PAST SYMPOSIA

2013:

Chemical Biology of Aging
November 1, 2013

Sixth Annual Chemical Biology Interface Summer Retreat
Tuesday, July 23, 2013

Biology of Cancer
January 10, 2013

2012:

Biological Thermodynamics
September 14, 2012

Fifth Annual Frontiers at the Chemistry-Biology Interface Symposium
April 28, 2012

2011:

Nucleic Acids
Friday, December 2, 2011

Fifth Annual Chemistry-Biology Interface Retreat
July 29, 2011

Drug Discovery
May 20, 2011

2010:

Protein Design
November 8, 2010

Fourth Annual Chemistry-Biology Interface Retreat
July 23, 2010

Molecular Imaging: Recent Advances and Medicinal Applications
April 15, 2010

2009:

Structural Biology
November 19, 2009

Third Annual Chemistry-Biology Interface Picnic
July 24, 2009

Lasers in Chemistry, Biochemistry, and Medicine
March 19, 2009

2008:

Oxidation and Reduction
November 18, 2008

Second Annual Chemistry-Biology Interface Scientific Picnic
July 25, 2008
Sponsor: NIH Chemistry-Biology Interface Fellowship

Membrane Structure, Assembly, and Traffic
May 6, 2008
Financial Sponsor: Avanti Polar Lipids

2007:

Chemical Genomics
December 13,2007
Financial Sponsors: PerkinElmer and ThermFisher Scientific

Chemistry/BMB/Wistar Trainee Retreat
July 13, 2007

Influenza Symposium
February 22, 2007
Financial Sponsor: Influmedix

2006:

The Nature and Role of Water as a Biological Solvent Symposium
October 12, 2006

Amyloid: Structure & Biology
April 27, 2006
Financial sponsors: OLIS, Inc.

Computational Analysis of Protein Structure and Function
March 9, 2006
Financial sponsors: Greater Philadelphia BioInformatics Alliance

2005:

Metallomolecules
November 17, 2005
Financial Sponsors: Bruker Biospin, GSAC

Trainee Symposium: Membranes and Molecular Recognition
October 25, 2005
Financial Sponsors: Optical Apparatus and GSAC

Single Molecule Studies
April 21, 2005
Financial Sponsors: Optical Apparatus, GSAC
On-Campus Co-Organizer*: Nano-Bio Interface Center (NBIC
)

Protein Design
March 10, 2005
Financial Sponsors: SynPep

2004:

Structure-Based Drug Design
November 18, 2004
Financial Sponsor: Merck Research Labs

Bioinorganic Chemistry: Metalloenzymes
April 22, 2004
Financial Sponsor: Polymedix

Protein Folding
February 26, 2004
Financial Sponsors: Proterion, GSAC

2003:

Inhibitors of Protein-Protein Interactions
November 20, 2003
Financial Sponsors: Biacore

*Organizer in addition to the Department of Chemistry and the Department of Biochemistry & Biophysics. 

All symposia from Fall 2003 – Spring 2006 received partial funding from the Provost’s Interdisciplinary Seminar Fund. 

 

Chemical Biology of Aging

November 1, 2013
Lynch Auditorium, Chemistry Building

12:30 p.m. - 1:20 p.m.
Gregory Verdine, Harvard University
The enemy within: Recognition and repair of 8-oxoguanine

1:20 p.m. – 1:40 p.m.
Brian Capell, Department of Cell and Developmental Biology, Berger Lab
Senescence leads to large-scale epigenomic destabilization marked by hallmarks of reprogramming

1:40 p.m. - 2:00 p.m.
David Frederick, Department of Physiology, Baur Lab
Increased synthesis of NAD is insufficient to promote the oxidative capacity of skeletal muscle in young mice

2:00 p.m. – 2:50 p.m.
Mary Armanios, Johns Hopkins University
Telomeres and age-related diseases

2:50 p.m. – 3:10 p.m.
Coffee Break

3:10 p.m. – 4:00 p.m.
Toren Finkel, Laboratory of Molecular Biology; National Heart, Lung, and Blood Institute, National Institutes of Health
Large lessons from small mice: mTOR, MCU, mitochondria and aging

4:00 p.m. – 4:20 p.m.
Daniel Ricketts, Department of Biochemistry and Biophysics, Marmorstein Lab
Molecular basis for histone H3.3-specific deposition by the HIRA/UBN1/CABIN1/ASF1a (HUCA) histone chaperone complex

4:20 p.m. – 4:40 p.m.
John Warner, Department of Chemistry, Petersson Lab
Protein semi-synthesis and modification of alpha synuclein

4:40 p.m. – 5:30 p.m.
Leonard Guarente, Massachusetts Institute of Technology
Sirtuins: aging and diseases

ORGANIZERS:
Stephanie Barros
Lyndsay Wood
Scott Ugras

FACULTY ADVISORS:
Shelley Berger, Cell & Developmental Biology
Brad Johnson, Pathology and Laboratory Medicine
Ronen Marmorstein, Wistar/Chemistry/BMB

SPONSORED BY:
Department of Chemistry
Department of Biochemistry and Biophysics
Biomedical Graduate Student Association

 
Sixth Annual Chemical Biology Interface Summer Retreat

Tuesday, July 23, 2013
Bryn Mawr College
10:00 a.m. - 6:00 p.m.

Keynote speaker: Tarun Kapoor, Rockefeller University

 

 
Biology of Cancer

January 10, 2013
Lynch Auditorium, Chemistry Building
12:30 p.m. - 5:30 p.m.

12:30 p.m. - 1:20 p.m.
Robert Weinberg, Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology
Malignant progression, the EMT and cancer stem cells

1:20 p.m. - 1:40 p.m.
Kevan Salimian
, Department of Biochemistry and Biophysics, Black Lab
CENP-A at human centromeres and neocentromeres forms octameric nucleosomes with loose superhelical termini

1:40 p.m. - 2:00 p.m.
Mark Mason
, Department of Chemistry, Skordalakes Lab
Oligimerization of the yeast Cdc13 is essential for proper telomere maintenance

2:00 p.m. - 2:50 p.m.
Steven Artandi
, Stanford University
Connecting chromosome ends to human disease

2:50 p.m. - 3:10 p.m.
Coffee Break

3:10 p.m. - 4:00 p.m.
Lorena Beese
, Duke University
Genesis and repair of DNA replication errors

4:00 p.m. - 4:20 p.m.
Peter Huwe
, Department of Biochemistry and Biophysics, Radhakrishnan Lab
Understanding kinase activation of ALK in neuroblastoma patients

4:20 p.m. - 4:40 p.m.
Yujie Liu
, Perelman School of Medicine, Hancock Lab
Inhibition of p300 impairs Foxp3+ T-regulatory cell function and promotes anti-tumor immunity

4:40 p.m. - 5:30 p.m.
Cynthia Wolberger
, Howard Hughes Medical Institute, The Johns Hopkins University
Mechanisms of ubiquitin signaling in transcription and the DNA damage response

ORGANIZING COMMITTEE:
Stephanie Barros
Morgan DeSantis
Jacob Goldberg
Scott Ugras
Lyndsay Wood

FACULTY ADVISORS:
Rahul Kohli
Ronen Marmorstein
Emmanuel Skordalakes

SPONSORED BY:

Penn logo tecan logo
Department of Chemistry
Department of Biochemistry and Biophysics
College Biochemistry Program
SASgov
Tecan Group Ltd.

Biological Thermodynamics

September 14, 2012
Lynch Auditorium, Chemistry Building
12:30 p.m. - 5:30 p.m.

 

12:30 p.m. – 1:20 p.m.
Thomas Record, University of Wisconsin-Madison
Interpreting and predicting solute and Hofmeister salt effects on biopolymer processes

1:20 p.m. – 1:40 p.m.
Ben Capraro, Department of Chemistry, Baumgart Lab
Membrane binding and dimerization of the endophilin N-BAR domain

1:40 p.m. – 2:00 p.m.
Robert Culik, Department of Biochemistry and Biophysics, Gai Lab
Experimentally interrogating the folding energy landscape of the Trp-cage miniprotein

2:00 p.m. – 2:50 p.m.
Angel García, Rensselaer Polytechnic Institute
Cosolvent effects on protein stability

2:50 p.m. – 3:10 p.m.
Coffee Break

3:10 p.m. – 4:00 p.m.
Bertrand Garcia-Moreno, Johns Hopkins University
Proton-coupled processes in proteins

4:00 p.m. – 4:20 p.m.
Nathaniel Nucci, Department of Biochemistry and Biophysics, Wand Lab
Site-resolved measurement of water-protein interactions by solution NMR

4:20 p.m. – 4:40 p.m.
Nick Bessman, Department of Biochemistry and Biophysics, Lemmon Lab
Understanding EGF receptor activation: Exploiting thermodynamics where structure has failed

4:40 p.m. – 5:30 p.m.
Ken Dill, Laufer Center for Physical & Quantitative Biology, Stony Brook University
Beyond the second law: The principles of maximum entropy and maximum caliber, with applications to biology and physics

ORGANIZING COMMITTEE:
Stephanie Barros
Morgan DeSantis
Jacob Goldberg
Scott Ugras
Lyndsay Wood

SPONSORED BY:

BGSA logo

Department of Chemistry
Department of Biochemistry and Biophysics
Penn Biomedical Graduate Students Association

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Fifth Annual Frontiers at the Chemistry-Biology Interface Symposium

April 28, 2012
Translational Research Center
8:30 a.m. - 6:30 p.m.

8:30 a.m. - 9:00 a.m.
Breakfast / Poster set up

9:00 a.m. - 9:05 a.m.
Opening remarks

9:05 a.m. - 9:30 a.m.
Ivan Dmochowski, University of Pennsylvania
Enabling chemical biology with hyperpolarized Xe

9:30 a.m. - 9:45 a.m.
Michael Taylor, Univeristy of Delaware

9:45 a.m. - 10:00 a.m.
Christopher Nabel, University of Pennsylvania

10:00 a.m. - 10:25 a.m.
Sharon Rozovsky, University of Delaware
77Se enrichment of proteins expands the biological NMR toolbox

10:25 a.m. - 10:40 a.m.
Coffee Break

10:40 a.m. - 11:05 a.m.
Emmanuel Skordalakes, The Wistar Institute, University of Pennsylvania
Telomerase structure function and cancer therapies

11:05 a.m. - 11:20 a.m.
Anabel Gonzalez Gil, Johns Hopkins University

11:20 a.m. - 11:35 a.m.
Kostyantyn Bobyk, University of Maryland College Park

11:35 a.m. - 12:00 noon
Dan Appella, National Institutes of Health
Nucleic acids for multi-valent display at the nanoscale

12:00 noon - 1:30 p.m.
Lunch/Poster session A

1:30 p.m. - 1:55 p.m.
Songon An, University of Maryland Baltimore County
Spatial Regulation of human de novo purine biosynthesis in cells

1:55 p.m. - 2:10 p.m.
Gabriel Rosenblum, University of Pennsylvania

2:10 p.m. - 2:35 p.m.
Herschel Wade, Johns Hopkins School of Medicine
When it's all a blur: Cracking the code for multidrug recognition

2:35 p.m. - 3:35 p.m.
Coffee break / Poster session B

3:35 p.m. - 4:00 p.m.
Herman Sintim, University of Maryland College Park
Chemical means to interrupt signaling in bacteria

4:00 p.m. - 4:25 p.m.
Doron Greenbaum, University of Pennsylvania, Perelman School of Medicine
Structure-guided design of stable helical inhibitors and probes for Cys proteases

4:25 p.m. - 4:30 p.m.
Poster award winner announcements

4:30 p.m. - 5:30 p.m.
KEYNOTE ADDRESS: Tom Muir, Princeton University
Chromatin: an expansive canvas for chemical biology

5:30 p.m. - 5:35 p.m.
Closing remarks

5:35 p.m. - 6:30 p.m.
Cocktails / H’ors d’oeuvres / Poster session B

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Nucleic Acids

Friday, December 2, 2011
Lynch Auditorium, Chemistry Building
12:30 p.m. - 5:30 p.m.

12:30 p.m. - 1:20 p.m.
Dinshaw Patel, Memorial Sloan-Kettering Cancer Center
Structural biology of RNA-mediated gene regulation

1:20 p.m. - 1:40 p.m.
Julie Griepenburg, Department of Chemistry, Dmochowski Lab
Regulating gene expression using light-activated oligonucleotides

1:40 p.m. - 2:00 p.m.
Sandya Ajith, Department of Biochemistry and Molecular Biophysics, Lynch Lab
Investigating the mechanism by which CELF2 regulates LEF1 alternative splicing

2:00 p.m. - 2:50 p.m.
Mark Behlke, Integrated DNA Technologies
A new generation of qPCR assays which use internally quenched probes

2:50 p.m. - 3:10 p.m.
Coffee Break

3:10 p.m. - 4:00 p.m.
Ruben Gonzalez, Columbia University
The structural dynamics of protein synthesis by the ribosome

4:00 p.m. - 4:20 p.m.
Ihab Younis, Department of Biochemistry and Molecular Biophysics, Dreyfuss Lab
A novel role for U1 snRNP in protecting pre-mRNA from premature cleavage and polyadenylation

4:20 p.m. - 4:40 p.m.
Henry Wang, Vagelos Scholar, Shorter Lab
Defining how Kapx2 affects the aggregation characteristics of FUS, an ALS-linked protein

4:40 p.m. - 5:30 p.m.
Eric Kool, Stanford University
Replacing the bases in DNA: Design of chemical and biological reporters

ORGANIZING COMMITTEE:
Robert Culik
Morgan DeSantis
Jacob Goldberg
Glen Liszczak
Scott Ugras

FACULTY ADVISORS:
David M. Chenoweth
Kristen W. Lynch
Ronen Marmorstein
E. James Petersson

SPONSORED BY:

IDT logo Penn LogoBGSA logo

Integrated DNA Technologies
Department of Chemistry
Department of Biochemistry and Biophysics
College Biochemistry Program
Biomedical Graduate Student Association

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2011 Chemistry-Biology Interface Retreat

Friday, July 29, 2011
10:00 a.m. – 6:00 p.m.
Villanova University

10:00 a.m. – 10:30 a.m.
Nataline Meinhardt
Design and application of alpha-helical calpain inhibitors

10:30 a.m. - 11:00 a.m.
Brittani Ruble
Photoregulatable hairpin-bandage hybrids for Transcriptome In Vivo Analysis (TIVA)

11:00 a.m. - 11:30 a.m.
Morgan Desantis
Understanding the mechanism of Hsp104-catalyzed disaggregation

11:30 a.m. - 12:00 noon
Chris Lanci
Computational design of a protein crystal: Moving from the nano-scale to the micro-scale

12:00 noon - 1:00 p.m.
Lunch

1:00 p.m. - 2:00 p.m.
Posters

2:00 p.m. - 2:30 p.m.
Jacob Goldberg
New tools for measuring conformational changes in proteins

2:30 p.m. - 3:00 p.m.
Mark Mason
Structural and biochemical characterization of yeast telomere binding protein Cdc13

3:00 p.m. - 4:00 p.m.
KEYNOTE SPEAKER: Craig Crews
Small molecule control of intracellular protein levels

4:00 p.m. - 6:00 p.m.
Barbeque and Happy Hour

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Drug Discovery

Friday, May 20, 2011
Grossman Auditorium, Wistar Institute
12:15 p.m. – 6:15 p.m.

12:15 p.m. – 1:00 p.m.
Nathanael S. Gray, Harvard Medical School, Dana-Farber Cancer Institute
Three strategies for overcoming kinase inhibitor resistance

1:00 p.m. – 1:20 p.m.
Jie Qin, Marmorstein Lab, Gene Expression and Regulation Program, Wistar Institute
Structure-based development of inhibitors to oncogenic BRAF kinase

1:20 p.m. – 1:40 p.m.
Shannon Telesco, Radhakrishnan Lab, Department of Bioengineering
A multiscale modeling approach to investigate molecular mechanisms of pseudokinase activation and drug resistance in the HER3/ErbB3 receptor tyrosine kinase signaling network

1:40 p.m. – 2:25 p.m.
Jeannie Rojas, Johnson and Johnson Ventures
Latest developments in alternative scaffolds based drug discovery at Johnson & Johnson

2:25 p.m. – 2:45 p.m.
Yao Zhang, DeGrado Lab, Department of Chemistry
The design and characterization for peptide-mimic based anticoagulant reversal

2:45 p.m. – 3:00 p.m.
Coffee Break

3:00 p.m. – 3: 45 p.m.
Michelle Arkin, University of California, San Francisco
Fragment-based ligand discovery for the "challenging" target

3:45 p.m. – 4:05 p.m.
Jun Wang, DeGrado Lab, Department of Biochemistry and Biophysics
Structure-based design of inhibitors targeting influenza A virus M2 proton channel (A/M2)

4:05 p.m. – 4:25 p.m.
Troy Messick, Vironika, LLC, Wistar Institute
Novel inhibitors of latent Epstein-Barr virus infection

4:25 p.m. – 4:45 p.m.
James Soper, Brunden Lab, Center for Neurodegenerative Disease Research, Institute on Aging
Development of brain-penetrant thromboxane receptor antagonists as novel therapeutics for Alzheimer’s disease

4:45 p.m. – 5:30 p.m.
Jun Liu, Johns Hopkins University
Exploration of the existing drug space for novel inhibitors of angiogenesis

5:30 p.m. – 6:15 p.m.
Reception, Wistar Atrium

SPONSORED BY:
Department of Chemistry
Department of Biochemistry and Biophysics, Dr. George W. Raiziss Foundation
The Wistar Institute

ORGANIZERS:
Morgan DeSantis
Daniela Fera
Gabriel Gonzalez
Shaoqing Zhang

FACULTY ADVISORS:
Doron Greenbaum
Ronen Marmorstein
James Shorter

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Protein Design

Monday, November 8, 2010
Dunlop Auditorium, Stemmler Hall

12:20 p.m. - 1:05 p.m.
Yi Lu, University of Illinois at Urbana-Champaign
Designing functional metalloproteins: unearthing the roles of non-covalent interactions in conferring and fine-tuning enzymatic activities

1:05 p.m. – 1:25 p.m.
Molly Sheehan, Dutton Lab, Department of Biochemistry and Biophysics
Designing superoxide oxidoreductase activity and mechanism in artificial protein

1:25 p.m. - 2:10 p.m.
Ting Xu, University of California, Berkeley
Hybrid biomaterials based on peptides and peptide-polymer conjugates

2:10 p.m. - 2:30 p.m.
Jose Manuel Perez-Aguilar, Saven Lab, Department of Chemistry
Design of Stromal Cell-Derived Factor 1x analogs with enhanced angiogenic properties

2:30 p.m. – 3:15 p.m.
Tanja Kortemme, University of California, San Francisco
Design and engineering of proteins, protein interactions and networks

3:15 p.m. - 3:30 p.m.
Coffee Break

3:30 p.m. - 4:15 p.m.
Karyn O’Neil, Johnson and Johnson Ventures
Advances in alternative scaffolds: a new biotherapeutic platform for Johnson & Johnson

4:15 p.m. - 4:35 p.m.
Ivan Korendovych, DeGrado Lab, Department of Biochemistry and Molecular Biophysics
Design of a switchable eliminase

4:35 p.m. - 5:20 p.m.
Sam Gellman, University of Wisconsin, Madison
Protein mimics with unnatural backbones

5:20 p.m. - 6:00 p.m.
Reception at the Johnson Foundation Library

SPONSORED BY:
The Department of Chemistry
The Department of Biochemistry and Biophysics
Graduate Student Government of the School of Arts and Sciences (SASgov)

ORGANIZERS:
Gabriel Gonzalez
Glen Liszczak
Yao Zhang
Shaoqing Zhang

FACULTY ADVISORS:
Ronen Marmorstein
Bill DeGrado

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CBI Retreat

Friday, July 23, 2010
Swarthmore College

9:00 a.m. - 10:00 a.m.
Breakfast (Science Center 101 lobby)

10:00 a.m. - 10:30 a.m.
Daniela Fera, Marmorstein Lab, Wister Insitute
Towards the structure-based design of HPV E7 inhibitors

10:30 a.m. - 11:00 a.m.
Lisa Lippert, Goldman Lab, Pennsylvania Muscle Institute, Department of Physiology
Observing conformational changes of yeast cytoplasmic dynein in real time using polarized total internal reflection fluorescence microscopy

11:00 a.m. - 11:30 a.m.
Jun Wang, DeGrado Lab, Department of Biochemistry and Biophysics
Discovery of potent inhibitors targeting influenza A virus M2 proton channel

11:30 a.m. - 12:00 noon
Graham Clinthorne, DeGrado Lab, Department of Biochemistry and Biophysics
Transmembrane histidine kinases: the role of polar residues offers clues to signaling mechanisms

12:00 p.m. - 1:00 p.m.
Lunch

1:00 p.m. - 2:00 p.m.
Poster Session

2:00 p.m. - 2:30 p.m.
Jennifer Greene, Harry Ischiropoulos, Department of Pediatrics
Unraveling the structural specificity of S-nitrosylation using global proteomic approaches

2:30 p.m. - 3:00 p.m.
Najat Khan, Dmchowski Lab, Department of Chemistry
Folate-conjugated 129-Xe biosensor for targeting cancer cells

3:00 p.m. - 3:30 p.m.
Mike Harbut, Greenbaum Lab, Department of Pharmacology
A chemical genetic approach defines a key role for the P. falciparum metallo-aminopeptidase, PfA-M1, in hemoglobin catabolism

3:30 p.m. - 4:00 p.m.
Kushol Gupta, Van Duyne Lab, Department of Biochemistry and Biophysics
The tyranny of the lattice: small-angle scattering studies of retroviral integrases and their complexes with DNA

4:00 p.m. - 6:00 p.m.
Happy Hour and Dinner

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Molecular Imaging: Recent Advances and Medicinal Applications

Thursday, April 15, 2010
12:00 p.m. – 6:00 p.m.
Reunion Hall, John Morgan Building and Austrian Auditorium, CRB

12:00 p.m. - 1:00 p.m.
Stephen Hell, Max Planck Institute, Göttingen
Nanoscopy with focused light

1:00 p.m. – 1:20 p.m.
Olena Taratula, Dmochowski Lab, Department of Chemistry
Targeted xenon@cryptophane biosensors for molecular imaging

1:20 p.m. – 1:40 p.m.
Yujie Sun, Goldman Lab, Pennsylvania Muscle Institute
Study of molecular motor proteins using single molecule fluorescence microscopy

1:40 p.m. 2:30 p.m.
Hank Kung, University of Pennsylvania
Molecular imaging in diagnosis and treatment of Alzheimer's disease

2:30 p.m. - 2:50 p.m.
Coffee Break

2:50 p.m. – 3:40 p.m.
Marina Kuimova, Imperial College, London
Imaging intracellular viscosity with molecular rotors

3:40 p.m. – 4:00 p.m.
Chih-Jung (CJ) Hsu, Baumgart Lab, Department of Chemistry
Spatial distribution of signaling proteins analyzed via photoactivation localization microscopy (PALM) in T-cells stimulated by surface-immobilized ligands

4:00 p.m. – 4:20 p.m.
Seung-Cheol Lee, Glickson Lab, Department of Radiology
In vivo magnetic resonance spectroscopy and imaging for therapeutic response detection in non-Hodgkin's lymphoma

4:20 p.m. – 5:10 p.m.
Dean Sherry, University of Texas, Dallas
Using chemical exchange principles in the design of MRI sensors

5:10 – 6:00 p.m.
Reception, JF Library, Anatomy-Chemistry Building

SPONSORED BY:

gapsa logo
Graduate and Professional Student Assembly (GAPSA)

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Structural Biology

Thursday, November 19, 2009
Class of '62 Auditorium, John Morgan Building

1:00 p.m. - 1:45 p.m.
Daniel Leahy, Johns Hopkins
Hedgehog Signaling: sorting out complex interactions

1:45 p.m.- 2:05 p.m.
Julie Aaron, Christianson Lab, Department of Chemistry
Epi-isozizaene synthase, a platform for the engineering of new terpenoid cyclization templates              

2:05 p.m. - 2:50 p.m.
Youxing Jiang, University of Texas Southwestern
Structural study of tetrameric cation channels  

2:50 p.m. - 3:10 p.m.
Coffee Break

3:10 p.m. - 3:55 p.m.
Charles Lesburg, Schering-Plough
Engineered PXR for inverse structure-based drug design

3:55 p.m. - 4:15 p.m.
Alexei Polishchuk, DeGrado Lab,Department of Biochemistry & Biophysics
Structure-based mechanism of proton transport through the influenza A M2 protein

4:15 p.m. - 5:00 p.m.
Lynne Regan, Yale University
Creating novel proteins by selection and design 

5:00 p.m. - 6:00 p.m.
Reception in Atrium

ORGANIZERS:
Julie Aaron
Daniela Fera
Glen Liszczak
Patrick Lombardi
Yao Zhang

FACULTY ADVISORS:
David Christianson, Department of Chemistry
Ronen Marmorstein, Wistar/Chemistry/BMB

SPONSORED BY:
Graduate and Professional Student Assembly (GAPSA)
Biomedical Graduate Student Association (BGSA)

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Third Annual Chemistry-Biology Interface Picnic

Friday, July 24, 2009
Swarthmore College 

10:00 a.m. – 12:00 p.m. / Morning Speakers / Science Center 101

Julia Richards, Department of Chemistry
Photoregulation of the 10-23 DNAzyme

Bryan Gibb, BMB
Breaking down the active site of Cre recombinase: understanding the mechanism of cleavage and ligation

Geronda Montalvo, BMB
Infrared spectroscopy and folding kinetics of a x-peptide helix

Ning Shangguan, Department of Chemistry
Roquefortine C and related biological activities

1:00 p.m. –  2:00 p.m. / Poster Session

Two hydrolase whodunits: on the trail of the yeast histone H4S1 phosphatase and the ant H3 tail clipping protease
Ed Ballister, Berger Lab, BMB

Bio-inorganic interface: Ferritin-nanoparticle systems
Jasmina Cheung-Lau, Dmochowski Lab, Department of Chemistry

Harnessing Hsp104 to eliminate Aß42 fibers implicated in Alzheimer’s Disease
Mimi Cushman, Shorter Lab, Neuroscience Graduate Group

Structure based drug design of human papillomavirus E7 inhibitors
Daniela Fera, Marmorstein Lab, Department of Chemistry/Wistar

Photoregulating gene expression with light activated oligonucleotides
Julie Griepenberg, Dmochowski Lab, Department of Chemistry

Molecular mechanism and specificity of substrate binding by the E3 Ubiquitin Ligase Pellino
Yu-San Huoh, Ferguson Lab, BMB

A mechanism of calcium binding for the regulation of myosin Ib in its role as a tension sensor
John Lewis, Goldman Lab, CAMB

The x-ray crystal structure of Acetylpolyamine Amidohydrolase (APAH) from Mycoplana ramosa
Pat Lombardi, Christianson Lab, Department of Chemistry

Characterization of novel PtdIns (4,5)P2 effector domains
Katarina Moravcevic, Lemmon Lab, BMB

Motor number controls cargo switching at actin-microtubule intersections in vitro
Trey Schroeder, Goldman Lab, BMB

Dynamics of tRNA motions during protein synthesis: Single molecule studies of ribosomes in the pre- and post-translocation states
Ben Stevens, Goldman Lab, Muscle Institute

Conformational changes of Hsp104 seen by Small Angle X-ray Scattering (SAXS)
Elizabeth Sweeny, Shorter Lab, BMB

The crystal structure of the Rtt109-Vps75 HAT-histone chaperone complex
Yong Tang & Katie Meeth, Marmorstein Lab, Wistar

Development of novel methods for the synthesis and control of protein structure
Mark Fagley & Anne Wagner, Petersson Lab, Department of Chemistry

Validation of 1-aminoanthracene as a fluorescent general anesthetic
Zhengzheng (Katie) Liao, Dmochowski Lab, Department of Chemistry

Mapping foldome changes in cell lysates with cysteine labeling kinetics
Brian Chase, Discher Lab, Bioengineering

2:00 p.m. –  4:00 p.m. / Afternoon Speakers / Science Center 101

Brandon Kelley, Department of Chemistry
Nucleophilic ring-opening of trisubstituted aziridines

Jasna Maksimoska, Department of Chemistry/Wistar
Structure-based design of organometallic PAK1 inhibitors

Kathryn Smith, BMB
Probing the mechanism of action of antimicrobial peptides through lipid diffusion

Daniel Dowling, Department of Chemistry
An unexpected protein superfamily: Arginase, Histone Deacetylase, and Acetylpolyamine Amidohydrolase

ORGANIZERS:
Julie Aaron
Daniela Fera
Brittani Ruble
Trey Schroeder
Kate Thorn

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LASERS IN CHEMISTRY, BIOCHEMISTRY, AND MEDICINE

Thursday, March 19, 2009
1:30 p.m. - 6:45 p.m.
Lynch Room, Chemistry Building

1:30 p.m. - 2:10 p.m.
Bruce Tromberg, University of California, Irvine
Spectroscopy and imaging in medicine: moving benchtop optical technologies to the bedside

2:10 p.m. - 2:25 p.m.
Patrick Mayes, El-Deiry Lab, Department of Pharmacology
Noninvasive vascular imaging in fluorescent tumors using multispectral unmixing

2:25 p.m. - 2:40 p.m.
XinJing Tang, Dmochowski Lab, Department of Chemistry
Using confocal laser scanning microscopy to probe the mechanism of anesthesia in animal models

2:40 p.m. - 2:55 p.m.
Louise Sinks, Vinogradov Lab, Department of Biochemistry and Biophysics
Oxygen microscopy with two-photon enhanced phosphorescence nanoprobes

2:55 p.m. - 3:35 p.m.
Charles Shank, Howard Hughes Medical Institute, Janelia Farm
Sculpting light for bioimaging and more

3:35 p.m. - 3:55 p.m.
Coffee Break

3:55 p.m. - 4:35 p.m.
William Eaton, National Institute of Health
Single molecule FRET trajectories and protein folding transition path times

4:35 p.m. - 4:50 p.m.
Matthias Waegele, Gai Lab, Department of Chemistry
Folding rates of protein secondary and supersecondary structures in crowded environments

4:50 p.m. - 5:05 p.m.
Dmitriy Vorobyev, Hochstrasser Lab, Department of Chemistry
Ultrafast dynamics of small ions

5:05 p.m. - 4:20 p.m.
Tim Sechler, Lester Lab, Department of Chemistry
The role of conical intersections in the quenching of excited electronic states

5:20 p.m. - 6:00 p.m.
Mostafa A. El-Sayed, Georgia Institute of Technology
Gold nanoparticles, properties and some applications in nano-biology and nano-medicine

6:00 p.m. - 6:45 p.m.
Reception in Nobel Hall, Chemistry Building (basement)

ORGANIZING COMMITTEE:
Smita Mukherjee, Graduate Student, Chemistry
Julie Glasscock Rogers, Graduate Student, BMB
Amanda Remorino, Graduate Student, Chemistry
Matt Tucker, Post-doctoral fellow, Chemistry

FACULTY ADVISORS:
Feng Gai, Professor, Departments of Chemistry and BMB
Robin Hochstrasser, Department of Chemistry and Director of the Regional Laser and Biomedical Technology Laboratories

SPONSORS:
Graduate and Professional Student Assembly (GAPSA)
Biomedical Graduate Student Association (BGSA)
The Regional Laser and Biomedical Technology Laboratories (RLBL)
The Department of Chemistry
The Department of Biochemistry & Biophysics

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OXIDATION AND REDUCTION

Tuesday, November 18, 2008
1:15 p.m. - 6:00 p.m.
Grossman Auditorium, The Wistar Institute

1:15 p.m. - 2:00 p.m.
John Caradonna, Boston University
Using synthetic models to re-evaluate the mechanisms of binuclear non-heme iron monooxygenases: do diamonds last forever?

2:00 p.m. - 2:20 p.m.
Jong-Heum Park, Penning Lab, Department of Pharmacology
Benzo[a]pyrene-7,8-dihydrodiol produces reactive oxygen species via the Aldo-Keto Reductase (AKR) pathway in A549 cells: Involvement of B[a]P-mediated redox cycling and alteration in redox status

2:20 p.m. - 2:40 p.m.
Luigi Di Costanzo, Christianson and Penning Labs, Department of Chemistry
Structure and catalytic mechanism of human steroid 5x-reductase (AKR1D1)

2:40 p.m. - 3:25 p.m.
Anne Jones, Arizona State University
Exploring and exploiting redox enzymes

3:45 p.m. - 4:00 p.m.                     
Bruce Lichtenstein, Dutton Lab, Department of Biochemistry and Biophysics
Addressing biological quinone control in de novo proteins

4:00 p.m. - 4:20 p.m.
Ivan Korendovych, DeGrado Lab, Department of Biochemistry and Biophysics
Computational design and experimental characterization of an electron transfer membrane protein

4:20 p.m. - 5:05 p.m. 
Gary Brudvig, Yale University
Water oxidation chemistry of photosystem II and artificial systems

5:05 p.m. - 6:00 p.m.
Reception, Wistar Atrium

SPONSORS:

gapsa logo

Graduate and Professional Student Assembly (GAPSA)
Biomedical Graduate Student Association (BGSA)
The Department of Chemistry
The Department of Biochemistry & Biophysics

SECOND ANNUAL CHEMISTRY-BIOLOGY INTERFACE

July 25, 2008
Scientific Picnic at Swarthmore College
9:20 a.m. – 10:00 a.m.

10:00 a.m. – 12:00 p.m.
Morning Speakers, Science Center 101

Peng Xie, Department of Chemistry/Wistar Institute
Structure-based design of a potent and specific organoruthenium PI3K inhibitor

Christopher Butts, Department of Chemistry
Fluorescence screening assay for apoferritin binders: A tool for gabaergic anesthetic discovery?

Julie Aaron, Department of Chemistry
Structure of a 129Xe-cryptophane biosensor complexed with human carbonic anhydrase II

Julie Glasscock, BMB
Using an amino-acid FRET pair to probe protein unfolding                                   

12:00 p.m. – 1:00 p.m.
Picnic Lunch

Upper Tarble, Clothier Hall
1:00 p.m. –  2:00 p.m.

Poster Session
Upper Tarble, Clothier Hall

Kim Malecka, Marmorstein Lab, Department of Chemistry/Wistar
Crystal structure of a p53 core tetramer bound to DNA

Julia Richards & Julie Griepenburg, Dmochowski Lab, Department of Chemistry
Photoactivatible oligonucleotides for controlling gene expression

Yong Tang, Marmorstein Lab, Department of Chemistry/Wistar
Structure/function studies on the H3K56-acetylating HAT Complex Rtt109-Vps75

Joe Swift & Jasmina C. Cheung-Lau, Dmochowski Lab, Department of Chemistry
Functionalization of colloidal gold using self-assembled ferritin-like systems

Seth Hayik, University of Florida and Fox Chase Cancer Center
Calculating binding affinities of zinc proteins using QM/MM methods

Smita Mukherjee, Gai Lab, Department of Chemistry
Folding kinetics of naturally occurring helical peptides

Lin Guo, Gai Lab, Department of Chemistry
Probing the role of hydration in the unfolding transitions of carbonmonoxy myoglobin and apomyoglobin

Jose Manuel Perez Aguilar, Saven Lab, Department of Chemistry                                           
Computational design of single-chain four-helix bundle proteins that bind non-biological cofactors

Christopher MacDermaid, Saven Lab, Department of Chemistry
Bundle builder: An efficient method for generating large ensembles of helical bundle structures for directed protein design

Aru Hill & Gary Seward, Dmochowski Lab, Department of Chemistry
Towards the development of Xenon-129 magnetic resonance biosensors

Carol Schultz, Penning Lab, BMB
Human AKRs display quinone reductase activity with PAH o-quinones

Michael Harbut, Greenbaum Lab, Department of Pharmacology
Development of bestatin-based activity-based probes

2:00 p.m. –  4:00 p.m. 
Afternoon Speakers, Science Center 101

Andre Isaacs, Department of Chemistry
Synthesis of novel steroidal analogs of cyclopamine

Yao Zhang, Department of Chemistry
Molecular design of TM helical bundle as a tool for probing the feature that drives folding in membrane

Claude Warzecha, Cell and Molecular Biology
Epithelial Splicing Regulatory Proteins 1 & 2 are novel cell type-specific splicing regulatory proteins identified through a genome-scale functional screen in mammalian cells

Venkata Krishnan, Department of Chemistry
Functional biomolecular materials incorporating non-biological cofactors into amphiphilic 4-helix bundle peptides

4:00 p.m. –  5:00 p.m.
Reception, Outdoor games, Parish Lawn

5:00 p.m. –  6:00 p.m.
Buffet Dinner, Upper Tarble, Clothier Hall

ORGANIZING COMMITTEE:
Julie Aaron, Department of Chemistry
Diana Cabral, Department of Chemistry
Sarah Chobot, BMB
Daniela Fera, Department of Chemistry
Andre Isaacs, Department of Chemistry

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MEMBRANE STRUCTURE, ASSEMBLY, AND TRAFFIC

Tuesday, May 6, 2008
Lynch Auditorium, Chemistry Building
1:00 – 6:00 p.m.

1:00 p.m. – 1:45 p.m.
Ken Jacobson, University of North Carolina, Chapel Hill
Post-raft era nano- and microdomains

1:45 p.m. – 2:05 p.m.
Aiwei Tian, Baumgart group, Department of Chemistry
Curvature and composition coupling in lipid bilayer membrane tubes

2:05 p.m. – 2:25 p.m.
Julie Glasscock, Gai group, Department of Chemistry
Single-molecule study of M2 proton channel conformational dynamics

2:25 p.m. – 3:10 p.m.
Wonhwa Cho, University of Illinois, Chicago
Spatiotemporal regulation of cellular processes by lipids and lipid-binding proteins: Proteomics and single molecule studies

3:30 p.m. – 4:15 p.m.
Frank Brown, University of California, Santa Barbara
Elastic and coarse-grained models for biomembranes

4:15 p.m. – 4:35 p.m.
Bryan Berger, DeGrado group, Department of Biochemistry and Molecular Biophysics
Transmembrane domain interactions in regulation of beta 1 integrins

4:35 p.m. – 5:20 p.m.
Randy Schekman, University of California, Berkeley
Developmental lesions associated with protein sorting defects in the secretory pathway

5:20 p.m. – 6:00 p.m.
Reception, Nobel Hall, Chemistry Building

CHAIR:
Julie Aaron

FACULTY ADVISORS:
Feng Gai, Department of Chemistry
Tobias Baumgart, Department of Chemistry
Bill DeGrado, Department of Biochemistry & Biophysics

SPONSORS:

gapsa logobgsa logo
Graduate and Professional Student Assembly (GAPSA)
Biomedical Graduate Student Association (BGSA)
The Department of Biochemistry & Biophysics
The Department of Chemistry

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CHEMICAL GENOMICS

Thursday, December 13, 2007
Grossman Auditorium, The Wistar Institute
12:45 P.M. - 6:00 P.M.

12:45 p.m. - 1:30 p.m.
Scott Diamond, University of Pennsylvania
The Penn Center for Molecular Discovery: lessons from the first million wells

1:30 p.m. - 1:50 p.m.
Peng Xie, Marmorstein Lab, The Wistar Institute
In search of potent and specific BRAF inhibitors through in vitro high-throughput screening

1:50 p.m. - 2:10 p.m.
Nancy Carillo, Bode Lab, Department of Chemistry
Aqueous synthesis of x3-oligopeptides

2:10 p.m.- 2:55 p.m.
Jon Ellman, University of California, Berkeley
Substrate activity screening – a powerful new method for inhibitor discovery

3:10 p.m. - 3:55 p.m.
Jun Liu, Johns Hopkins University
Forward and reverse chemical genetic approaches toward angiogenesis

3:55 p.m. - 4:15 p.m. 
Ryan Coleman, Sharp Lab, Department of Genomics and Computational Biology
Two computational tools to analyze small molecule binding sites in proteins: Travel Depth and Geometric Patch Generation           

4:15 p.m. - 4:35 p.m.
XinJing Tang, Dmochowski Lab, Department of Chemistry
Controlling gene silencing with caged oligonucleotides in K562 and zebrafish

4:35 p.m. – 5:20 p.m.
Suzanne Walker, Harvard University
Glycosyltransferase inhibitors

5:20 p.m. - 6:00 p.m.
Reception in the Wistar Atrium

CHAIR:
Julia Richards

FACULTY ADVISORS:
Amos Smith, Chemistry
Ronen Marmorstein, Wistar/Chemistry/BMB
Doron Greenbaum, Pharmacology
Donna Huryn, Penn Center for Molecular Discovery

SPONSORS:

gapsa
Graduate and Professional Student Assembly (GAPSA)
The Department of Chemistry
The Department of Biochemistry & Biophysics

 

CHEMISTRY/BMB/WISTAR TRAINEE RETREAT

Friday, July 13, 2007
Swarthmore College

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INFLUENZA SYMPOSIUM

February 22, 2007, 12:50 p.m. - 6:00 p.m.
Location: Grossman Auditorium, The Wistar Institute

12:50 p.m. – 1:40 p.m.
Michael Silverman and Farhad Abtahian, University of Pennsylvania MD/PhD Program
Dissecting a deadly virus: lessons from Avian Influenza and the Pandemic of 1918

1:40 p.m. - 1:55 p.m.
Sarah Abdulla, Ertl Group, The Wistar Institute
A flu vaccine for the elderly

1:55 p.m. - 2:10 p.m.
Vilma Decman (Post-Doctoral Fellow) Wherry Group, The Wistar Institute
Influenza infection in aged and young mice

2:10 p.m. - 2:55 p.m.
Larry Pinto, Northwestern University
Influenza proton channels: their role in infection and mechanism for transport

2:55 p.m. - 3:10 p.m.
Amanda Stouffer (Post-Doctoral Fellow) DeGrado Group, Department of Biochemistry and Biophysics
Amantadine binding to the M2 proton channel and the new wild type

3:25 p.m. - 3:40 p.m.
Matteo Dal Peraro (Post-Doctoral Fellow) Klein Group, Department of Chemistry
Blocking and resistance mechanisms of M2 channel explored by molecular dynamics simulations

3:40 p.m. - 4:25 p.m.
Ted Jardetzky, Northwestern University
Structural insights into the membrane fusion mechanism of parainfluenza viruses

4:25 p.m. - 4:40 p.m.
Darya Zharikova (Post-Doctoral Fellow) Gerhard Group, The Wistar Institute
Potential of Influenza A virus to escape protection mediated by antibodies to the matrix protein 2

4:40 p.m. - 5:25 p.m.
Judith White, University of Virginia
The fusion proteins of Influenza and Ebola Viruses

5:25 p.m. - 6:00 p.m.
Reception

ORGANIZERS:
Alexei Polishchuk, Chair, BMB graduate studen

FACULTY ADVISORS:
Bill DeGrado, Faculty Advisor, Biochemistry/Biophysics Faculty
Jeff Saven, Faculty Advisor, Chemistry Faculty
Robert Doms,Faculty Advisor, Microbiology Faculty

ORGANIZING DEPARTMENTS:
Department of Biochemistry and Biophysics
Department of Chemistry
Department of Microbiology
The Wistar Institute

SPONSORS:
Graduate Student Associations Council (GSAC)
Influmedix
The departments listed above

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THE NATURE AND ROLE OF WATER AS A BIOLOGICAL SOLVENT SYMPOSIUM

Thursday, October 12, 2006
Location: Carolyn Hoff Lynch Room, First Floor, Cret Wing, Chemistry Complex
1 p.m. - 6 p.m.

1:00 p.m. - 1:45 p.m.
Dongping Zhong, Ohio State University
Surface hydration dynamics and protein-water interactions

1:45 p.m. - 2:00 p.m.
Jennifer Dashnau (Graduate Student)
Vanderkooi Group, BMB Graduate Group
Small molecule effects on H-bonding in water: polyalcohol case studies

2:00 p.m. - 2:15 p.m.
Yung Sam Kim (Post-Doctoral Fellow)
Hochstrasser Group, Department of Chemistry
Ultrafast dynamics of water-peptide interactions

2:15 p.m. - 2:30 p.m.
Walter Witschey (Graduate Student)
Reddy Group, Radiology, BMB Graduate Group
Structural and functional characteristics of biological water: Lessons from MRI

2:30 p.m. - 3:15 p.m.
Theresa Head-Gordon, University of California, Berkeley
Theoretical and experimental studies of bulk water and aqueous solutions

3:30 p.m. - 4:15 p.m.
Steve Granick, University of Illinois at Urbana-Champaign
Studies of interfacial water

4:15 p.m. - 4:30 p.m.
Marco De Vivo (Post-Doctoral Fellow)
Klein Group, Department of Chemistry
The role of water in phosphatase activity in soluble epoxide hydrolase

4:30 p.m. - 4:45 p.m.
Maxim Pometun (Post-Doctoral Fellow)
Wand Group, Department of Biochemistry and Biophysics
Cold-induced unfolding of encapsulated proteins

4:45 p.m. - 5:30 p.m.
Ken Dill, University of California, San Francisco
Modeling water, the hydrophobic effect, and ion solvation

5:30 p.m. - 6:00 p.m.
Reception

CHAIR:
Nathaniel Nucci, Chair, BMB graduate student

FACULTY ADVISORS:
Jeff Saven, Department of Chemistry
Jane Vanderkooi, Department of Biochemistry and Biophysics

SPONSORS:

gapsa logo
The Graduate and Professional Student Assembly (GAPSA)

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AMYLOID: STRUCTURE & BIOLOGY

Thursday, April 27, 2006
Class of '62 Auditorium, Ground Floor, John Morgan Bldg.
1 p.m. - 6 p.m.

1:00 p.m. - 1:35 p.m.
Jeffery Kelly, The Scripps Research Institute
Understanding and ameliorating misfolding diseases

1:40 p.m. - 1:52 p.m.
Eric Greenbaum, Department of Pharmacology
Advisor: Walter Englander
The structure and folding of alpha synuclein amyloid: insights from hydrogen exchange and electron microscopy

1:55 p.m. - 2:07 p.m.
Pramit Chowdhury, Department of Chemistry
Advisor: Feng Gai
Computer aided design of small peptides for serpin depolymerization 

2:10 p.m. - 2:45 p.m. 
Peter Lansbury, Harvard Medical School
Therapeutic approaches to disease-modifying drugs for Parkinson's Disease

2:50 p.m. - 3:02 p.m.
Casey H. Londergan, Department of Chemistry
Advisor: R.M. Hochstrasser
The onset of peptide aggregation monitored by two-dimensional infrared spectroscopy

3:25 p.m. - 4:00 p.m.
Ron Wetzel, University of Tennessee
Energetics of amyloid assembly

4:05 p.m. - 4:17 p.m.
Sheldon Park, Department of Chemistry
Advisor: Jeff Saven
Simulation of pH-dependent edge strand rearrangement in human b-2 microglobulin

4:20 p.m. - 4:32 p.m.
Jun Han, Department of Chemistry
Advisor: Hai-Lung Dai
Detection of b-Amyloid peptide oligomers in Alzheimer's Disease through single-pair FRET microscopy

4:35 p.m. - 5:10 p.m.
Robert Tycko, National Institutes of Health
Molecular structures of fibrils associated with amyloid diseases and yeast prions

5:15 p.m. - 6:00 p.m.
Reception

CHAIR:
Kesav Kumar, Chair, Chemistry Graduate Student

FACULTY ADVISORS:
Walter Englander, Department of Biochemistry and Biophysics
Robin Hochstrasser, Department of Chemistry
Virginia Lee, Center for Neurodegenerative Research

SPONSORS:
OLIS, Inc.
The Provost’s Interdisciplinary Seminar Fund
Graduate Student Associations Council (GSAC)

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COMPUTATIONAL ANALYSIS OF PROTEIN STRUCTURE AND FUNCTION

Thursday, March 9, 2006
Austrian Auditorium, Clinical Research Building
1 p.m. - 6 p.m.

1:00 - 1:35 p.m.
Eugene Koonin, NCBI-NIH
Unifying measures of protein function and evolution

1:40 - 1:55 p.m.
Feng Chen, Advisor: Jeff Saven/David Roos, Department of Chemistry
A quantitative comparative analysis of ortholog identification methods

2:00 - 2:15 p.m.
Tammer Farid, Advisor: Les Dutton/Chris Moser, Department of Biochemistry and Biophysics
Electron tunneling simulations in the mitochondrial respiratory chain

2:20 - 2:55 p.m.
Roland Dunbrack, Fox Chase Cancer Center
Predicting the structure of proteins and protein complexes

3:20 - 3:55 p.m.
Olivier Lichtarge, Baylor University
Annotation and re-design of proteins"

4:00 - 4:15 p.m.
Ravindra Venkatramani, Advisor: Ravi Radhakrishnan, Department of Bioengineering
Studying the DNA replication cycle in a high fidelity polymerase by molecular dynamics simulations

4:20 - 4:35 p.m.
John Skinner, Advisor: Kim Sharp, Department of Biochemistry and Biophysicss
Pump probe MD: locating allosteric pathways

4:40 - 5:15 p.m.
Mark Gerstein, Yale University, Understanding protein function on a genome-scale using networks

5:20 - 6:00 p.m.
Reception

CHAIR:
Thomas Petty, Chair
Genomics and Computational Biology (GCB) Graduate Student

FACULTY ADVISORS:
Jeff Saven, Chemistry Faculty
Kim Sharp, Biochemistry/Biophysics Faculty
Lyle Unger, Computer and Informations Sciences Faculty
David Roos, Biology Faculty
Junhyong Kim, Biology Faculty
Sridhar Hannenhalli, Genetics Faculty

GPBA logo

This event was sponsored by the
Greater Philadelphia Bioinformatics Alliance and The Provost’s Interdisciplinary Seminar Fund

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METALLOMOLECULES IN CHEMICAL TECHNOLOGY, DYNAMICS AND DISEASE

November 17, 2005
Auditorium, Biomedical Research Building II/III
1 p.m. - 6 p.m.

1:00 - 1:40 p.m.
David Bocian, University of California Riverside
Hybrid semiconductor/molecular memories

1:40 - 2:00 p.m.
H. Chris Fry, Department of Chemistry
De novo designed proteins binding non-biological cofactors

2:00 - 2:20 p.m.
Hongling Zou (Graduate Student), Department of Chemistry
Molecular dynamics study of heme cofactor binding to amphiphilic 4-helix bundle peptides at soft interfaces

2:20 - 3:00 p.m.
Joan Valentine, University of California, Los Angeles
Copper-zinc superoxide dismutase and amyotrophic lateral sclerosis (ALS)

3:20 - 4:00 p.m.
John Shelnutt, Sandia National Laboratories & University of New Mexico
Ionic self-assembly of porphyrin nanostructures for artificial photosynthesis

4:00 - 4:20 p.m.
Olga Finikova (Postdoctoral Fellow), Department of Biochemistry and Biophysics
Symmetrically x-extended porphyrins: versatile near-infrared chromophores for biomedical applications

4:20 - 4:40 p.m.
Gretchen Bender (Graduate Student), Department of Biochemistry and Biophysics
Correlating structure and function of de novo designed metalloporphyrin proteins

4:40 - 5:20 p.m.
Joel Friedman, Albert Einstein College of Medicine
Probing the functional role of equilibrium & non-equilibrium protein dynamics in hemeproteins using sol-gel encapsulation protocols

5:25 - 6:00 p.m.
Reception

CHAIR:
David Finkelstein, BMB Graduate Student

FACULTY ADVISORS:
Michael Therien, Department of Chemistry
Jane Vanderkooi, Department of Biochemistry and Biophysics

SPONSORS:
Bruker Biospin
The Provost’s Interdisciplinary Seminar Fund
Graduate Student Associations Council (GSAC)

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Trainee Symposium: MEMBRANES AND MOLECULAR RECOGNITION

October 25, 2005
Grossman Auditorium, Wistar Institute, 36 & Spruce Streets
1 p.m. - 6 p.m.

Novel Membrane Studies:

1:00 - 1:30 p.m.
Ian Murray (Postdoctoral Fellow)
Advisor: Paul Axelsen, Pharmacology
Membrane-mediated amyloidogenesis

1:30 - 2:00 p.m.
Jia Zeng (Graduate Student)
Advisor: Hai-Lung Dai, Chemistry
Real-time, nonlinear optical probe of molecular transport across living E.coli cell membranes

2:00 - 2:30 p.m.
Matthew J. Tucker (Graduate Student)
Advisor: Feng Gai, Chemistry
A new FRET technique to probe the folding dynamics of membrane binding peptides

2:30 - 3:00 p.m.
Qing Luo (Postdoctoral Fellow)
Advisor: Britton Chance, BMB
Non-invasive optical probing of prefrontal cortex function in students

Mechanisms of Molecular Recognition

3:15 - 3:45 p.m.
Joe Swift (Graduate Student)
Advisor: Ivan Dmochowski, Chemistry
Application and optimization of ferritin: nature’s template for inorganic nanoparticle synthesis

3:45 - 4:15 p.m.
Troy Messick (Postdoctoral Fellow)
Advisor: Ronen Marmorstein, Wistar
Structure of the OTU deubiquitinating enzyme bound to ubiquitin

4:15 - 4:45 p.m.
Sung-wook Choi (Graduate Student)
Advisors: Bill DeGrado and Jeffrey Winkler, Chemistry
"Bioactive arylamide foldamer"

4:45 - 5:15 p.m.
Sheldon Park (Postdoctoral Fellow)
Advisor: J.G. Saven, Chemistry
Biophysical studies and computational design of a DNA binding protein

5:15 - 6:00  Reception

CHAIR:
Daniel Dowling, Chair, Department of Chemistry

FACULTY ADVISORS:
Dewey McCafferty,Department of Biochemistry and Biophysics
Bill DeGrado, Department of Biochemistry and Biophysics
Feng Gai, Department of Chemistry

SPONSORS:
Optical Apparatus Company
The Provost’s Interdisciplinary Seminar Fund
Graduate Student Associations Council (GSAC)

SINGLE MOLECULE STUDIES

Thursday, April 21, 2005
Carolyn Hoff Lynch Room, First Floor, Cret Wing, Chemistry Complex
1:00 p.m. – 6:00 p.m.

1:00 p.m. - 1:40 p.m.
Enrico Gratton, University of Illinois at Urbana-Champaign
Tracking molecules in cells using a two-photon microscope

1:40 p.m. - 1:55 p.m.
Jia Tang (Graduate Student)
Advisor: Feng Gai, Department of Chemistry
Single molecule study of protein polymerization

2:00 p.m. - 2:15 p.m.
Jennifer Ross (Postdoctoral Fellow)
Advisor: Yale Goldman, Dept. of Biochemistry and Biophysics
Direct observation of single dynein-dynactin complexes walking along microtubules in vitro

2:20 p.m. - 2:55 p.m.
Julio Fernandez, Columbia University
Force-quench studies of protein folding

3:20 p.m. - 3:55 p.m.
Sunney Xie, Harvard University
From in vitro to in vivo single molecule studies

4:00 p.m. - 4:15 p.m.
Alexey Sharonov (Postdoctoral Fellow)
Advisor: Robin Hochstrasser,Department of Chemistry
Real time imaging of protein interactions with living cells

4:20 p.m. - 4:35 p.m.
Nishant Bhasin (Graduate Student)
Advisor: Dennis Discher, Dept. of Chemical Engineering
Chemistry on a single protein, VCAM-1, during forced unfolding

4:40 p.m. - 5:15 p.m. 
Justin Molloy,National Institute for Medical Research, London
Single molecule mechanical and optical studies: in vitro and inside live mammalian cells

5:20 - 6:00 p.m.
Reception

CHAIR:
Joe Laakso

FACULTY ADVISORS:
Yale Goldman, Department of Physiology
Feng Gai, Department of Chemistry

SPONSORS:
Optical Apparatus Company
The Provost’s Interdisciplinary Seminar Fund
Graduate Student Associations Council (GSAC)

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PROTEIN DESIGN

Thursday, March 10, 2005
Austrian Auditorium, Clinical Research Building
1:00 p.m. – 6:00 p.m.

1:00 p.m. - 1:40 p.m.
Lynne Regan, Yale University
Structure, function, and folding of designed repeat proteins

1:40 p.m. - 1:55 p.m.
Jing He (Graduate Student) Advisor: Jeff Saven, Department of Chemistry
Computational design of anesthetic binding ion channel model

2:00 p.m. - 2:15 p.m.
Michelle DeRitter (Graduate Student) Advisor: Feng Gai, Department of Chemistry
Fast folding of Trp-cage mini-proteins

2:20 p.m. - 3:00 p.m.
Themis Lazaridis, City College of New York
Energy functions for membrane proteins

3:20 p.m. - 4:00 p.m.
Karyn O’Neil, Centocor, Inc
Epitope directed panning for selection of an anti-tissue factor surrogate antibody

4:00 p.m. - 4:15 p.m.
Vikas Nanda (Postdoctoral Fellow) Advisor: Bill DeGrado, Dept. of Biochemistry & Biophysics
Doubling the design alphabet - varying backbone and sidechain stereochemistry

4:20 p.m. - 4:35 p.m.
Ting Xu (Postdoctoral Fellow) Advisor: Kent Blasie, Department of Chemistry
Design, synthesis & characterization of novel electronic biomolecular materials

4:40 p.m. - 5:20 p.m.
Michael Hecht, Princeton University
Protein design unplugged: novel proteins from combinatorial libraries

5:20 p.m. - 6:00 p.m.
Reception

CHAIR:
Scott Shandler

FACULTY ADVISOR:
Bill DeGrado, Department of Biochemistry and Biophysics
Jeff Saven, Department of Chemistry

SPONSORS:
SynPep
The Provost’s Interdisciplinary Seminar Fund

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STRUCTURE-BASED DRUG DESIGN

Thursday, November 18, 2004
JMB Reunion Hall, John Morgan Building
1:00 p.m. – 6:00 p.m

1:00 p.m. - 1:40 p.m.
Eddy Arnold, Rutgers University
Aiming at a rapidly evolving target: drug and vaccine design against HIV/AIDS

1:40 p.m. - 1:55 p.m.
Brandi Sanders (Graduate Student) Advisor: Ronen Marmorstein, The Wistar Institute
Structure-based activation of Sir2 proteins

2:00 p.m. - 2:15 p.m.
Klara Stefflova (Graduate Student) Advisor: Gang Zheng, Department of Radiology, UPHS
Photodynamic therapy agent with built-in apoptosis sensor (PDT-BIAS)

2:20 p.m. - 3:00 p.m.  
William Jorgensen, Yale University
Protein-ligand binding and structure-based drug design

3:20 p.m. - 4:00 p.m.
William Moore Jr, Locus Pharmaceuticals
Pharmaceutical discovery: The war on drudgery

4:00 p.m. - 4:15 p.m.  
Howard Bregman (Graduate Student) Advisor: Eric Meggers, Department of Chemistry
A new avenue to highly potent protein kinase inhibitors

4:20 p.m. - 4:35 p.m.  
Seth Snyder (Postdoctoral Fellow) Advisor: Bill DeGrado, Department of Biochemistry and Biophysics
Design, synthesis, and evaluation of small-molecule antagonists targeting collagen receptors on platelets

4:40 p.m. - 5:20 p.m.  
Chris Walsh, Harvard Medical School
Glycosyltransferases dedicated to the maturation of antibiotics

5:20 - 6:00 p.m.
Reception

CHAIR:
Michael Brent

FACULTY ADVISORS:
Dewey McCafferty, Department of Biochemistry and Biophysics
Ronen Marmorstein, Department of Chemistry

SPONSORS:
Merck Research Laboratories
The Provost’s Interdisciplinary Seminar Fund

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BIOINORGANIC CHEMISTRY: METALLOENZYMES

Thursday, April 22, 2004
Carolyn Hoff Lynch Seminar Room, Cret Chemistry Building
1:00 p.m. – 6:00 p.m.

1:00 p.m. - 1:45 p.m.
Paul A. Lindahl, Texas A&M University, College Station, TX
Acetyl-coenzyme A synthase: the case for a Ni(0)-based mechanism of catalysis

1:50 p.m. - 2:05 p.m.  
Frank V. Cochran (Postdoctoral Fellow) Department of Biochemistry and Biophysics
de novo design and characterization of a four-helix bundle protein that selectively binds a non-biological cofactor

2:10 p.m. - 2:55 p.m.
Carol A. Fierke, University of Michigan, Ann Arbor, MI
Function of Zn(II) and Mg(II) in protein prenyltransferases

3:20 p.m. - 4:05 p.m.
Tom L. Poulos, University of California, Irvine, CA
Transfer in heme enzymes: intermediates, radicals, and electron transfer in heme enzymes: peroxidases as a model system"

4:10 p.m. - 4:25 p.m.
German Gomez (Graduate Student) Department of Chemistry
Phosphatase activity in human epoxide hydrolase

4:30 p.m. - 5:15 p.m.
John D. Lipscomb, University of Minnesota, MN
Keys to the castle gate: the basis for specificity in methanse oxidation by methane monooxygenase

5:20 - 6:00 p.m.
Reception

CHAIR:
Herschel Wade

FACULTY ADVISORS:
Joe Jarrett, Department of Biochemistry and Biophysics
Ivan Dmochowski, Department of Chemistry

SPONSORS:
Polymedix
Provost’s Interdisciplinary Seminar Fund

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PROTEIN FOLDING

Thursday, February 26, 2004
Austrian Auditorium, Clinical Research Building
1:00 p.m. – 6:00 p.m.

1:00 p.m. - 1:40 p.m.  
Donald M. Engelman, Yale University
Membrane protein folding and evolution

1:50 p.m. - 2:05 p.m.  
Ronald Peterson (Postdoctoral Fellow) Department of Biochemistry and Biophysics
Induced folding of metastable proteins

2:10 p.m. - 2:25 p.m.  
Mallela M. G. Krishna (Postdoctoral Fellow) Department of Biochemistry and Biophysics
Residue resolved structure, stability, folding and unfolding rates of a kinetic protein folding intermediate

2:30 p.m. - 3:10 p.m.  
George Rose, Johns Hopkins University
Proteins: the unfolding story

3:40 p.m.- 3:55 p.m.
Ting Wang (Postdoctoral Fellow) Department of Chemistry
Ultrafast folding of a three-helix bundle:1prb

4:00 p.m. - 4:15 p.m.  
Chong Fang (Graduate Student) Department of Chemistry
Dynamics and interactions within alpha-helices by 2D IR

4:20 p.m. - 5:00 p.m.  
Martin Gruebele, University of Illinois at Urbana-Champaign
Folding kinetics and dynamics of proteins on rough energy landscapes

5:15 - 6:00 p.m.
Reception

CHAIR:
Sabrina Bédard

FACULTY ADVISORS:
Walter Englander, Department of Biochemistry and Biophysics
Feng Gai, Department of Chemistry

SPONSORS:
Proterion
Graduate Student Associations Council (GSAC)

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INHIBITORS OF PROTEIN-PROTEIN INTERACTIONS

Thursday, November 20, 2003
Carolyn Hoff Lynch Room, Chemistry Building, Cret Wing
1:00 p.m. - 5:15 p.m.

1:00 p.m. - 1:40 p.m.
Phil Cole, Johns Hopkins University
Bisubstrate analogs for probing structure and function of protein kinases and HATs

1:50 p.m. - 2:05 p.m.
Jason Chruma (Postdoctoral Fellow) Department of Chemistry
Inhibition of the protein-protein interaction that occurs when the AIDS virus attacts T-cells

2:10 p.m. - 2:25 p.m.
Jaskiran Kaur (Postdoctoral Fellow) Department of Chemistry
Design and testing of peptides as inhibitors of ribonucleotide reductase

2:30 p.m. - 3:10 p.m.  
Zhiping Weng, Boston Univesity
An integrated approach to protein-protein docking

3:40 p.m. - 3:55 p.m.  
Kendra Frederick (Graduate Student) Department of Biochemistry and Biophysics
Comparison of the dynamics of complex formation between calmodulin and different calmodulin binding domain peptides

4:00 p.m. - 4:15 p.m.  
Lumelle Schneeweis (Graduate Student) Department of Biochemistry and Biophysics
Elucidation of the stoichiometry of binding of RANKL to its receptor, RANK, and to its decoy receptor, osteoprotegerin

4:20 p.m. - 5:00 p.m.  
Craig Crews, Yale University
Chemical genetics: probing protein function with small molecules

CHAIR:
Lumelle Schneeweis

FACULTY ADVISORS:
Jeff Saven, Department of Chemistry
Marcos Milla, Department of Biochemistry and Biophysics

SPONSORS:
Biacore
Provost’s Interdisciplinary Seminar Fund