Conference Program
 
Protein Folding Dynamics

January 8-13, 2006
Four Points Sheraton / Holiday Inn Express
Ventura, CA

Chair:
Jane Clarke

Vice Chair:
Charles L. Brooks

The Gordon Research Conference on Protein Folding Dynamics will follow the Gordon-Kenan Graduate Research Seminar on Protein Folding Dynamics (January 6-8, 2006).

Protein folding is a multidisciplinary area of research addressing one of the fundamental problems in biology. Understanding the dynamical and energetic features of folding, are keys to elucidating issues of protein function, design and the origin of misfolding diseases. Consequently, few other fields have seen such a successful blend of physical and biological sciences. Progressively, more studies that bring together experiment and theory are being published, and this combination is advancing our fundamental quantitative understanding of the folding process. Technological and theoretical advances have altered our view of the how protein folding occurs. Fast events can be observed experimentally on timescales that approach those accessible by all-atom molecular dynamics simulations. New, sophisticated "simple" models of proteins allow ensemble kinetics to be sampled and compared to experiment. The Gordon Research Conference in Protein Folding Dynamics is a relatively new conference, set up to specifically bring experiment and theory together to explore advances in the field, and as a forum to discuss fundamental problems from polypeptide energetics and dynamics; to chaperone assisted folding and the relationship between protein misfolding and disease.


CONTRIBUTORS

We are grateful to D.E. Shaw Research and Development, LLC and IBM for their generous support for the meeting. We also acknowledge support from the National Science Foundation.


SUNDAY
4:00 pm - 9:00 pmArrival and Check-in
6:00 pmDinner
7:30 pm - 9:30 pmPLENARY SESSION I
Discussion Leader: Jane Clarke (University of Cambridge)
7:30 pm - 8:20 pm Peter Wolynes (University of California, San Diego)
"Recent Successes of the Energy Landscape Theory of Protein Folding"
8:20 pm - 8:30 pm Discussion
8:30 pm - 9:20 pmJeffery Kelly (Scripps Research Institute)
"Backbone Mutations to Probe H-bond Energetics in Folding and Misfolding"
9:20 pm - 9:30 pmDiscussion
MONDAY
7:30 am - 8:30 amBreakfast
8:30 amGroup Photo
9:00 am - 12:30 pmFOLDING AND AGGREGATION
Discussion Leader: Sheena Radford (University of Leeds)
9:10 am - 9:40 amValerie Daggett (University of Washington)
"Simulation of Conformational Changes Associated with Amyloidosis"
9:40 am - 9:50 am Discussion
9:50 am - 10:20 amYugi Goto (Osaka University)
"Comparison of Protein Folding and Amyloid Fibril Formation"
10:20 am - 10:30 amDiscussion
10:30 am Coffee Break
10:50 am - 11:05 amWilliam Swope (IBM Almaden Research Center)
"Computer Simulations of Peptides and Small Proteins"
11:05 am - 11:10 amDiscussion
11:10 am - 11:25 amThomas Jahn (University of Leeds)
"Amyloid Fibril Formation Proceeds Via Trapped Protein Folding Intermediates"
11:25 am - 11:30 amDiscussion
11:30 am - 12:00 pmCarol Hall (North Carolina State University)
"Molecular Dynamics Simulation of Fibril Formation"
12:00 pm - 12:10 pmDiscussion
12:20 pm - 12:30 pmGeneral Discussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session I
6:00 pmDinner
7:30 pm - 9:30 pmPROTEIN EVOLUTION
Discussion Leader: Zan Luthey-Schulten (University of Illinois, Urbana-Champaign)
7:40 pm - 8:05 pmCyrus Chothia (MRC LMB)
"Sequence Divergence: Limitations and Effects"
8:05 pm - 8:15 pmDiscussion
8:15 pm - 8:40 pmTeresa Head Gordon (University of California, Berkeley)
"Designing Sequences to Fold or Aggregate using the Denatured State Ensemble"
8:40 pm - 8:50 pmDiscussion
8:50 pm - 9:15 pmSarah Teichmann (MRC LMB)
"Evolution of Multi-Domain Proteins"
9:15 pm - 9:30 pmDiscussion / General Discussion
TUESDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmINVESTIGATING SPECIES ON THE FOLDING PATHWAY
Discussion Leader: Joan Shea (University of California, Santa Barbara)
9:10 am - 9:40 amDan Raleigh (State University of New York, Stony Brook)
"The Role of the Unfolded State in Protein Folding and Stability"
9:40 am - 9:50 amDiscussion
9:50 am - 10:20 amMichele Vendruscolo (University of Cambridge)
"Determination of Ensembles of Structures Representing the Dynamics of Proteins"
10:20 am - 10:30 amDiscussion
10:30 amCoffee Break
10:50 am - 11:05 amSarah Batey (University of Cambridge)
"Cooperative Folding in a Multidomain Protein"
11:05 am - 11:10 amDiscussion
11:10 am - 11:25 amJin Wang (State University of New York, Stony Brook)
"Diffusion Dynamics of Protein Folding"
11:25 am - 11:30 amDiscussion
11:30 am - 12:00 pmPeter Wright (Scripps Research Institute)
"Mapping the apomyoglobin folding landscape by NMR: New insights into folding intermediates"
12:00 pm - 12:10 pmDiscussion
12:20 pm - 12:30 pmGeneral Discussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session II
6:00 pmDinner
7:30 pm - 8:15 pmINVESTIGATING SPECIES ON THE FOLDING PATHWAY (continued)
Discussion Leader: Joan Shea (University of California, Santa Barbara)
7:30 pm - 8:00 pmHarold Scheraga (Cornell University)
"Computation of Protein Folding Pathways using Molecular Dynamics with a United-Residue (UNRES) Model of Polypeptide Chains"
8:00 pm - 8:15 pmDiscussion
8:15 pm - 9:30 pmPLENARY SESSION II
Discussion Leader: Charles Brooks (Scripps Research Institute)
8:15 pm - 9:10 pm Chris Dobson (University of Cambridge)
"Protein Folding & Human Disease"
9:10 pm - 9:30 pmDiscussion
WEDNESDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmEXPLORING THE FOLDING LANDSCAPE I
Discussion Leader: Kevin Plaxco (University of California, Santa Barbara)
9:10 am - 9:40 amJosé Onuchic (University of California, San Diego)
"The Energy Landscape for Protein Folding and Function"
9:40 am - 9:50 amDiscussion
9:50 am - 10:20 amMikael Oliveberg (University of Stockholm)
"Panning for the minimal protein folding nucleus through loop-entropy perturbations"
10:20 am - 10:30 amDiscussion
10:30 am Coffee Break
10:50 am - 11:05 amMichelle DeRitter (University of Pennsylvania)
"Ultrafast Folding of Trp Cage Mini Proteins"
11:05 am - 11:10 amDiscussion
11:10 am - 11:25 am Elisha Haas (Bar Ilan University)
"Non Local Interactions are Effective Key Contributions to the Structure of Early Folding Intermediates"
11:25 am - 11:30 amDiscussion
11:30 am - 12:00 pmEugene Shakhnovich (Harvard University)
"Protein Folding Dynamics: A Global View from High-Resolution All Atom Simulations with Transferable Potentials"
12:00 pm - 12:10 pmDiscussion
12:10 pm - 12:30 pmGeneral Discussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session III
6:00 pmDinner
7:00 pm - 7:30 pmBusiness Meeting
(Nominations for the next Vice Chair; Fill out Conference Evaluation Forms; Discuss future Site & Scheduling preferences; Election of the next Vice Chair)
7:30 pm - 9:30 pmEXPLORING THE FOLDING LANDSCAPE II
Discussion Leader: Angel Garcia (Rensselaer Polytechnic Institute)
7:40 pm - 8:10 pmPhil Dawson (Scripps Research Institute)
"Unnatural backbone and side chain structures: an expanded toolkit for protein engineering"
8:10 pm - 8:20 pm Discussion
8:20 pm - 8:35 pmMiriam Friedel (University of California, Santa Barbara)
"Tethering a protein to a surface changes its folding mechanism"
8:35 pm - 8:40 pmDiscussion
8:40 pm - 9:10 pmVijay Pande
"Simulating Folding and Misfolding in Biological Contexts"
9:10 pm - 9:20 pmDiscussion
9:20 pm - 9:30 pmGeneral Discussion
THURSDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmFAST AND EARLY EVENTS / SINGLE MOLECULE FOLDING STUDIES
Discussion Leader: Tobin Sosnick (University of Chicago)
9:10 am - 9:40 amBill Eaton (National Institutes of Health)
"Ultrafast Folding"
9:40 am - 9:50 am Discussion
9:50 am - 10:20 amSteve Hagen (University of Florida)
"Diffusion and Friction-Limited Folding in Small Proteins"
10:20 am - 10:30 amDiscussion
10:30 amCoffee Break
10:50 am - 11:20 am Susan Marqusee (University of California, Berkeley)
"Single Molecule Studies of Protein Folding using the Optical Tweezers"
11:20 am - 11:30 amDiscussion
11:30 am - 12:00 pmGilad Haran (Weizmann Institute)
"Probing Collapse and Folding Transitions with Single-Molecule Fluorescence"
12:00 pm - 12:10 pmDiscussion
12:20 pm - 12:30 pmGeneral Discussion
12:30 pmLunch
1:30 pm - 6:00 pmFree Time
6:00 pmDinner
7:30 pm - 9:30 pmFOLDING IN THE CELL
Discussion Leader: Amnon Horovitz (Weizmann Institute)
7:40 pm - 8:10 pmSilvia Cavagnero (University of Wisconsin, Madison)
"Protein Folding as a Function of Chain Elongation: Off and On the Ribosome"
8:10 pm - 8:20 pm Discussion
8:20 pm - 8:35 pmBeena Krishnan (University of Massachusetts, Amherst)
"Developing New Strategies to Monitor In Vivo Protein Folding"
8:35 pm - 8:40 pmDiscussion
8:40 pm - 9:10 pm Art Horwich (Yale University)
"The Chaperonin Reaction: Observing Substrate Proteins"
9:10 pm - 9:20 pmDiscussion
9:20 pm - 9:30 pm General Discussion
FRIDAY
7:30 am - 8:30 amBreakfast
9:00 amDepart

Last Updated: October 11, 2006