May 18, 2006 to May 21, 2006
Proteins self-organize into exquisitely precise structures, but the actual conformation of a protein fluctuates, and almost never coincides exactly with the average structure observed via X-ray crystallography or other methods. Mounting evidence suggests that these induced motions play specific and essential roles in protein function, but the mechanism is rarely clear, owing in part to the difficulty of direct observation of protein motions. X-ray crystallography reports the magnitude of atomic fluctuations, but the measurements are reliable only for well-ordered regions, where fluctuations are low. Crystals can be subjected to time-resolved experiments, but the range of applications is limited to reactions that can be triggered by light or trapped by clever manipulations. NMR spectroscopy is used to probe the dynamics of particular regions of a protein, but has limitations on interpretation depending on whether the dynamics can be defined as slowly or quickly exchanging and the density of through-space couplings. Mass spectrometry coupled with hydrogen/deuterium exchange and proteolysis has been used in some cases to determine changes in the relative solvent accessibility of amide hydrogens.
Computational methods have been utilized for several decades to study the motion of proteins, but traditional all-atom methods alone remain too computationally expensive to tackle functionally interesting long-time dynamics. Simplified models have been proposed to describe the equilibrium fluctuations near the native state, as opposed to nonequilibrium processes, such as folding or induced-fit relaxation. Normal mode analysis allows the decomposition of the fluctuations into collective modes with shared frequencies. Those with the lowest vibrational frequencies are the most global in scope, and presumably the most relevant for function. Classification of modes can, in fact, be used to describe and predict key conformational changes. Increasingly, computed normal modes of motion in proteins have been found to coincide with experimentally observed changes. This leads us to the purpose of this symposium, which is to foster interactions that will lead to improved methods of calculating motions and relating them to biological functions.
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Schedule
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
Organizers
Sponsors
Bruker AXS delivers analytical X-ray systems for elemental analysis, materials research and structural investigations. Our innovative solutions enable a wide range of customers in heavy industry, chemistry, pharmacy, semiconductor, life science and nanotechnology to make technological advancements and to accelerate their progress.
Graduate Training in Computation and Informatics in Biology and Medicine at the University of Wisconsin–Madison. The CIBM mission is to provide modern training for a new generation of researchers wishing to solve biomedical problems requiring strengths in both computational and biological science.