Daily Schedule

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Wednesday, September 10


Welcome & Session I: Allosteric Transition in Proteins and How They        
Relate to Function

4:00 - 4:20 PM

Welcome/Opening Remarks:
Ivet Bahar, University of Pittsburgh School of Medicine, USA
Ozlem Keskin, Koc University, Turkey
4:20 - 4:50 PM         Amnon Horovitz, Weizmann Institute of Science, Israel
Distinguishing Between Allosteric Mechanisms Using Structural Mass-
Spectrometry is Demonstrated for the Chaperonin GroEL

4:50 - 5:20 PMRuth Nussinov, Tel-Aviv University, Israel, and NIH, USA
Ras: a Structural Biologist View and Questions
5:20 - 5:50 PMRebecca Wade, Heidelberg University, Germany
Organism-adapted Specificity of Allosteric Regulation of Central Metabolic
Enzymes in Lactic Acid Bacteria

5:50 - 6:10 PM Tom McLeish, Durham University, United Kingdom *
Predicting Global Low Frequency Protein Motions in Allostery Without
Conformational Change: Application to CRP/FNR Family Transcription Factors
6:10 - 6:30 PM Vanessa Ortiz, Columbia University, USA *
Quantifying Signal Propagation and Conformational Changes in Allosteric Proteins
6:30 - 7:00 PM        Banu Ozkan, University of Arizona, USA
Mechanism of Protein Evolution: Conformationaly Dynamics and Allostery
7:15 - 9:30 PM  Welcome Reception

  *Short talks selected from among submitted abstracts

Thursday, September 11

Session II:  Protein Interactions and Complex Systems Modeling I:
Evolution and Function

8:45 - 9:15 AMJanet Thornton, European Bioinformatics Institute (EMBL-EBI), United Kingdom
The Evolution of Enzyme Mechanisms and Functional Diversity
9:15 - 9:45 AMAnne-Claude Gavin, EMBL Heidelberg, Germany
Lipid-Protein Networks
9:45 - 10:00 AM Savas Tay, ETH Zurich, Switzerland *
Molecular Noise Facilitates NF-κB Entrainment under Complex Dynamic Inputs
10:00 - 10:30 AM Burkhard Rost, Technical University of Munich, Germany
Evolution Teaches Predicting Protein Interactions from Sequence
10:30 - 10:45 AM Andrew Pohorille, NASA Ames Research Center, USA *
Proteins with Novel Function, Structure and Dynamics
10:45 - 11:00 AM                                Srinath Krishnamurthy, National University of Singapore, Singapore *
How Enzymes Access Caged Substrates? Phosphodiesterase-Protein Kinase A Interactions Mediate Hydrolysis of PKA Receptor Bound Cyclic AMP
11:00 - 11:30 AM Coffee Break

Session III: Protein Interactions and Complex Systems Modeling II:
Cell Regulatory and Signaling Mechanisms

11:30 AM - 12:00 PM Leslie Loew, University of Connecticut Health Center, USA
Clusters and Comets: Regulation of Actin Assembly
12:00 - 12:30 PM Anna Panchenko, National Center for Biotechnology Information, NIH, USA
Regulation of Protein-Protein Binding and Pathway Crosstalk
12:30 - 1:00 PM Zaida Luthey-Schulten, University of Illinois at Urbana-Champaign, USA
Stochastic Simulations of Cellular Processes: From Single Cells to Colonies
1:00 - 1:15 PM       Yaman Arkun, Koc University, Turkey *
Modeling and Dynamic Analysis of Feedback Loops of Insulin and Angiotensin
II Signalling Systems
1:15 - 3:00 PM
Lunch & Poster Session I
3:00 PMFree Afternoon

 *Short talks selected from among submitted abstracts

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Friday, September 12


Session IV: Structure and Dynamics I:
From Molecular Fluctuations to Supramolecular Machinery

9:00 - 9:30 AM Ada Yonath, Weizmann Institute of Science, Israel
What Was First, the Genetic Code or Its Products?
9:30 - 10:00 AM Klaus Schulten, Beckman Institute, University of Illinois at Urbana-Champaign, USA
The Photosynthetic Membrane of Purple Bacteria as a Clockwork of Atomic and Electronic Level Processes
10:00 - 10:30 AM Canan Atilgan, Sabanci University, Turkey
How Much Can Local Dynamical Features of Proteins Can Inform on Conformational Possibilities?
10:30 - 10:45 AM Short Talk *
10:45 - 11:00 AM Günther Peters, Technical University of Denmark, Denmark *
Self-assembly of a Glucagon-like Peptide 1 Analogue: Bridging Experiment and Simulations
11:00 - 11:30 PM Coffee Break

Session V: Membrane Proteins II:
Interactions and (Neuro) Signal Transduction

11:30 AM - 12:00 PM Lukas Tamm, University of Virginia, USA
Fold to Fuse: The F2F Code of SNAREs on Membranes
12:00 - 12:30 PM Ingo Greger, MRC Laboratory of Molecular Biology, United Kingdom
Dynamics and Function of the AMPA Receptor N-terminal Domain
12:30 - 1:00 PM Christine Ziegler, The Max Planck Institute for Biophysics, Germany
Two Is Better Than One: Molecular Mechanism of Sodium Coupling in the Betaine Transporter BetP
1:00 - 1:15 PM Liviu Movileanu, Syracuse University, USA *
Engineered Protein Nanopores for Challenging Tasks in Molecular Diagnosis
1:15 - 3:00 PMLunch & Poster Session II
3:00 PMFree Afternooon

 *Short talks selected from among submitted abstracts

Saturday, September 13

Session VI: Drug Discovery I:
From Molecular Modeling to Systems Pharmacology

8:45 - 9:15 AM John Overington, European Bioinformatics Institute (EMBL-EBI), United Kingdom
Data Mining Large-Scale Bioactivity Datasets to Find Patterns in Ligand Recognition
9:15 - 9:45 AM Celia Schiffer, University of Massachusetts Medical School, USA
Combating Drug Resistance: Lessons from the Viral Proteases of HIV and HCV
9:45 - 10:00 AM Serdar Durdagi, Bahcesehir University, Turkey *
In Silico Studies on K-RAS-PDEδ Interaction Inhibition to Design Novel Anti-Cancer Drugs

10:00 - 10:30 AM William Eaton, NIDDK, NIH, USA
Sickle Cell Hemoglobin: Allostery, Aggregation Kinetics, and Search for a Drug
10:30 - 10:45 AM Serdar Kuyucak, University of Sydney, Australia *
Computational Design of Drugs for Autoimmune Diseases from Peptide Toxins
10:45 - 11:00 AM Judith Klein-Seetharaman, University of Warwick, United Kingdom *
Molecular Speciation, Dynamics and Interactions of Lipid Droplets with Proteins
11:00 - 11:30 AM Coffee Break

Session VII: Protein-Protein Interactions 

11:30 AM - 12:00 PM  Zhiping Weng, University of Massachusetts Medical School, USA
Protein-Protein Docking and Design
12:00 - 12:30 PM       Attila Gursoy, Koc University, Turkey
Structural Networks of Signaling Pathways on Proteome Scale: Challenges and Opportunities
12:30 - 1:00 PM Nikolay Dokholyan, University of North Carolina at Chapel Hill, USA
Controlling Allosteric Networks in Proteins
1:00 - 1:15 PM Lee-Wei Yang, National Tsing Hua University, Taiwan*
Intramolecular Communication Based on Time-dependent Linear Response Theories
1:15 - 3:00 PM Lunch & Poster Session III

Session VIII: Protein Structure & Dynamics II:
From Molecular Fluctuations to Supramolecular Machinery                     "In Honor of Professor Erman - Celebrating 40 Years of Science" 

3:15 - 3:30 PM Introduction (by Ivet Bahar)
3:30 - 4:00 PM  Ken A. Dill, SUNY at Stony Brook, USA
Integrative Modeling of Proteins
4:00 - 4:20 PM
Batu Erman, Sabanci University, Turkey
Protein-Protein Interactions that Inhibit the Activity of the p53 Tumor Suppressor 
4:20 - 4:40 PM Andrzej Kloczkowski, The Ohio State University, USA
From Polymer Rubberlike Elasticity to Protein Dynamics – How Simple Physical Models of Rubber Influenced Modern Biophysics.
4:40 - 5:05 PM Malcolm Walkinshaw, University of Edinburgh, United Kingdom
Allosteric Regulation of the Glycolytic Pathway in Mammals and Trypanosomes
5:05 - 5:30 PM Turkan Haliloglu, Bogazici University, Turkey
Sequence Variations and Allosteric Dynamics in Binding
5:30 - 5:55 PM Robert Jernigan, Iowa State University, USA
Extracting Dynamics Information from Multiple Molecular Structures and Computationally Generating Their Transition Pathways
5:55 - 6:20 PM Burak Erman, Koc University, Turkey
Fractal Structure of Interaction Pathways in Proteins and Prediction of Allosteric Paths
6:20 PM   Dinner

 *Short talks selected from among submitted abstracts

Sunday, September 14


Session IX: Protein Interactions, Dynamics, and Dysfunction

9:00 - 9:30 AM                                     Shoshana Wodak, The Hospital for Sick Children, and University of Toronto, Canada
Role of Histidine Protonation in the pH Induced Changes in Prion Protein Stability
9:30 - 9:45 AM Pemra Doruker, Bogazici University, Turkey
Effect of Ligand Binding on Enzyme Global Dynamics and Function
9:45 - 10:15 AM          David Perahia, CNRS, France
A New Approach for Exploring Free Energy Landscapes of Large Structural Changes: Molecular Dynamics with Excited Collective Motions (MDeNM)   
10:15 - 10:30 AM     Erik Marklund, University of Oxford, United Kingdom *
Restraining Molecular Dynamics and Modeling With Ion-Mobility Mass Spectrometry
10:30 - 10:45 AM Jocelyne Vreede, University of Amsterdam, The Netherlands *
Modeling the Binding of H-NS to AT-rich DNA
10:45 - 11:00 AMYaakov (Koby) Levy, Weizmann Institute of Science, Israel *
Protein-DNA Interactions: Fine Balance between High Affinity and Fast Kinetics
11:00 - 11:30 AMClosing Remarks
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