BIOCHEMISTRY

Activities at the Pyle Center, 702 Langdon Street, Madison, Wisconsin

Thursday, May 18, 2006

4:30pm-6:30pm - Reception and registration - Pick up conference materials, Alumni Lounge.

Session #1 - Multiple Scales for Difficult Questions - Chair, George Phillips

6:45pm - Welcome - Room 326

7:00pm - 7:45pm - Multi-Scale Modeling from Multi-Resolution Data: Unveiling Functional Motions of Macromolecular Machines [PDF]
Florence Tama - University of Arizonia

​7:45pm - 8:20pm - Towards Understanding Membrane Fusion: Course-Grained and All-Atom Models for Fusion and Bilayer:Bilayer interaction [PDF]
Tom Woolf - Johns Hopkins University

Friday, May 19, 2006

Session #2 - Structure Determination and Prediction - Chair, Dmitry Kondrashov

​8:30am - 9:05am - Minimalist Representations and the Importance of Nearest Neighbor Effects in Protein Folding Simulations [PDF]
Karl Freed - University of Chicago

9:05am - 10:15am - Refinement of Protein Structures with Database Derived Distance Constraints and Mean-Force Potentials [PDF]
Zhijun Wu - Iowa State University

9:40am - 10:15am - Break

10:15am - 10:50am - Protein Structure Refinement with Normal-mode based Sampling [PDF]
Michael Feig - Michigan State

​10:50am - 11:35am - New Methods for Coarse-grained Normal Mode Analysis and Their Applications in Structural Refinement [PDF]
Jianpeng Ma - Baylor College of Medicine

11:45am - 1:00pm - Lunch

1:30pm - 3:00pm - Poster Session 1

Session #3 - Correlated Motion in Macromolecules - Chair, Ivet Bahar

​3:00pm - 3:45pm - Computationally Enhanced Dynamics Analysis of Protein NMR Data [PDF]
Rafael Bruschweiler - Florida State University

3:45pm - 4:30pm - Probing Macromolecular Motions and Couplings Using Elastic Network Models [PDF]
Bernard Brooks - NIH

4:30pm - 5:05pm - Dynamic Coupling and Allosteric Behavior in a Non-Allosteric Protein [PDF]
Andrew Lee - UNC

5:05pm - 7:00pm - Dinner & Independent Evening Activities

Session #4 - Vibrational Methods for Studying Protein Motion - Chair, George Phillips

7:00pm - 7:45pm - Terahertz Absorption Spectroscopy: A New Experimental Probe of Collective Vibrational Motions in Solvated Proteins [PDF]
Kevin Plaxco - UCSB

​7:45pm - 8:20pm - Low Frequency Dynamics in Proteins [PDF]
Robert Bryant - University of Virginia

Saturday, May 20, 2006

Session #5 - Modeling of Functional Conformational Changes - Chair, Qiang Cui

8:30am - 9:15am - Common Mechanism of Pore Opening Shared by Five Potassium Channels Elucidated by Gaussian Network Model [PDF]
Ivet Bahar - University of Pittsburg

9:15am - 9:50am - Plastic Network Model of Large Amplitude Conformational Change [PDF]
Paul Maragakis - Harvard

9:50am - 10:35am - Mechanisms for Supercoil Relaxation by DNA Topoisomerase [PDF]
​Ioan Andricioaei - University of Michigan, Ann Arbor

10:35am - 11:10am - Break

11:10am - 11:45am - Hinge-Bending Motion in S-adenosyl-L-homocysteine Hydrolase: Mutagenesis, Fluorescence and Modeling Studies [PDF]
Krzysztof Kuczera - University of Kansas

11:45am - 12:20pm - Src Kinase Activation: A Switched Electrostatic Network [PDF]
Carol B. Post - Purdue University

12:20pm - 1:30pm - Box Lunch - Eat inside or outside

1:30pm - 3:00pm - Poster Session 2

Session #6 - Coarse-Grained Methodology - Chair, Robert Jernigan

3:00pm - 3:45pm - Flexibility, Rigidity and Coarse Graining in Biomolecules [PDF]
Michael Thorpe - Arizona State–Tempe

3:45pm - 4:20pm - Accounting for Short Time-Scale Dynamics in Simplified Models of Proteins [PDF]
Maria Kurnikova - Carniegie-Mellon University

​4:20pm - 4:45pm - Break

4:45pm - 5:20pm - Continuum Elastic Models of Protein Secondary Structures [PDF]
Sean Sun - Johns Hopkins University

5:20pm - 5:55pm - Optimization, Validation, and Application of Coarse-Grained Models of Residue Interaction [PDF]
Dmitry Kondrashov - University of Wisconsin-Madison

​6:00pm - 7:00pm - Reception

7:00pm - 9:00pm - Banquet

Sunday, May 21, 2006

Session #7 - Dynamic Interactions in Macromolecular Assemblies - Chair, Julie Mitchell

8:30am - 9:15am - Viral Capsid Dynamics: From Maturation to Assembly [PDF]
Charles Brooks - Scripps

9:15am - 9:50am - The Unfolding Action of GroEL [PDF]
​Arjan Van Der Vaart - Harvard University

9:50am - 10:10am - Break

10:10am - 10:45am - Single Molecule Dynamics Reveals the Role of Flexibility in Bio-molecular Recognition [PDF]
Jin Wang - SUNY-Stony Brook

10:45am - 11:30am - Prediction of Protein Structure, Function and Druggability on a Proteomic Scale [PDF]
Jeff Skolnick - Georgia Institute of Technology