innate
Immunity
$1,857,000 5/15/2007 4/30/2012
$1,545,000 2/1/2008 1/31/2012
$1,388,000 1/1/2007 6/1/2010
$46,000 7/1/2008 5/31/2010
Miyagi, Masaru P01 CA-06220 CCF IFNS and Cytokines: Signalling $82,000 6/1/2008 4/30/2010
Mukherjee, Pranab R21 AI-074077 NIH
Role of Extracellular Matrix Proteins
in Candida Biofilm Formation
$431,750 6/1/2009 5/31/2011

Active Projects, continued
Principal
Investigator
Palczewski,
Krzysztof
Palczewski,
Krzysztof
Completed Projects
Type of Grant Agency Title Total Cost Start Date End Date
P30 EY-011373 NIH
Core Grant Vision Research-
Proteomics Core
15
$390,000 4/1/2007 3/31/2012
R01 EY-008061 NIH Phototransduction Enzymes $3,680,000 1/1/2009 12/31/2013
Qu, Cheng-Kui R01 Hl-068212 NIH
Ramachandra,
Lakshmi
R21 AI-076792 NIH
Protein Tyrosine Phosophatases
and Hematopoietic Cell Regulation
Mycobacterium Tuberculosis
Phagosome Maturation
$1,930,000 12/1/2007 11/30/2012
$431,750 9/24/2008 2/28/2011
Rote, Neal R21 HD-052803 NIH Trophoblast Intercellular Fusion $428,000 7/1/2008 6/30/2010
Surewicz, Witold R01 NS-044158 NIH
Weinberg, Aaron R01 DE-018276 NIH
Weinberg, Aaron P01 DE-019089 NIH
Weinberg, Aaron R01 DE-016334 NIH
Weinberg, Aaron P01 DE-019759 NIH
Wintrode, Patrick R01 HL-085469 NIH
Principal
Investigator
Confrontational conversions of prion
protein
Ontogeny of Oral Epithelial
Anitmicrobial Peptides
Epithelial Immunity and Oral
Complications of HIV
Beta Defensin Protection of Human
Oral Epithelial Cells
Oral Musosal Immunity in
Vulnerable HIV Infected Populations
Molecular Basis of Serpin Function
and Disfunction
Other Federal and Non-Federal
Revenue
$2,262,000 2/15/2009 1/31/2014
$1,296,000 5/1/2007 4/30/2011
$527,500 8/1/2008 7/31/2009
$1,400,000 8/1/2005 7/31/2009
$9,600,000 6/15/2009 5/31/2014
$1,545,000 6/1/2007 5/31/2012
$2,282,759 7/1/2005 6/30/2009
$56,802,267
Type of Grant Agency Title Total Cost Start Date End Date
Chance, Mark R21 DK-069952 NIH
Chance, Mark R21 DK-070992 NIH
Chance, Mark P41 EB-01979 NIH
Chance, Mark U54 NIH
Alagramam, Kumar R21 DC-007866 NIH
Dearborn, Dorr R21 ES-014653 NIH
Nibbe, Rod AMS
Cellular Footprinting of the
Transferrin: Receptor
Proteomics of Type 1 Diabetes
Progression
Center for Synchrotron Biosciences-
Supplement
Genomics and Structural
Proteomics Core
Proteome and Transcriptome of
Defined Cell Types in the Ear
Following Noise Exposure
Biomarkers for Exposure to
Stachybotrys
Discovery Proteomics of Colorectal
Cancer
$431,000 9/1/2005 8/31/2007
$628,000 9/1/2005 8/31/2007
$216,000 3/1/2006 8/31/2008
$54,000 11/1/2006 7/31/2007
$436,000 3/1/2007 2/28/2010
$419,000 5/1/2006 4/30/2009
$2,000 7/1/2007 10/31/2007
$2,186,000

Training Grant Summary
Trainee Type of Grant Agency Title
Bohon, Jennifer T32 DK-007678 NIH
Bebek, Gurkan R25 CA-094186 NIH
Bohon, Jennifer T32 HL-007887 NIH
Nibbe, Rod T32 GM-008803 NIH
Patel, Vishal T32 GM-08613 NIH
Undergrads Majoring
in Systems Biology
Majors, BME Majors,
PPSP- Medicine
Students. Masters
Students in STEP
and Public Health
Nutrition
Pending Projects
Principal
Investigator
Type of
Grant
Scholarships
Chance, Mark R01 NIH
Chance, Mark
P30 EB-
009866
Chance, Mark U01 NIH
Ohio
Board of
Regents
Cell Physiology Project: Examination of
the ClpAP Protease via Synchrotron Xray
Hydroxyl-Radical Protein
Footprinting and Mass Spectrometry
Training on Computational Genomics
Project: Biological Networks
Heart Lung Physiology Project:
Structural Mapping of the ClpAP
Protease and its Assembly
Predoctural Training Program Project:
Late Stage Human Colon Cancer
Genetics Project: Network Crosstalk in
Complex Genetic Models of Colon
Cancer
Choose Ohio First Engaged Scholarship
Program in Bioscience and Healthcare
16
Trainee
Support
Start Date End Date
$39,000 7/1/2007 6/30/2008
$160,000 8/31/2007 7/30/2009
$45,000 7/1/2008 6/30/2009
$45,000 8/1/2008 7/31/2009
$83,000 7/1/2007 6/30/2009
$355,000 7/1/2008 8/31/2013
$727,000
Agency Title Total Cost Start Date End Date
Radiolytic Footprinting Methods for Structural Mass
Spectrometry
$1,570,000 4/1/2010 3/31/2015
NIH Case Center for Synchrotron Biosciences $4,667,000 9/1/2009 8/31/2014
Novel Biomarkers for Chronic Kidney Disease in
Diabetes- Subcontract with University of Denver
$902,000 9/1/2009 8/30/2014
Chance, Mark DOD Molecular Signatures in Colon Cancer $1,177,500 3/1/2010 2/28/2013
Chance, Mark S10 NIH Thermo Electron LTQ Orbitrap XL $1,189,642 12/1/2009 11/30/2010
Chance, Mark S10 NIH Canberra 100 Element Germanium Detector $1,480,000 12/1/2009 11/30/2010
Chance, Mark P30 NIH
Chance, Mark P30 NIH
Adams, Mark R01 NIH
Baron, Elma R21 NIH
Bebek, Gurkan K25 NIH
Biomedical Research Core in Proteomics and
Systems Biology
Biomedical Research Core in Bioinformatics and
Systems Biology
Mechanism of colistin resistance in Acinetobacter
baumannii
Treatment of Mycosis Fungoides with Silicon
Phthalocyanine Pc 4 Photodynamic Therapy
Cellular Signaling Signatures in Colorectal Cancer
Carcinogenesis
$1,463,807 10/1/2009 9/30/2011
$744,765 10/1/2009 9/30/2011
$1,570,000 12/1/2009 11/30/2014
$431,750 12/1/2009 11/30/2011
$722,000 4/1/2010 3/31/2015
Bonomo, Robert ARRA NIH PBPs in Acinebacter Baumannii $818,404 9/1/2009 8/31/2010
Cho, Michael R01 NIH
Enhancing B cell Immune Responses Against HIV-1
Using Maltivalent Antigens
$2,557,331 7/1/2009 6/30/2014

Pending Projects, continued
Principal
Investigator
Type of
Grant
Cobb, Brian R01 NIH/NIGMS
Davis, Pamela UL1 NIH
Dealwis, Chris R01 NIH
Ghannoum,
Mahmoud
Ghannoum,
Mahmoud
R01 NIH
RC2 NIH
Hoppel, Chuck R01 NIH
Jackson, Mark R01 NIH
Agency Title Total Cost Start Date End Date
Structure and Function Relationships in
carbohydrate antigen recognition
CWRU/CCF CTSA NCRR ARRA Supplement
Translational
Antibodies and Neurodegenerative Disease
Research, Diagnosis and Treatment
Modulations of Candida Biofilms by ADH Involves
Aconitas-based Mechanism
Effects of HIV Infection and Antiretroviral Therapy
on Oral Mycobiome and Metabolome
Protein Acetylation: Enhanced Sythesis of
Mitoochondrial Proteincs in Aged Heart
Identification of a Novel Oncogene Involved in
EGFR-RAS Signaling
17
$1,766,250 7/1/2009 6/30/2014
$938,228 9/1/2009 8/31/2011
$1,441,000 7/1/2009 6/30/2014
$1,962,500 12/1/2009 11/30/2014
$1,570,000 9/30/2009 8/31/2011
$1,970,000 4/1/2010 3/31/2015
$800,000 1/1/2010 12/31/2014
Karn, Jonathan NIH Center for AIDS Research - Proteomics Core $1,041,000 4/1/2010 3/31/2015
Kern, Timothy RC1 NIH Pharmacoproteomics fo Diabetic Retinopathy $942,000 10/1/2009 9/30/2011
Koyuturt, Mehmet NSF
CDI-Type 1: Network Algorithms for Integrating
'omics Data in the Study of Complex Phenotypes
$602,247 9/1/2009 8/31/2012
Maguire, Mike R01 NIH Structure-Function of the MgtE Mg 2t Channel $1,570,000 4/1/2010 3/31/2015
Miyagi, Masaru NSF
Serine Protease Catalyzed Carboxyl Oxygen
Exchange Reaction
$519,455 9/1/2009 8/30/2012
Miyagi, Masaru R21 NIH Ante-Mortem Diagnosis of Prion Infection $392,500 12/1/2009 11/30/2011
Miyagi, Masaru R01 NIH
Miyagi, Masaru RC1 NIH
Moore, John R01 NIH
Qu, Cheng-Kui R01 NIH
Histidine Hydrogen-deuterium Exchange Mass
Spectrometry for Structural Biology
Histidine Hydrogen-deuterium Exchange Mass
Spectrometry for Structural Analysis of
Macromolecular Complexes
Stretch and Apoptosis Cause Fetal Membrane
Rupture
PTPMT1 Phosphatases and Oxidative stress of
Hematopoietic Stem Cells
$1,962,500 4/1/2010 3/31/2015
$1,000,000 10/1/2009 9/30/2012
$1,962,500 12/1/2009 11/30/2014
$1,962,500 12/1/2009 6/30/2013
Rote, Neal R01 NIH Apoptosis and Trophoblast Fusion $1,962,500 12/1/2009 11/30/2013
Stark, George P01 NIH
Weinberg, Aaron RC1 NIH
Weiss, Michael R01 NIH
Project 4: Reversible Lysine Methylation of
Chromatin-bound Inducible Transcription Factors
Using Fusobacterium Nucleaturm Associated
Defensin Inducer to Boos Indigenous Immune
Response; Enhancing Treatment of HIV/Aids
Related Manifistations
How Mutations in Proinsulin Cause Neonatal
Diabetes: A Protein-Misfolding Disease
$2,590,000 5/1/2010 4/30/2015
$999,934 9/1/2009 8/31/2011
$2,147,000 12/1/2009 11/30/2014
Wintrode, Patrick S10 NIH LTQ Mass Spectrometer $394,000 4/1/2010 3/31/2011
$49,790,313

Pilot Awards
PI Title of Project Amount Year
Betapudi, Venk
A Proteomics approach to understand the regulatory mechanisms of
nonmuscle myosin II mediated breast cancer cell migration
18
$10,000 2008
Lee, Hyoung-Gon Pathogenic mechanism of MYC cardiomyopathy $10,000 2008
Nock, Nora
Ramachandra,
Lakshmi
Romani, Andrea
Feng, Zhaoyang
(John)
Harris, Michael
Lu, Tao
Sanders, Steven
Tesar, Paul
Genotype-Phenotype Modeling of Polycyclic Aromatic Hydrocarbon
Response System Pathways in Prostrate Carcinogenesis
$10,000 2008
Analyses of Mycobacterium tuberculosis phagosomes by proteomics $10,000 2008
Proteomic Identification of Proteins Modified by HNE in the Heart of
type-1 diabetic rats
Proteomic Analysis of Diet Restriction Pathway and the Role of TOR
Signaling Using a Novel Stable Isotopic Lysine Labeling technique in
C. elegans
Analysis of Enzyme Mechanism Using Kinetic Isotope Effects by
Applying ESI-Q/TOF Tandem MS
Identification and Functional Characterization of Novel Protein
Substrates of the F-box Leucine Rich Protein (FBXL 11)
A Proteomics Screen to Identify Recognition Modules for Methylated
Histone H3 Lysine 20
Understanding the Molecular Networks Underlying stem cell
Pluripotency: a Proteomics Approach
$10,000 2008
$10,000 2009
$10,000 2009
$10,000 2009
$10,000 2009
$10,000 2009
$100,000

10/29/2008
10/30/2008
11/6/2008
11/13/2008
11/20/2008
SEMINAR SERIES
11/29/2008
2/5/2009
WORKSHOPS
Thermo Scientific's Workshop Label Free Quantitation Using Mass
Spectrometry
Expression Proteomics Workshop: Global proteome profiling using label
free technology in human clinical studies and animal models of disease
19
Daniela Schlatzer & Chao
Yuan
3/5/2009 Quantitative proteomic analysis using stable isotopic labeling Masaru Miyagi & Chao Yuan
4/2/2009
High Throughput Urine Proteome Analysis by AMT-Tag Method
Using Mass Spectrometry of high mass accuracy
CTSC: Diet-Induced Metabolic Disease and Cancers in
genetically predisposed mice
Locating Disease Genes: Haplotype inference, linkage,
association and integrative studies
CTSC: Genomics of Multidrug Resistance in Acinetobacter
baumannii
Human Placental Development: A Target for Proteomics
Analysis
12/4/2008 Target validation principles: Using bioinformatics workflow
Igor Popov
Joseph
Nadeau
Jing Li
2-D DIGE Workshop: An applied quantitative proteomics tool to identify
molecular signatures for urogenital dysfunction in diabetic rat model
Emanuel Institute of Biochemical Physics
Russian Academy of Science
CWRU, Dept. of Genetics
CWRU, Dept. of Electrical Engineering and
Computer Science
Mark Adams CWRU, Dept. of Genetics
Neal Rote CWRU, Dept. of Reproductive Biology
Mahesh
Visvanathan
University of Kansas, EECS
12/11/2008 CTSC: Going outside the box with carboxylase Belinda Willard Cleveland Clinic Foundation, Proteomics Core
1/12/2009
1/20/2009
Intrinsic disorder and protein evolution: Amino acid composition
of proteins in last universal ancestor
Development of Bioinformatics Tools for Phylogenetics and
Genomics Analyses
Sai Harish
Babu Karne
Yu Liu
Indiana University –Purdue University at
Indianapolis, School of Informatics
University of Toronto, Dept. of Molecular
Genetics
1/22/2009 High resolution immunophenotyping flow cytometric analysis David Kaplan CWRU, Dept. of Pathology
2/19/2009
From Structural Genomics to Metagenomics: Making Tracks in
Protein Structure and Function Space
3/12/2009 Class Mode Discovery by Local Sparse Bump Hunting
3/19/2009
3/30/2009
3/31/2009
Multistep Tumorigenesis in Lung Cancer and Glioblastoma:
Insights from high dimensional data mining
Computational Method Development for Proteomics Data
Analysis
Candidate Gene Selection and Networks for Complex Disease:
Schizophrenia as a Case
4/9/2009 Using Mass Spectrometry for rapid Bacterial Diagnosis
5/7/2009
Study of interactions between the axon guidance receptor plexin-
B1 and small GTPases
6/11/2009 Using Ancestry Estimates in Genetic Studies
6/25/2009
A new class of acyl-CoA esters, 4-phosphoacyl-CoAs, are
intermediates in one of two new catabolic pathways of 4hydroxyacids
(products of lipid peroxidation and drugs of abuse)
Iddo Friedberg
Jean-Eudes
Dazard
Thomas
LaFramboise
Bingwen Lu
Zhongming
Zhao
Robert
Bonomo
UCSD, California Institute for
Telecommunications and Information
Technology
CWRU, Dept. of Epidemiology and Biostatistics
CWRU, Dept. of Genetics
The Scripps Research Institute, Dept. of
Chemical Physiology
Virginia Commonwealth University, Dept. of
Bioinformatics
CWRU, Division of Infectious Diseases and HIV
Medicine
Matthias Buck CWRU, Dept. of Physiology and Biophysics
Jill Barnholtz-
Sloan
Henri
Brunengraber
CWRU, General Medical Sciences (Oncology)
CWRU, Dept. of Nutrition
Elizabeth Yohannes &
Chao Yuan

Posters and Presentations by Center Members
Posters and Presentations by Center Members
(Underlined names represent summer students)
1. Zheng, L., Liu, S.Q., Sun, M.Z., Chang, J., Howell, S.J., Mishra, R., Chance, M.R., Kern, T.S. Alteration
of transcriptional machinery in the retina of diabetic rats, Amer Diabetes Assoc, abstract, Alexandria,
VA, June 2008.
2. Ghosh, S.K., Yohannes, E., McCormick, T., Chance, M.R., Weinberg, A. Proteomic profiling of oral
epithelial cells from HIV-positive and healthy subjects, IADR-2008, abstract, Toronto, Canada, July 2-5,
2008.
3. Rodriguez, E., Brown, R.C., Crish, J., Chance, M.R., Gobezie, R. Proteomic Analysis of the Human
Synovium from Patients Clinically Diagnosed with Early and Late Osteoarthrits, Summer Research
Symposium for Undergraduate Research, poster, Athens, OH, August 2008.
4. Daniels, E.W., Brown, R.C., Crish, J., Chance, M.R., Grant, R.E., Gobezie, R. Proteomic Analysis of
Synovial Fluid of Healthy vs Osteoarthritic Patinents Using 2D-DIGE and Mass Spectrometry
(Validation of Putative Protein Markers Gelsolin and Afamin), Nth Dimensions Education Solutions
meeting, poster, Miami, FL, August 2008.
5. Takamoto, K., Han, D., Qin, Y., et al. Structural and antigenic properties of a novel immunogen
containing HIV-1 gp41 membrane-proximal external region, Aids Research and Human Retroviruses,
abstract, 24: 23, 2008
6. Lu, T., Jackson, M.W., Singhi, A.D., et al. Promoter insertion reveals lysine demethylase FBXL11 as a
negative regulator of NF-kappa B, Cytokine, abstract, 43(3): 326, 2008
7. Gupta, S., D'Mello, R., Chance, M.R., Structural Probing of Snap-Freeze Protein Samples by
Synchrotron Fooprinting: Radiation Damage at Work, New York Structural Biology Discussion Group,
Summer Session, poster, Cold Spring Harbor Laboratory, New York, NY, August 6, 2008.
8. Gupta, S., X-ray Footprinting at Beamline X28C, New York Structural Biology Discussion Group,
Summer Session, poster, Cold Spring Harbor Laboratory, New York, NY, August 6, 2008.
9. Berman, L.E., Allaire, M., Chance, M.R., Hendrickson, W., Heroux, A., Manjasetty, B., Orville, A.
Robinson, H., Saxena, A., Schneider, D., Shi, W., Soares, A., Stojanoff, V., Sweet, R. A suite of
macromolecular crystallography facilities being planned for NSLS-II, XXI Congress and General
Assembly of the IUCr, poster, Osaka, Japan, August 23-31, 2008.
10. Miyagi, M., Nakazawa, T. Sensitive and Unequivocal Determination of pKa Values of Individual
Histidine Residues in Proteins Using Mass Spectrometry, 17th Meeting of Methods in Protein Structure
Analysis, poster, Sapporo, Japan, August 26-29, 2008.
11. Ewing, R.M. Refining network topology through mining human AP-MS data. CSHL/Wellcome Trust
Network Biology meeting, presentation, Hinxton, Cambridge, GB, August 2008.
12. Dealwis, C. Passive immunotherapy of Alzheimer’s disease, presentation, Roskamp Institute,
Sarasota, Florida, August 2008.
13. Chance, M.R. Integrating Gene and Protein Expression Biomarkers in a Systems Biology Approach to
Colon Cancer, Cambridge Healthtech Institute Biomarker Discovery Summit, Philadelphia, PA,
September 2008.
14. Ewing, R.M. Large-scale protein interaction mapping: moving towards dynamic networks, presentation,
Department of Genetics, CWRU, Sept. 2008.
15. Manjasetty B.A., Zhu, W., Chance, M.R. Structure and function analysis of E.coli L-Arabinose
Isomerase through structural genomics approach, Genomics, Proteomics and Systems Biology,
presentation, J.N Tata Auditorium, Indian Institute of Science, Bangalore, India, October 1-3, 2008.
16. Azizi, F., Wan, Q., Radivoyevitch, T., Dealwis, C., Mastrangelo, C.H. A Combinatorial Multicomponent
Plug Mixer for Systems Chemistry, MicroTAS2008, poster, October 12-17, 2008.
17. Patterson, N., Zheng, X., Chance, M.R. Advancing Computational Methods for Protein Structure
Determination: Rosetta + Footprinting, ABRCMS Conference, poster, Orlando, FL, November 5-8,
2008.
20

Posters and Presentations, continued
18. Ewing, R.M. “Large-scale protein interaction mapping: moving towards dynamic networks”, Department
of Plant Breeding and Genetics, Cornell University, November 11, 2008.
19. Chance, M.R. “Integrative Approaches in Translational Medicine”, NCRR/NIBIB - P41 Center Directors
Meeting, presentation, Washington DC, November 13-14, 2008.
20. Yohannes, E., Chang, J., Davies, K.P., Chance, M.R. “Proteomics Analysis Identified Molecular
Signatures for Diabetes Mullitus Associated Erectile Dysfunction”, 5 th Annual Diabetes Research
Symposium, poster, Cleveland, OH, November 14, 2008.
21. Ewing, R.M. “Large-scale protein mapping: computational and statistical challenges”, Biostatistics
Seminar Series, School of Medicine, Case Western Reserve University, November 20, 2008.
22. Gupta, S. “X-ray Footprinting at Beamline X28C”, New York Structural Biology Discussion Group,
Winter Session, New York Academy of Sciences, poster, New York, NY. January 22, 2009
23. Bohon, J., Jennings, L.D., Philips, C.M., Licht, S., Chance, M.R. “Structural Mass Spectrometry of a
Molecular Machine: Oligomerization and Gating in the ClpAP Protease”, New York Structural Biology
Discussion Group 4 th Winter Meeting, NY Academy of Sciences, poster, New York, NY, January 22,
2009.
24. Schlatzer, D. “Global Proteome Profiling Using Label Free Technology in Human Clinical Studies and
Animal Models of Disease”, Center for Proteomics and Bioinformatics Workshop, Case Western
Reserve University, workshop presenter, Cleveland. OH 44106, February 5, 2009.
25. Lindsay, A., Chance, M.R., Liu, S., Chen, D., Zheng, Q., Alagramam, K. “Inner Ear Protein Networks
and Biomarkers in a Mouse Model for Deafness in Usher Syndrome 1F and Nonsyndromic Deafness
DFNB23”, Association for Research in Otolaryngology, poster, Baltimore, MD, February 14-19, 2009.
26. Zheng, XJ, Vernon, R.M., Baker, D., Chance, M.R. “Protein Structure Determination by Combining
Structural Mass Spectrometry Data with Rosetta”, US HUPO 5 th Annual Conference, oral presentation,
San Diego, CA, February 2009.
27. Bebek, G., “Virtual Screening to Identify Signal Transduction Pathway Segments in the APC(Min/+)
Mouse”, US HUPO 5 th Annual Conference, oral presentation, San Diego, CA, February 25, 2009.
28. Bohon, J., Jennings, L.D., Philips, C.M., Licht, S., Chance, M.R. “Structural Mass Spectrometry of a
Molecular Machine: Functional Consequences of Confirmational Changes in the ClpAP Protease”, 5 th
Annual US HUPO Conference, presentation, San Diego, CA, February 24, 2009.
29. Chance, M.R. “Discovery and scoring of protein interaction sub-networks discriminative of late stage
human colon cancer”, 5 th Annual US HUPO Conference, presentation, San Diego, CA, February 24,
2009.
30. Chance, M.R. “Conserved waters define a structural and functional channel involved in activation of the
G protein-coupled receptor rhodopsin”, 5 th Annual US HUPO Conference, presentation, San Diego, CA,
February 24, 2009.
31. D’Mello, R., Gupta, S., Bohon, J., Sullivan, M., Chance, M.R. “Footprinting at Beamline X28C: A
National Resource for Studying Macromolecular Structure and Dynamics”, Biophysical Society 53 rd
Annual Meeting, poster, Boston, MA, February 28 – March 4, 2009.
32. Gupta, S., Angel, T., Jastrzebska, B, Palczewski, K., Chance, M.R. “X-ray Footprinting Studies on
Photoactivation of Bovine Rhodopsin", Biophysical Society 53 rd Annual Meeting, presentation, Boston,
MA, February 28 – March 4, 2009
33. Chance, M.R. “Systems Biology for Clinical Diagnosis and Therapy”, presentation, Department of
Medicine Grand Rounds, University Hospitals, Cleveland, OH, March 3, 2009.
34. Zheng, XJ., Vernon, R.M., Baker, D., Chance, M.R. “Structure Determination by Combining
Footprinting Data with Rosetta”, 2009 NIGMS workshop, NIH, Bethesda, MA, March 2009.
35. Yohannes, E “2D-DIGE Workflow: An applied quantitative proteomics tool to identify molecular
signatures for urogenital dysfunction in diabetic rat model”, Center for Proteomics and Bioinformatics,
Case Western Reserve University, oral presentation, Cleveland, OH, April 2, 2009.
21

Posters and Presentations, continued
36. Saha, S. “An affinity Purification Mass Spectrometry (AP-MS) platform for characterizing protein
interaction networks”, Research Showcase, Case Western Reserve University, poster, Cleveland, OH,
April 16, 2009.
37. Schlatzer, D. “An integrative Biology Approach for plasma biomarker discovery in idiopathic
pneumonia syndrome”, 6 th Annual Ohio Valley Mass Spectrometry Symposium, presentation,
Columbus, OH, April 21, 2009.
38. Gokulrangan, G., Levinson, R., Rana, G., Chen, D., Alagramam, K., Chance, M.R. “Hearing Loss
Phenomenon in Usher Syndrome1: Protein Profiling of the Cochlea using Proteomic Methodologies”,
6 th Ohio Valley Mass Spectrometry Symposium, presentation, Columbus, OH, April 22, 2009.
39. Chance, M.R. “Nuts and Bolts of Grant Writing: How to Sell Your Science”, Professional Skills
Program, presentation, Dept. Physiology & Biophysics, Case Western Reserve University, Cleveland,
OH, May 2009.
40. Gupta, S. “Introduction to X-ray Protein Footprinting Workshop: Solution Studies of Macromolecules:
Global and Local Structure”, 2009 Joint National Synchrotron Light Source and Center for Functional
Nanomaterials Users’ Meeting, Brookhaven National Laboratory, presentation, Upton, NY, May 18 –
20, 2009.
41. Chance, M.R. “Footprinting and Conformational Dynamics: Synergy with SAXS”, 2009 Joint National
Synchrotron Light Source and Center for Functional Nanomaterials Users’ Meeting, Brookhaven
National Laboratory, presentation, Upton, NY, May 18 – 20, 2009.
42. Yohannes, E., Chang, J., Davies, K.P., Chance, M.R. “Molecular Targets for Diabetes Mellitus
Associated Erectile Dysfunction”, CERAMACS 2009, presentation, Cleveland, OH, May 20 – 23, 2009.
43. Yohannes, E., Anni, H., Gonye, G.E., Ilchenko, S., Rubin, E., Chance, M.R. “Quantitative Proteomics
Analysis of Alcohol-induced Cardiomyopathy using Label Free LC-MS Approach”, 57 th ASMS
Conference on Mass Spectrometry, poster, Philadelphia, PA, May 31 – June 4, 2009.
44. Gokulrangan, G., Levinson, R., Rana, G., Chen, D., Alagramam, K., Chance, M.R. “Identification of
Biomarkers in Cochlear Pathogenesis in the Usher Syndrome 1F Mouse Model”. 57 th ASMS
Conference on Mass Spectrometry, poster, Philadelphia, PA, May 31 – June 4, 2009.
45. Gupta, S., Chance, M.R. “X-ray Footprinting Studies on Integral Membrane Protein”, 57 th ASMS
Conference on Mass Spectrometry, poster, Philadelphia, PA, May 31 – June 4, 2009.
46. Schlatzer D., Chance, M.R., Ewing, R., Ilchenko S., Rana, G., Cooke, K. “An Integrative Biology
Approach for Plasma Biomarker Discovery in Idiopathic Pneumonia Syndrome”, 57 th ASMS Conference
on Mass Spectrometry, oral presentation, Philadelphia, PA, June 1, 2009.
47. Nibbe, R., Chance, M.R. “Quantitative Top-Down Proteomics and Systems Biology of Colon Cancer”,
57 th ASMS Conference on Mass Spectrometry, oral presentations, Philadelphia, PA, June 2, 2009.
48. Zheng, XJ, Vernon, R., Baker, D., Sauder, JM, Burley, S., Chance, M.R. “Structure Determination by
Combining Footprinting Data with Rosetta”, 57 th ASMS Conference on Mass Spectrometry, poster,
Philadelphia, PA, May 31 – June 4, 2009.
49. Lundberg, K., Gokulrangan, G., Rana, G., Schlatzer, D., Wolfram, J., Yuan, C., Chance, M.R.,
Ward, N. “Identification of Differentially Expressed Proteins in Transgenic Mouse Models of Psoriasis
using Label Free Analysis”, 57 th ASMS Conference on Mass Spectrometry, poster, Philadelphia, PA,
May 31 – June 4, 2009.
50. Kaur, P., Kiselar, J., Chance, M.R. “Computational Methods for Probing Covalently Labeled
Biomolecules using Structural Proteomics”, 57 th ASMS Conference on Mass Spectrometry, poster,
Philadelphia, PA, May 31 – June 4, 2009.
51. Kiselar, J., Phillips, N., Chance, M.R., Weiss, M. “Probing the Structure of Proinsulin by MS-Based
Footprinting”, 57 th ASMS Conference on Mass Spectrometry, poster, Philadelphia, PA, May 31 – June
4, 2009.
52. Lattif A., Mukherjee, P., Yohannes, E., Zhao, H., Chance, M.R. “Quantitative Proteomic Analysis of
Parental and adh1 Mutant Isolates of Candida albicans in Mature Phase Biofilm”, 57 th ASMS
Conference on Mass Spectrometry, poster, Philadelphia, PA, May 31 – June 4, 2009.
22

53. Wang, B., Lu. T., Miyagi, M., Stark, G., Chance, M.R. “Post-Translational Modifications on the Subunit
p65 of NfkB”, 57 th ASMS Conference on Mass Spectrometry, poster, Philadelphia, PA, May 31 – June
4, 2009.
54. Yuan, C., DiNuoscio, G., Keller, A., Rana, G., Romani, A., Chance, M.R. “Quantitative Proteomic
Analysis of Diabetic Cardiomyopathy Using Label-free Mass Spectrometry” 57 th ASMS Conference on
Mass Spectrometry, poster, Philadelphia, PA, May 31 – June 4, 2009.
55. Chance, M.R. “Overview of and Statistical Analysis of “-omic” Data”, OCCBIO ’09, presentation, Case
Western Reserve University, Cleveland, OH, June 15, 2009.
56. Saha, S., Kaur, P., Song, J., Skomorovska-Prokvolit, Y., Rana, G., Ewing, R. “Computational
challenges and solutions in interaction proteomics”, OCCBIO ’09, poster, Case Western Reserve
University, Cleveland, OH, June 15, 2009.
57. D'Mello, R., Gupta, S., Bohon, J., Abel, D., Toomey, J., Sullivan, M., Chance, M.R. X-ray
Footprinting at Beamline X28C: A National Resource for Studying Macromolecular Structure and
Dynamics, Biophys. J., 96(3), 66a-67a (2009).
58. Chang, J., Kanika, N.D., Tar, M., et al. Diabetic Cystopathy is Associated with Changes in the Oxidative
Stress Status of the Bladder, Journal of Urology, abstract, 181(4): 80-81, 2009.
59. Bennett, M., Cooper, K., Chance, M.R., et al. Ultraviolet irradiation alters keratinocyte ephrin receptor
and calcium signaling pathways following exposure to a chemical sensitizer, dinitrobenzene sulfonic
acid, Journal of the American Academy of Dermatology, abstract, 60(3): AB32, 2009.
Publications
(Underlined citations represent theses)
Center & Collaborative Research
Posters and Presentations, continued
1. Shi, W., Chance, M.R. Metallomics and Metalloproteomics, Cell Mol. Life Sci., 65(19), 3040-3048,
2008.
2. Chang, J., Chance, M.R., Nicholas, C., Ahmed, N., Guilmeau, S., Flandez, M., Wang, D., Byun, D.S.,
Nasser, S., Albanese, J.M., Corner, G.A., Heerdt, B.G., Wilson, A.J., Augenlicht, L.H., Mariadason,
J.M. Proteomic changes during intestinal cell maturation in vivo, J. Proteomics, 71(5):530-46, 2008.
3. Mailankot, M., Smith, D., Howell, S., Wang, B., Jacobberger, J., Stefan, T., Nagaraj, R.H. Cell Cycle
Arrest by Kynurenine in Lens Epithelial Cells. Invest Ophthalmol Vis Sci., 49(12):5466-75, 2008.
4. Goc, A., Angel, T.E., Jastrzebska, B., Wang, B., Wintrode, P.L., Palczewski, K. Differences in
properties of native and reconstituted heterotrimeric G protein transducin, Biochemisty, 47(47):12409-
19, 2008.
5. Szymanski, J., Wilson, D.W., Zhang, G.-Q. MIMI: Multimodality, Multiresource, Information Integration
Environment for Biomedical Core Facilities, Journal of Digital Imaging, 2008 [Epub ahead of print].
6. Yuan, C., Solaro R.J. Myofilament proteins: from cardiac disorder to proteomic changes, Proteomics-
Clinical Applications, 2:788-99, 2008.
7. Yuan, C., Sheng, Q., Tang, H., Li, Y., Zeng, R., Solaro, R.J. Quantitative comparison of sarcomeric
phosphoproteomes of neonatal and adult rat hearts, Am J Physiol Heart Circ Physiol, 295(2):H647-56,
2008.
8. Tsutsui, Y., Kuri, B., Sengupta, T., Wintrode, P.L. The structural basis of serpin polymerization studied
by hydrogen/deuterium exchange and mass spectrometry, J. Biol. Chem., 283(45):30804-11, 2008.
9. Jennings, L.D., Bohon, J., Chance, M.R., Licht, S. “The ClpP N-terminus Coordinates Substrate
Access with Protease Active Site Reactivity, Biochemistry, 47, 11031-11040, 2008.
10.Zheng, L., Liu, S., Sun, M.Z., Chang, J., Chance, M.R., Kern, T.S. Pharmacologic intervention
targeting glycolytic-related pathways protects against retinal injury due to ischemia and reperfusion,
Proteomics, 9(7):1869-82, 2009.
23

Publications
Center & Collaborative Research, continued
11. Pieper, U., Chiang, R., Seffernick, J.J., Brown, S.D., Glasner, M.E., Kelly, L., Eswar, N., Sauder, J.M.,
Bonanno, J.B., Swaminathan, S., Burley, S.K., Zheng, X., Chance, M.R., Almo, S.C., Gerlt, J.A.,
Raushel, F., Shoichet, B.K., Jacobson, M.P., Babbitt, P.C., Sali, A. Target Selection and Annotation
for the Structural Genomics of the Amidohydrolase and Enolase Superfamilies, J Struct Funct
Genomics, 10(2):107-25, 2009.
12. Mailankot, M., Staniszewska, M.M., Butler, H., Caprara, M.H., Howell, S., Wang, B., Doller, C.,
Reneker, L.W., Nagaraj, R.H. Indoleamine 2,3-dioxygenase overexpression causes kynureninemodification
of proteins, fiber cell apoptosis and cataract formation in the mouse lens, Lab Invest, 89
(5):498-512, 2009.
13. Shin, K., Nigrovic, P.A., Crish, J., Boilard, E., McNeil, H.P., Larabee, K.S., Adachi, R., Gurish, M.F.,
Gobezie, R., Stevens, R.L., Lee, D.M. Mast cells contribute to autoimmune inflammatory arthritis via
their tryptase/heparin complexes, J Immunol. 182(1):647-56, 2009.
14. Nibbe, R.K., Markowitz, S., Myeroff, L., Ewing, R., Chance, M.R. “Discovery and scoring of protein
interaction subnetworks discriminative of late stage human colon cancer,” Mol. Cell. Proteomics, 8
(4):827-45, 2009.
15. Moore, R.M., Redline, R.W., Kumar, D., Mercer, B.M., Mansour, J.M., Yohannes, E., Novak, J.B.,
Chance. M.R., Moore, J.J. “Differential expression of fibulin family proteins in the para-cervical weak
zone and other areas of human fetal membranes”, Placenta, 30(4):335-41, 2009.
16. Bennett, B.C., Wan, Q., Ahmad, M.F., Langan, P., Dealwis, C.G. X-ray structure of the ternary
MTX.NADPH complex of the anthrax dihydrofolate reductase: a pharmacophore for dual-site inhibitor
design J Struct Biol. 166(2):162-71, 2009.
17. Kiser, J.Z., Post, M., Wang, B., Miyagi, M. Streptomyces erythraeus Trypsin for Proteomics
Applications J Proteome Res. 8(4):1810-1817, 2009.
18. Strachan, R.T., Sheffler, D.J., Willard, B., Kinter, M., Kiselar, J.G., Roth, B.L. Ribosomal S6 kinase 2
directly phosphorylates the 5-hydroxytryptamine 2A (5-HT2A) serotonin receptor, thereby modulating
5-HT2A signaling J Biol Chem. 284(9):5557-73, 2009.
19. Pattanaik, P., Bethel, C.R., Hujer, A.M., Hujer, K.M., Distler, A.M., Taracila, M., Anderson, V.E.,
Fritsche, T.R., Jones, R.N., Pagadala, S.R., van den Akker, F., Buynak, J.D., Bonomo, R.A.
Strategic design of an effective beta-lactamase inhibitor: LN-1-255, a 6-alkylidene-2'-substituted
penicillin sulfone, J Biol Chem. 284(2):945-53, 2009.
20. Mathivanan, S., Ahmed, M., … Ewing, R.M., … Pandey, A. Human Proteinpedia enables sharing of
human protein data, Nat Biotechnol, 26(2):164-7, 2009.
21. Lodowski, D.T., Angel, T.E., Palczewski, K. Comparative analysis of GPCR crystal structures,
Photochem Photobiol, 85(2):425-30, 2009.
22. Tian, G., Zhou, Y., Hajkova, D., Miyagi, M., Dinculescu, A., Hauswirth, W.W., Palczewski, K., Geng,
R., Alagramam, K.N., Isosomppi, J., Sankila, E.M., Flannery, J.G., Imanishi, Y. Clarin-1, encoded by
the Usher syndrome III causative gene, forms a membranous microdomain: Possible role of Clarin-1
in organizing the actin cytoskeleton. J Biol Chem. 2009 May 7. [Epub ahead of print]
23. Angel, T., Chance, M.R., and Palczewski, K. Conserved waters mediate structural and functional
activation of family A (rhodopsin-like) G protein-coupled receptors, Proc. Nat. Acad. Sci., 106
(21):8555-60, 2009.
24. Rojanathammanee, L., Harmon, E.B., Grisanti, L.A., Govitrapong, P., Ebadi, M., Grove, B.D., Miyagi,
M., Porter, J.E. The 27-kDa heat shock protein confers cytoprotective effects through a beta2adrenergic
receptor agonist-initiated complex with beta-arrestin. Molecular pharmacology, 75(4): 855-
65, 2009.
25. Burley, S.K., Almo, S.C., Bonanno, J.B., Chance, M.R., Emtage, S., Fiser, A., Sali, A., Sauder, J.M.,
and Swaminathan, S. “Chapter 40: Structural Genomics of Protein Superfamilies”, in Structural
Bioinformatics, 2 nd Ed., eds. J. Gu & P.E. Bourne, Wiley-Blackwell, p. 983, 2009.
24

26. Gomez, J.A., Sun, W., Gama, V., Hajkova, D., Yoshida, T., Wu, Z., Miyagi, M., Pink, J.J., Jackson,
M.W., Danielpour, D., Matsuyama, S. The C-terminus of Interferon Gamma Receptor Beta Chain
(IFNγR2) has antiapoptotic activity as a Bax inhibitor, Cancer Biology and Therapy, 2009, in press.
27. Chance, M.R., Chang, J., Schlatzer, D.M., Miyagi, M. Quantitative Proteomics, in Enclyclopedia of
Analytical Chemistry, R.A. Meyers, Ed., Wiley Publishing, in press.
28. Angel, T.E., Gupta, S., Jastrzebska, B., Palczewski, K., Chance, M.R. (2009) “Structural waters
define a functional channel mediating activation of the GPCR, rhodopsin”, Proc. Nat. Acad. Sci. USA,
in press.
29. Yuan, C., Rana, G., Chang, J., Ewing, R., Chance, M.R., Comparison of label free and O 18 labeling
mass spectrometry in relative protein quantification, IEEE: 2009 Ohio Collaborative Conference on
Bioinformatics proceedings, p. 14-18.
30. Li, X., Erten, S., Bebek, G., Koyuturk, M., Li, J. Comparative Analysis of Modularity in Biological
Systems. IEEE: 2009 Ohio Collaborative Conference on Bioinformatics proceedings, pp. 104-109,
doi: 10.1109/OCCBIO.2009.29
31. Schlatzer, D.M., Christ, G., Dharseei, M., Dazard, J.E., Ewing, R.M., Ilchenko, S., Stewart, I.,
Chance, M.R. (2009) “Urinary protein profiles in a rat model for diabetic complications”, Mol. Cell.
Proteomics, Jun 4. [Epub ahead of print].
32. Kaur, P., Kiselar, J., Chance, M.R. Integrated Algorithms for High Throughput Examination of
Covalently Labeled Biomolecules by Structural Mass Spectrometry, Analytical Chemistry, in press.
33. Nibbe, R.K., Chance, M.R. “Biomarkers in human colorectal cancer: looking back, to go forward”,
Future Medicine, in press.
34. Lu, T., Jackson, M.W., Singhi, A.D., Kandel, E., Wang, B., Yang, M., Zhang, Y., Chance, M.R.,
Miyagi, M., Gudkov, A.V., Stark, G.R. (2009) “Regulation of NFĸB by NSD1/FBXL11-dependent
reversible lysine methylation of p65”, Genes and Development, submitted.
35. Zhang, L., Howell, S.J., Liu, S., Sun, M.Z., Chang, J., Mishra, R., Chance, M.R., Kern, T.S. (2009)
“Alteration of transcriptional machinery in the retina of diabetic rats”, Diabetes, submitted.
36. Nibbe, R.K., Chance, M.R., Koyuturk, M. “Integrative Proteomics Approaches to Identify Important
Sub-networks in Human Colorectal Cancer”, PLoS Comp. Bio., submitted.
37. Dagdanova, A.V., Ilchenko, S.A., Yang, Q., Obrenovich, M.E., Hatcher, K., Dogterom, A., McAnulty,
P., Huang, L., Zou, W., Kong, Q., Gambetti, P., Chen, S.G. Mass Spectrometry Characterization of
the Prion Protein in Human Urine, Biochemistry, submitted.
38. Cafasso, J., Sandman, K., Karr, E., Manjasetty, B., Reeve, J., Chance, M.R. “A preliminary
crystallography study reveals the DNA binding protein Archaeal Tryptophan Regulator, TrpY is a
dimer,” J. Undergraduate Research, submitted.
39. Yohannes, E., Chang, J., Tar, M.T., Davies, K.P., Chance, M.R. Molecular Targets for Diabetes
Mellitus Associated Erectile Dysfunction, Mol Cell Prot, submitted.
40. Kiser, P., Golczak, M., Lodowski, D., Chance, M.R., Palczewski, K., “Crystal Structure of Native
RPE65, the Retinoid Isomerase of the Visual Cycle”, Proc. Nat. Acad. Sci, in revisions.
Service Research: Proteomics & Genomics
41. Jennings, L. Translocation and Proteolysis by the Energy-Dependent Protease ClpAP: Coordination
of Conformational Changes and Active Site Chemistry, Ph.D. Thesis. Massachusetts Institute of
Technology, Cambridge (2008).
42. Adilakshmi, T., Bellur, D.L., Woodson, S.A. Concurrent nucleation of 16S folding and induced fit in
30S ribosome assembly, Nature, 455, 1268-1272 (2008). [ premier ].
43. Distler, A.M., Kerner, J., Hoppel, C.L. Proteomics of mitochondrial inner and outer membranes,
Proteomics 8(19):4066-82, 2008.
44. Distler, A.M., Kerner, J., Lee, K., Hoppel, C.L. Post-translational modifications of mitochondrial outer
membrane proteins. Methods Enzymol., 457:97-115, 2009.
45. Distler, A.M., Kerner, J., Hoppel, C.L. Mass spectrometric demonstration of the presence of liver
carnitine palmitoyltransferase-I (CPT-I) in heart mitochondria of adult rats, Biochim Biophys Acta.
1794(3):431-7, 2009.
25

Publications
Service Research: Proteomics & Genomics, continued
46. Wolfram, J.A., Diaconu, D., Hatala, D.A., Rastegar, J., Knutsen, D., Lowther, A., Askew, A., Gilliam,
A.C., McCormick, T.S., Ward, N.L. Keratinocyte but not endothelial cell specific overexpression of
Tie2 leads to the development of psoriasis, American Journal of Pathology, 174:1443–1458, 2009.
47. Kombu, R.S., Zhang, G., Abbas, R., Mieyal, J.J., Anderson, V.E., Kelleher, J.K., Sanabria, J.R.,
Brunengraber, H. Dynamics of glutathione and ophthalmate traced with 2H-enriched body water in
rats and humans. Am J Physiol Endocrinol Metab., 2009 Apr 28. [Epub ahead of print]
48. Hota, P.K., Buck, M. Thermodynamic characterization of two homologous protein complexes:
associations of the semaphorin receptor plexin-B1 RhoGTPase binding domain with Rnd1 and active
Rac1. Protein Sci., 18(5):1060-71, 2009.
49. Shelton, M.D., Distler, A.M., Kern, T.S., Mieyal, J.J. Glutaredoxin regulates autocrine and paracrine
proinflammatory responses in retinal glial (muller) cells, J. Biol. Chem., 284(8):4760-6, 2009.
50. Schneider, K.D., Bethel, C.R., Distler, A.M., Hujer, A.M., Bonomo, R.A., Leonard, D.A. Mutation of
the Active Site Carboxy-Lysine (K70) of OXA-1 beta-Lactamase Results in a Deacylation-Deficient
Enzyme, Biochemistry, 2009 Jun 15. [Epub ahead of print]
51. Seckler, J.M., Howard, K.J., Barkley, M.D., Wintrode, P.L. Solution Structural Dynamics of HIV-1
Reverse Transcriptase Heterodimer, Biochemistry, in press.
52. Sengupta, T., Tsutsui, Y., Wintrode, P.L. Local and Global Effects of a Cavity Filling Mutation in a
Metastable Serpin, Biochemistry, accepted.
Service Research: X-Ray X Ray Absorption Spectroscopy
53. Hakemian, A., Kondapalli, K., Telser, J., Hoffman, B., Stemmler, T., Rosenzweig, A. The Metal
Centers of Particulate Methane Monooxygenase from Methylosinus trichosporium OB3b,
Biochemistry, 47: 6793–6801, 2008.
54. Sagi, I., Milla, M. Application of structural-dynamic approaches provide novel insights into the
enzymatic mechanism of the tumor necrosis factor-alpha converting enzyme (TACE), Analytical
Biochemistry, 372(1): 1-10, 2008.
55. Shearer, J, Soh, P., Leintz, S. Both Met(109) and Met(112) are utilized for Cu(II) coordination by the
amyloidogenic fragment of the human prion protein at physiological pH. J Inorg Biochem, 102: 2103-
2113, 2008.
56. Smith, S., Bencze, K., Wasiukanis, K., Benore-Parsons, M, Stemmler, T. XAS and Pulsed EPR
Studies of the Copper Binding Site in Riboflavin Binding Protein, Inorg. Chem., 47: 6867-72, 2008.
57. Smith, S., Bencze, K., Wasiukanis, K., Stemmler, T., Benore-Parsons, M. Association of Copper to
Riboflavin Binding Protein; Characterization by EPR and XAS, Open Inorg. Chem. J., 2: 39-41, 2008.
58. Kondapalli, K., Kok, N., Dancis, A., Stemmler, T. Drosophila Frataxin: an Iron Chaperone During
Cellular [2Fe-2S] Cluster Bioassembly, Biochemistry, 47: 6917-27, 2008.
59. Abriata, L.A., Gonzalez, L.J., Llarrull, L.I., Tomatis, P.E., Myers, W.K., Costello, A.L., Tierney, D.L.,
Vila, A.J. Engineered Mononuclear Variants in Bacillus cereus Metallo-b-Lactamase BcII are Inactive,
Biochemistry, 47(33): 8590-8599, 2008.
60. Shearer, J., Szalai, V. A. The Amyloid-beta peptide of Alzheimer's Disease Binds Cu(I) in a linear bis-
His coordination environment: Insight into a possible neuroprotective mechanism, J Amer Chem Soc,
130(52): 17826–17835, 2008. [premier]
61. Fiedler, A. T., Shan, X., Mehn, M. P., Kaizer, J., Torelli, S., Frisch, J. R., Kodera, M., Que, L., Jr.
Spectroscopic and Computational Studies of (m-Oxo)(m-1,2-Peroxo)diiron(III) Complexes of
Relevance to Nonheme Diiron Oxygenase Intermediates, J. Phys. Chem. A, 112: 13037-13044,
2008.
26

62. Jackson, T. A., Rohde, J.-U., Seo, M. S., Sastri, C. V., DeHont, R., Ohta, T., Kitagawa, T., Münck, E.,
Nam, W., Que, L., Jr. Axial Ligand Effects on the Geometric and Electronic Structures of Nonheme
Oxoiron(IV) Complexes, J. Am. Chem. Soc., 130(37): 12394-12407, 2008. [premier]
63. Ordóñez, E., Thiyagarajan, S., Cook, J., Stemmler, T, Gil, J., Mateos, L., Rosen, B. Evolution of metal
(loid) binding sites in transcriptional regulators, J. Biol. Chem., 283, 25706-14, 2008.
64. Hirota, S., Kawahara, T., Beltramini, M., Di Muro, P., Magliozzo, R., Peisach, J., Powers, L., Tanaka,
N., Nagao, S., Bubacco, L. Molecular Basis of the Bohr Effect in Arthropod Hemocyanin, J. Biol.
Chem., 283, 31941-31948, 2008.
65. Soh Fri, P. Metal Binding to Peptide Fragments Derived From the Neurotoxic Domain of the Human
Prion Protein, Ph.D. Thesis, University of Nevada, Reno, (2009).
66. Neupane, K.P. Metallopeptide Based Models of Nickel Superoxide Dismutase, Ph.D. Thesis,
University of Nevada, Reno, (2009).
67. England, J., Martinho, M., Farquhar, E., Frisch, J., Bominaar, E., Munck, E., Que, L. A Synthetic High
-Spin Oxoiron(IV) Complex: Generation, Spectroscopic Characterization, and Reactivity, Angew.
Chem. Int. Ed., 48, 3622-3626 (2009).[ premier]
68. Akabayov, B., Lee, S., Akabayov, S., Rekhi, S., Zhu, B., Richardson, C., DNA Recognition by the
DNA Primase of Bacteriophage T7: A Structure Function Study of the Zinc-Binding Domain,
Biochemistry, 48(8), 1763–73 (2009).
69. Kandegedara, A., Thiyagarajan, S., Kondapalli, K.C., Stemmler, T.L., Rosen, B.P. Role of bound Zn
(II) in the CadC Cd(II)/Pb(II)/Zn(II)-responsive repressor. J. Biol. Chem., 284(22):14958-65 (2009).
70. Herbst, R.W., Guce, A., Bryngelson, P., Higgins, K., Ryan, K., Cabelli, D., Garman, S., Maroney, M.J.
The Role of Conserved Tyrosine Residues in NiSOD Catalysis: A Case of Convergent Evolution,
Biochemistry, 48: 3354-3369 (2009).
71. Kumar, R., Rekhi, S., Prabhakaran, D., Kim, E., Somyazulu, M., Cook, J., Stemmler, T., Bootrhoyd,
A., Chance, M.R., Cornelius, A. Structural Studies on Na0.75CoO2 Thermoelectric Material at High
Pressures, Solid State Communications, doi:10.1016/j.ssc.2009.06.012, 2009.
72. Solomon, A., Selzer, T., Milla, M., Sagi, I. New frontiers in the biophysics and chemistry of
metalloproteinases, in Wiley Encyclopedia of Chemical Biology, in press.
73. Akabayov, B., Eberhardt Gottschalk, K., le Maire, M., Sagi, I., Karlish, S.J.D. Divalent metal binding
sites of Na+,K+-ATPase and Ca2+-ATPase. Two Mg2+ ions are bound together with ATP, J Biol
Chem, submitted.
74. Moore, A. L., Shearer, J., Kim, J., Cline, J. I., Catalano, V. J. Highly luminescent Au(I)-(Cu(I)-X)2
butterfly dimers utilizing the ligands [(CH3imCH2py)]BF4, and [(CH3imCH2quin)]BF4, Inorg Chem,
submitted.
75. Selzer, T., Vash, B., Ali, S., Sertchook, R., Grossmann, J.G., Atadja, P., Stams, T., Cohen, D., Sagi, I.
Human histone deacetylases are flexible enzymes: insights from solution structural analysis of human
apo-histone deacetylase 8, Biophys J, submitted.
76. Kumar, R., Rekhi, S., Prabhakaran, D., Kim, E., Somyazulu, M., Cook, J., Stemmler, T., Bootrhoyd,
A., Chance, M.R., Cornelius, A. High Pressure Structural Studies on Na0.75CoO2, Solid State
Communication, submitted.
77. Shearer, J., Neupane, K.P., Callan, P. Use of unnatural amino-acids in Nickel Superoxide Dismutase
metallopeptide mimics to probe the influence of a key hydrogen-binding network in the
metalloenzyme, Inorg. Chem., submitted.
78. Frisch, J.R., Vu, V.V., Martinho, M., Münck, E., Que, L., Jr. Characterization of Two Distinct Addducts
in the Reaction of a Non-heme Diiron(II) Complex with O2, Inorg. Chem., submitted.
79. Vu, V.V., Emerson, J.P., Martinho, M., Kim, Y.S., Münck, E., Park, M.H., Que, L., Jr. Cell growthregulating
deoxyhypusine hydroxylase from humans has a nonheme diiron active site that activates
O2. Proc. Natl. Acad. Sci. U. S. A., submitted.
27

Publications
Service Research: Macromolecular Crystallography
80. Lamour, V., Kuznedelov, K., Rutherford, S. T., Ramagopal, U. A., Gourse, R. L., Severinov, K., Darst,
S. A. Crystal structure of Escherichia coli Rnk, a new RNA polymerase-interacting protein, J. Mol.
Biol., 383, 367-379 (2008).
81. Debler, E., Ma, Y., Seo, H., Hsia, K., Noriega, T., Blobel, G., Hoelz, A. A Fence-like Coat for the
Nuclear Pore Membrane, Mol. Cell, 32, 815–826 (2008). [ premier ]
82. Stavropoulos, P., Nagy, V., Blobel, G., Hoelz, A. Molecular Basis for the Autoregulation of the Protein
Acetyl Transferase Rtt109, Proc Natl Acad Sci USA, 105(34), 12236-12241 (2008). [ premier ]
83. Hsu, Y., Jubelin, G., Taieb, F., Nougayrède, J., Oswald, E., Stebbins, C. Structure of the
Cyclomodulin Cif from Pathogenic Escherichia coli, J. Mol. Biol., 384(2), 465-477 (2008).
84. Kim, J., Tsai, P., Chen, S., Himo, F., Almo, S., Raushel, F. Structure of Diethyl Phosphate Bound to
the Binuclear Metal Center of Phosphotriesterase, Biochemistry, 47(36), 9497-9504 (2008).
85. Rao, Y., Greener, J., Avila-Orta, C., Hsiao, B., Blanton, T. The Relationship between Microstructure
and Toughness of Biaxially Oriented Semicrytalline Polyester Films, Polymer, 49(10), 2507-2514
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86. Mancias, J., Goldberg, J. Structural Basis of Cargo Membrane Protein Discrimination by the Human
COPll Coat Machinery, EMBO J., 27, 2918 (2008). [ premier ]
87. Messing, S., Structure and Function of the RNA Pyrophosphohydrolase BdRppH and the 9-cis-epoxy
Carotenoid Dioxygenase VP14 , Ph.D Thesis. Johns Hopkins University, Baltimore (2008).
88. Serganov, A., Huang, L., Patel, D. Structural Insights Into Amino Acid Binding and Gene Control by a
Lysine Riboswitch, Nature, 455, 1263-1267 (2008). [ premier ]
89. Jayaram, H., Accardi, A., Wu, F., Williams, C., Miller, C. Ion Permeation Through a Cl--Selective
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90. Lazar-Molnar, E., Yan, Q., Cao, E., Ramagopal, U., Nathenson, S., Almo, S. Crystal Structure of the
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91. Song, J., Kingston, R. WDR5 Intearcts with Mixed Lineage Leukemia (MLL) Protein via the Histone
H3-binding Pocket, J. Biol. Chem., 238(50), 35258 (2008).
92. Beierlein, J., Frey, K., Bolstad, D., Pelphrey, P., Joska, T., Smith, A., Priestley, N., Wright, D.,
Anderson, A. Synthetic and Crystallographic Studies of a New Inhibitor Series Targeting Bacillus
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93. Moldoveanu, T., Gehring, K., Green, D. Concerted Multi-Pronged Attack by Calpastatin to Occlude
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94. Zhou, X., Tan, T., Valiyaveettil, S., Go, M., Kini, R., Velazquez-Campoy, A., Sivaraman, J. Structural
Characterization of Myotoxic Ecarpholin S From Echis carinatus Venom, Biophys. J., 95, 3366–3380
(2008).
95. Zimmer, J., Nam, Y., Rapoport, T. Structure of a Complex of the ATPase SecA and the Protein-
Translocation Channel, Nature, 455, 936-943 (2008).
96. Lee, I., Schindelin, H. Structural Insights into E1-Catalyzed Ubiquitin Activation and Transfer to
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97. Sunita, S., Tkaczuk, K., Purta, E., Kasprzak, J., Douthwaite, S., Bujnicki, J., Sivaraman, J. Crystal
Structure of the Escherichia coli 23S rRNA: m{5}C Methyltransferase RlmI (YccW) Reveals
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98. Altieri, S., Clayton, G., Silverman, W., Olivares, A., De La Cruz, E., Thomas, L., Morais-Cabral, J.
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99. Collard, F., Zhang, J., Nemet, I., Qanungo, K., Monnier, V., Yee, V, Crystal Structure of the
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100.Hsu, Y., Jubelin, G., Taieb, F., Nougayrède, J., Oswald, E., Stebbins, C. Structure of the
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101.Wing, R., Bailey, S., Steitz, T. Insights into the Replisome from the Structure of a Ternary Complex of
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102.Nolen, B., Pollard, T. Structure and Biochemical Properties of Fission Yeast Arp2/3 Complex Lacking
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103.Samanta, U., Bahnson, B. Crystal Structure of Human Plasma Platelet-Activating Factor
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104.Stanley, B., Ehrlich, E., Short, L., Yu, Y., Xiao, Z., Yu, X., Xiong, Y. Structural Insight into the Human
Immunodeficiency Virus Vif SOCS Box and Its Role in Human E3 Ubiquitin Ligase Assembly, J.
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105.Zhang, W., Cho, Y., Lolis, E., Howe, J. Structural and Single-Channel Results Indicate that the Rates
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106.Schubert, H., Phillips, J., Heroux, A., Hill, C. Structure and Mechanistic Implications of a
Uroporphyrinogen III Synthase−Product Complex, Biochemistry, 47(33), 8648-8655 (2008).
107.Martucci, W., Vargo, M., Anderson, K. Explaining an Unusually Fast Parasitic Enzyme: Folate Tail-
Binding Residues Dictate Substrate Positioning and Catalysis in Cryptosporidium hominis
Thymidylate Synthase, Biochemistry, 47(34), 8902-8911 (2008).
108.Meinke, G., Ezeokonkwo, C., Balbo, P., Stafford, W., Moore, C., Bohm, A. Structure of Yeast Poly(A)
Polymerase in Complex with a Peptide from Fip1, an Intrinsically Disordered Protein, Biochemistry,
47, 6859–6869 (2008).
109.Bowley, S., Merenbloom, B., Heroux, A., Betts, L., Okumura, N., Gorkun, O., Lord, S. Polymerization
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110.Dowling, D., Gantt, S., Gattis, S., Fierke, C., Christianson, D. Structural Studies of Human Histone
Deacetylase 8 and Its Site-Specific Variants Complexed with Substrate and Inhibitors, Biochemistry,
47, 13554-13563 (2008).
111.Jones, L., Colf, L., Bankovich, A., Stone, J., Gao, Y., Chan, C., Huang, R., Garcia, K., Kranz, D.
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Panel of Structurally Similar High-Affinity T Cell Receptors, Biochemistry, 47, 12398-12408 (2008).
112.Wang, H., Yan, Z., Yang, S., Cai, J., Robinson, H., Ke, H. Kinetic and Structural Studies of
Phosphodiesterase-8A and Implication on the Inhibitor Selectivity, Biochemistry, 47, 12760-12768
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113.Hu, X., Wang, H., Ke, H., Kuhlman, B. Computer-Based Redesign of a Beta Sandwich Protein
Suggests That Extensive Negative Design is not Required for de novo beta Sheet Design, Structure,
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114.Demirci, H., Gregory, S., Dahlberg, A., Jogl, G. Multiple-Site Trimethylation of Ribosomal Protein L11
by the PrmA Methyltransferase, Structure, 16(7), 1059-1066 (2008).
115.Biswas, S., Mohammad, M., Movileanu, L., van den Berg, B. Crystal Structure of the Outer
Membrane Protein OpdK from Pseudomonas aeruginosa, Structure, 16(7), 1027-1035 (2008).
116.Xu, Y., Chen, Y., Zhang, P., Jeffrey, P., Shi, Y. Structure of a Protein Phosphatase 2A Holoenzyme:
Insights into B55-Mediated Tau Dephosphorylation, Mol. Cell, 31, 873–885 (2008). [ premier ]
117.Singh, S., Piscitelli, C., Yamashita, A., Gouaux, E. A Competitive Inhibitor Traps LeuT in an Open-to-
Out Conformation, Science, 322, 1655-1661 (2008). [ premier ]
118.Chen, W., Lam, S., Srinath, H., Jiang, Z., Correia, J., Schiffer, C., Fitzgerald, K., Lin, K., Royer, Jr.,
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119.Ragumani, S., Kumaran, D., Burley, S., Swaminathan, S. Crystal Structure of a Putative Lysostaphin
Peptidase from Vibrio cholerae, Proteins: Struc. Func. Bioinformatics, 72(3), 1096-1103 (2008).
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120.Cappadocia, L., Sygusch, J., Brisson, N. Purification, Crystallization and Preliminary X-ray Diffraction
Analysis of the Whirly Domain of StWhy2 in Complex with Single-Stranded DNA, Acta Cryst. F, 64,
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121.Pan, Y., Weng, J., Kabaleeswaran, V., Li, H., Cao, Y., Bholse, R., Zhou, M. Cortisone Dissociates
the Shaker Family K Channels from their Beta Subunit, Nat. Chem. Biol., 4(11), 708-714 (2008).
122.Lietha, D., Eck, M. Crystal Structures of the FAK Kinase in Complex with TAE226 and Related bisanilino
Pyrimidine Inhibitors Reveal a Helical DFG Conformation, PLoS One, 33(11), e3800 (2008).
123.Han, Q., Cai, T., Tagle, D., Robinson, H., Li, J. Substrate Specificity and Structure of Human
Aminoadipate Aminotransferase/kynurenine Aminotransferase II, Bioscience Rep., 28(4), 205-215
(2008).
124.Kumaran, D., Rawat, R., Ahmed, A., Swaminathan, S. Substrate Binding Mode and its Implication on
Drug Design for Botulinum Neurotoxin A, Plos Pathog., 4(9), 1-9 (2008).
125.Zhou, X., Sun, Q., Kini, R.M., Sivaraman, J. A universal method for fishing target proteins from
mixtures of biomolecules using isothermal titration calorimetry, Protein Sci, 17(10):1798-804 (2008).
126.Tan YW, Yu HB, Leung KY, Sivaraman J, Mok YK. Structure of AscE and induced burial regions in
AscE and AscG upon formation of the chaperone needle-subunit complex of type III secretion system
in Aeromonas hydrophila, Protein Sci, 17(10):1748-60 (2008).
127.Quezada, C., Hicks, S., Galan, J., Stebbins, C. A Family of Salmonella Virulence Factors Functions
as a Distinct Class of Autoregulated E3 Ubiquitin Ligases, Proc Natl Acad Sci USA, 106(12):4864-9,
(2009). [ premier ]
128.Overgaard, J., Larsen, F., Timco, G., Iversen, B. Experimental Charge Density in an Oxidized
Trinuclear Iron Complex using 15 K Synchrotron and 100 K Conventional Single-Crystal X-ray
Diffraction, Dalton Trans., 2009, 664–671 (2009).
129.Buchko, G., Robinson, H., Addlagatta, A. Structural Characterization of the Protein cce_0567 from
Cyanothece 51142, a Metalloprotein Associated with Nitrogen Fixation in the DUF683 Family,
Biochim Biophys Acta, 1794(4), 627-633 (2009).
130.Serganov, A., Huang, L., Patel, D. Coenzyme Recognition and Gene Regulation by a Flavin
Mononucleotide Riboswitch, Nature, 458, 233-237 (2009). [ premier ]
131.Ho, M., Menetret, J., Tsuruta, H., Allen, K. The Origin of the electrostatic Perturbation in
Acetoacetate Decarboxylase, Nature, 459, 393 (2009). [ premier ]
132.Scott, F., Stec, B., Pop, C., Dobaczewska, M., Lee, J., Monosov, E., Robinson, H., Salvesen, G.,
Schwarzenbacher, R., Riedl, S. The Fas-FADD Death Domain Complex Structure Unravels Signalling
by Receptor Clustering, Nature, 457, 1019-1022 (2009). [ premier ]
133.Woo, J., Lim, J., Shin, H., Suh, M., Ku, B., Lee, H., Joo, K., Robinson, H., Lee, J. Structural Studies
of a Bacterial Condensin Complex Reveal ATP-Dependent Disruption of Intersubunit Interactions,
Cell, 136, 85–96 (2009). [ premier ]
134.Ezezika, O., Younger, N., Lu, J., Kaiser, D., Corbin, Z., Nolen, B., Kovar, D., Pollard, T.
Incompatibility with Formin Cdc12p Prevents Human Profilin from Substituting for Fission Yeast
Profilin: Insights from Crystal Structures of Fission Yeast Proflin, J. Biol. Chem., 284(4), 2088-2097
(2009).
135.Tan, Y., Chan, S., Ong, T., Yit, L., Tiong, Y., Chew, F., Sivaraman, J., Mok, Y. Structures of Two
Major Allergens, Bla g 4 and Per a 4, From Cockroaches and Their IgE Binding Epitopes, J. Biol.
Chem., 284, 3148-3157 (2009).
136.Lafrance-Vanasse, J., Lefebvre, M., Di Lello, P., Sygusch, J., Omichinski, J. Crystal Structures of the
Organomercurial Lyase MerB in Its Free and Mercury-Bound Forms, J. Biol. Chem., 284, 938-944
(2009).
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137.Gallagher, D., Smith, N., Kim, S., Robinson, H., Reddy, P. Profound Asymmetry in the Structure of
the cAMP-free cAMP Receptor Protein (CRP) from Mycobacterium tuberculosis, J. Biol. Chem., 284,
8228–8232 (2009).
138.Nayak, V., Dessau, M., Kucera, K., Anthony, K., Ledizet, M., Modis, Y. Crystal Structure of Dengue
Type 1 Envelope Protein in the Postfusion Conformation and its Implication for Receptor Binding,
Membrane Fusion and Antibody Recognition, J. Virology, 83, 4338 (2009).
139.Brandao, T., Robinson, H., Johnson, S., Hengge, A. Impaired Acid Catalysis by Mutation of a Protein
Loop Hinge Residue in a YopH Mutant Revealed by Crystal Structures, J. Am. Chem. Soc., 131(2),
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140.Orville, A., Lountos, G., Finnegan, S., Gadda, G., Prabhakar, R. Crystallographic, Spectroscopic, and
Computational Analysis of a Flavin C4a-Oxygen Adduct in Choline Oxidase, Biochemistry, 48, 720–
728 (2009).
141.Li, Y., Cao, C., Jia, W., Yu, L., Mo, M., Wang, Q., Huang, Y., Lim, J., Ishihara, M. Structure of the F-
Spondin Domain of Mindin, an Integrin Ligand and Pattern Recognition Molecule, EMBO J., 28(3),
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142.Tripathi, A., Ren, Y., Jeffrey, P., Hughson, F. Structural Characterization of Tip20p and Dsl1p,
Subunits of the Dsl1p Vesicle Tethering Complex, Nat. Struct. Mol. Biol., 16(2), 114 (2009).
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143.Han, Q., Robinson, H., Cai, T., Tagle, D., Li, J. Biochemical and Structural Properties of Mouse
Kynurenine Aminotransferase III, Mol. Cell. Bio., 29(3), 784-793 (2009). [ premier ]
144.Gutierrez, J., Crowder, T., Rinaldo-Matthis, A., Ho, M, Almo, S., Schramm, V. Transition state
analogs of 5'-methylthioadenosine nucleosidase disrupt quorum sensing., Nat. Chem. Biol., 5(4), 251-
257 (2009).
145.Liu, J., Bolstad, D., Smith, A., Priestley, N., Wright, D., Anderson, A. Probing the Active Site of
Candida Glabrata Dihydrofolate Reductase with High Resolution Crystal Structures and the Synthesis
of New Inhibitors, Chem. Biol. Drug Des., 73, 62-74 (2009).
146.Clark, L., Boriack-Sjodin, P., Day, E., Eldredge, J., Fitch, C., Jarpe, M., Miller, S., Li, Y., Simon, K.,
van Vlijmen, H. An Antibody Loop Replacement Design Feasibility Study and a Loop-Swapped Dimer
Structure, Protein Eng. Des. Sel., 22(2), 93-101 (2009).
147.Lim, H., Miller, C. Intracellular Proton-Transfer Mutants in a CLC Cl–/H+ Exchanger, J Gen. Physiol.,
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148.Sun, Q., Collins, R., Huang, S., Holmberg-Schiavone, L., Anand, G.S., Tan, C.H., van-den-Berg, S.,
Deng, L.W., Moore, P.K., Karlberg, T., Sivaraman, J. Structural basis for the inhibition mechanism of
human cystathionine gamma-lyase, an enzyme responsible for the production of H(2)S, J Biol Chem,
284(5):3076-85 (2009).
149.Jobichen, C., Fernandis, A.Z., Velazquez-Campoy, A., Leung, K.Y., Mok, Y.K., Wenk, M.R.,
Sivaraman, J. Identification and characterization of the lipid-binding property of GrlR, a locus of
enterocyte effacement regulator, Biochem J, 420(2):191-9 (2009).
150.Tulsidas, S.R., Thangamani, S., Ho, B., Sivaraman, J., Ding, J.L. Crystallization of a nonclassical
Kazal-type Carcinoscorpius rotundicauda serine protease inhibitor, CrSPI-1, complexed with
subtilisin, Acta Crystallogr Sect F Struct Biol Cryst Commun, 65(Pt 5):533-5 (2009).
151.F., Shoichet, B.K., Jacobson, M.P., Babbitt, P.C., Sali, A. Target Selection and Annotation for the
Structural Genomics of the Amidohydrolase and Enolase Superfamilies, J Struct Funct Genomics, 10
(2):107-25 (2009).
152.Schalch, T., Job, G., Noffsinger, V.J., Shanker, S., Kuscu, C., Joshua-Tor, L., Partridge, J.F. High
affinity binding of Chp1 chromodomain to K9 methylated histone H3 is required to establish
centromeric heterochromatin, Mol. Cell, 34, 36-46 (2009).
153.Kapoor, N., Menon, S., Devi, R., Sachdev, P. & Sakmar, T.P. Structural Evidence for a Sequential
Release Mechanism for Activation of Heterotrimeric G Proteins, Mol Cell, submitted.
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154.Song, J.J., Kingston, R.E. Structure insights into the WDR5-MLL interaction and the methylated
histone H3 binding properties of WDR5-MLL complex, Nat. Struct. Mol. Biol, submitted. [premier]
155.Nolen, B.J., Tomasevic, N., Russell, A., Pierce, D., Jia, Z., Hartman, J., Sakowicz, R., Pollard, T.D.
Structural basis for inhibition of Arp2/3 complex by two classes of small molecule inhibitors, Nature,
submitted.
156.Yeung, N., Zhao, X., Gao, Y.G., Robinson, H., Miner, K., Lei, L., Lu, Y. Rational Design of a
Structural and Functional Nitric Oxide Reductase, Nature, submitted.
157.Marshall, N.M., Garner, D.K., Wilson, T.D., Gao, Y.G., Robinson, H., Lu, Y. Rationally Tuning the
Reduction Potential of a Single Electron Transfer Protein over a 700 mV Range, Nature, submitted.
158.Buchko, G.W. Pentapeptide repeat proteins and cyanobacteria. In: Gault P.M. and Marler, H.J.
(eds.) Handbook on Cyanobacteria: Biochemistry, Biotechnology, and Applications, Nova Science
Publishers, in press.
159.Zhan, C., Yan, Q., Patskovsky, Y., Li, Z., Toro, R., Meyer, A., Cheng, H., Brenowitz, M.D.,
Nathenson SG, Almo SC Biochemical and Structural Characterization of the Human TL1A
Ectodomain, Biochemistry, in press.
Service Research: Infrared Spectroscopy
160.Police, S., Harris, J., Lodder, R., Cassis, L. Effect of Diets Containing Sucrose vs. D-tagatose in
Hypercholesterolemic Mice, Obes., epub (2008).
161.Mak, K., Sfeir, M., Wu, Y., Lui, C., Misewich, J., Heinz, T. Measurement of the Optical Conductivity of
Graphene, Phys. Rev. Lett., 101, 196405 (2008). [ premier ]
162.Bonwell, E., Fisher, T., Fritz, A., Wetzel, D. Determination of Endosperm Protein Secondary
Structure in Hard Wheat Breeding Lines using Synchrotron Infrared Microspectroscopy, Vib.
Spectrosc., 48, 76-81 (2008).
163.Yu, P. Synchrotron-Based Microspectroscopic Analysis of Molecular and Biopolymer Structures
Using Multivariate Techniques and Advanced Multi-Components Modeling. Canadian Journal of
Analytical Sciences and Spectroscopy, 53: 220-231, (2008).
164.Doiron, K. Characterization Of Autoclaved Flaxseed As Feed For Ruminants Using Conventional
And Mid-IR Spectroscopic Based Approaches, Ph.D. Thesis, University of Saskatchewan, Canada,
2009.
165.Yu, P., Block, H., Doiron, K. Understanding the Differences in Molecular Conformation of
Carbohydrate and Protein in Endosperm Tissues of Grains with Different Biodegradation Kinetics
Using Advanced Synchrotron Technology, Spectrochim. Acta A, 71, 1837–1844 (2009).
166.Miller, S.S., Fulcher, R.G. Microstructure and Chemistry of the Oat Kernel. In: Oats: Chemistry and
Technology. Edited by P.J. Wood and F. H. Webster. AACC International Press, in press.
167.Doiron, K.J., Yu, P., McKinnon, J.J., Christensen, D.A. Heat-Induced Protein Structures and Protein
Subfractions In Relation to Protein Degradation Kinetics and Intestinal Availability In Dairy Cattle,
Journal of Dairy Science, in press.
168.Yu, P., Jonker, A., Gruber, M. Molecular Basis of Protein Structure and Nutritive Value in
Proanthocyanidin-enhanced Lc-Transgenic Alfalfa using Synchrotron-Radiation FTIR
Microspectroscopy, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, Elsevier,
in press.
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