Conference Program
 
Proteins
June 21-26, 2009
Holderness School
Holderness, NH
Chairs:
Jacquelyn S. Fetrow & Terrence G. Oas

Vice Chairs:
James U. Bowie & Patricia L. Clark

The Proteins Gordon Research Conference has established a rich history of bringing together experimental and computational biochemists, biophysicists and biologists who study the many aspects of proteins science, including protein structure, folding, function and dynamics. Recent Proteins GRC programs have reflected a current broad interest in the properties and function of proteins in the cellular environment. The 2009 Proteins GRC will continue this focus on post-reductionist protein science, but will also highlight the contributions of classical protein science.

Topics will include recent and unpublished results describing the chemical and physical basis of protein structure and interaction networks, in-cell visualization of proteins, the role of co-solutes in structure and stability, the functional consequences of structural heterogeneity, among others. Discussion leaders with a substantial history in this field will be invited to provide their own historical and scientific perspective on each session topic and presented results.

This conference will thus emphasize the field’s substantial knowledge about the physical and chemical properties of proteins, while encouraging the application of this knowledge to understand how proteins behave and function in their biological contexts. The diverse presentations of new science and historically-informed discussions will provide researchers at all levels - institutional and industrial research scientists, faculty, post-doctoral fellows, and graduate students - with a rigorous and comprehensive view of contemporary protein science.

Contributors
SUNDAY
2:00 pm - 9:00 pmArrival and Check-in (Office Closed 6:00 pm - 7:00 pm)
6:00 pmDinner
7:30 pm - 7:40 pmWelcome / Introductory Comments by GRC Site Staff
7:40 pm - 9:30 pmPost Reductionist Protein Science
A plethora of new methods to study proteins in living cells were inspired by experiments originally developed to study purified proteins in simple solutions. The tension (sometimes literally) between reductionists and non-reductionists can be both thought provoking and inspiring. This session aims to explore this tension.
Discussion Leader: Lila Gierasch (University of Massachusetts)
7:40 pm - 8:00 pm Lila Gierasch (University of Massachusetts, Amherst)
"Perspectives on Post-Reductionist Protein Science"
8:00 pm - 8:30 pm Tom Kerppola (University of Michigan)
"Visualization of molecular processes in living cells"
8:30 pm - 8:40 pm Discussion
8:40 pm - 9:10 pm Zemer Gitai (Princeton University)
"Quantitative high-throughput analysis of bacterial protein localization identifies new cytoskeletal proteins and regulators"
9:10 pm - 9:15 pm Discussion
9:15 pm - 9:30 pm General Discussion (led by Lila Gierasch)
MONDAY
7:30 am - 8:30 amBreakfast
8:45 amGroup Photo
9:00 am - 12:30 pmRole of Co-Solutes and Water in Protein Stability
Remarkable advances have been made recently in our understanding of the effect of small molecules as co-solutes on the behavior of proteins under physiological conditions. Not only have these advances improved our understanding of the basic physics of proteins in aqueous solution, but they have also opened up new experimental approaches. This session will explore some of these advances and the interpretation of their results.
Discussion Leader: George Rose (Johns Hopkins University)
9:00 am - 9:25 am Wayne Bolen (University of Texas Medical Branch)
"Naturally occurring osmolytes: an ontology of solvent effects on protein stability"
9:25 am - 9:35 am Discussion
9:35 am - 10:00 am Bertil Halle (Lund University)
"Dynamics of water-protein interactions: from solution to cell"
10:00 am - 10:10 am Discussion
10:10 am - 10:20 am John Qvist (Lund University)
"Protein hydration dynamics unveiled by temperature dependent NMR measurements"
10:20 am - 10:30 am Discussion
10:30 am - 10:50 am Coffee Break
10:50 am - 11:15 am Adrian Elcock (University of Iowa)
"From salt water to the bacterial cytoplasm: studying environmental effects on biomolecular behavior with molecular simulations"
11:15 am - 11:25 am Discussion
11:25 am - 11:50 am Janet Wood (University of Guelph)
"Proton-osmolyte symporter ProP of Escherichia coli: osmosensor and osmoregulator"
11:50 am - 12:00 pm Discussion
12:00 pm - 12:15 pm George Rose (Johns Hopkins University)
"Perspectives on the role of co-solutes and water on protein stability"
12:15 pm - 12:30 pm General Discussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session A
6:00 pmDinner
7:30 pm - 9:30 pmProtein-RNA Interactions and the Biology of Translation
With the publication of the ribosome structure, the field of RNA-protein biology has exploded. This session will explore some of the recent developments in this field.
Discussion Leader: Ignacio Tinoco, Jr. (University of California, Berkeley)
7:30 pm - 8:00 pm Jamie Williamson (The Scripps Research Institute)
"Assembly of the ribosome in vitro and in cells"
8:00 pm - 8:10 pm Discussion
8:10 pm - 8:20 pm Mee-Ngan Yap (National Institutes of Health)
"Recognition of a translation arrest motif inside the ribosome tunnel"
8:20 pm - 8:25 pm Discussion
8:25 pm - 8:55 pm Ruben Gonzalez, Jr. (Columbia University)
"Coupling of tRNA and ribosome dynamics during translation"
8:55 pm - 9:05 pm Discussion
9:05 pm - 9:15 pm Ignacio Tinoco, Jr. (University of California, Berkeley)
"Perspectives on protein-RNA interactions and the biology of translation"
9:15 pm - 9:30 pm General Discussion
TUESDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmThe Hydrogen Bond and Hydrophobicity, Revisited
The hydrogen bond and hydrophobicity are the two most important molecular driving forces in proteins and these have been studied throughout the history of protein science. This session will explore recent advances in the theoretical understanding of these forces and their role in important biological functions.
Discussion Leader: Robert Baldwin (Stanford)
9:00 am - 9:15 am Robert Baldwin (Stanford)
"Recent perspectives on the hydrogen bond and hydrophobicity"
9:15 am - 9:40 am Michele Vendruscolo (University of Cambridge)
"Hydrogen bonding and hydrophobicity as the driving forces in protein ordered aggregation"
9:40 am - 9:50 am Discussion
9:50 am - 10:15 am Joseph Dannenberg (Hunter College)
"A density functional theory (DFT) approach to the hydrophobic effect"
10:15 am - 10:25 am Discussion
10:25 am - 10:35 am Silvina Matysiak (University Of Texas At Austin)
"Dissecting the role of hydrophobic hydration in protein stability: A 3D water-explicit minimalist protein model of cold and heat-denaturation"
10:35 am - 10:45 am Discussion
10:45 am - 11:05 am Coffee Break
11:05 am - 11:30 am Bertrand Garcia-Moreno (Johns Hopkins University)
"Charges in the hydrophobic interior of a protein"
11:30 am - 11:40 am Discussion
11:40 am - 12:05 pm Stephen White (University of California, Irvine)
"Hydrogen bonding and the stability of helix-gating proteins in membranes"
12:05 pm - 12:15 pm Discussion
12:15 pm - 12:30 pm General Discussion (led by Robert Baldwin)
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session B
6:00 pmDinner
7:30 pm - 9:30 pmTheory of Amyloid Formation
The misfolding of proteins in the cellular environment is arguably the most important property of proteins from a biomedical point of view. Because of the increased sophistication of the theory of protein structure and dynamics, researchers are beginning to see the physical basis for some of the key elementary steps leading to the formation of pathological misfolding products such as amyloid fibrils. This session is designed to present the state-of-the-art descriptions of amyloid formation.
Discussion Leader: Harold Scheraga (Cornell University)
7:30 pm - 7:45 pm Harold Scheraga (Cornell University)
"Challenges in understanding amyloid formation"
7:45 pm - 8:15 pm Devarajan Thirumalai (University of Maryland)
"Growth mechanism of oligomers and fibrils of amyloidogenic peptides"
8:15 pm - 8:25 pm Discussion
8:25 pm - 8:35 pm Brenda Watt (University of Pennsylvania)
"Dissecting the Pmel17 amyloid"
8:35 pm - 8:40 pm Discussion
8:40 pm - 9:10 pm Charles Brooks (University of Michigan)
"pH and membranes in amyloid peptide aggregation"
9:10 pm - 9:15 pm Discussion
9:15 pm - 9:30 pm General Discussion (led by Harold Scheraga)
WEDNESDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmFunctional Consequences of Heterogeneity in Protein Structure
Interconversion of multiple conformations has long been known to be a crucial part of protein function. However, only recently have experimental methods and theory been developed to describe this dynamics in terms of relatively large ensembles of protein conformations. This session will explore the tools for observing and analyzing these multiple conformations, both experimentally and theoretically.
Discussion Leader: Ken Dill (University of California, San Francisco)
9:00 am - 9:25 am Kingshuk Ghosh (University of Denver)
"Heterogeneity in the Folding and Stability of Proteins: A Statistical Mechanics Perspective"
9:25 am - 9:35 am Discussion
9:35 am - 10:00 am Vincent Hilser (University of Texas Medical Branch)
"Intrinsic Disorder, Local Unfolding and Allostery in an Ensemble"
10:00 am - 10:10 am Discussion
10:10 am - 10:20 am Dan Bolon (University of Massachusetts, Worcester)
"Harnessing design to probe the essential Hsp90 protein interaction network in vivo"
10:20 am - 10:30 am Discussion
10:30 am - 10:50 am Coffee Break
10:50 am - 11:15 am Elan Eisenmesser (University of Colorado at Denver)
"Cyclophilins and their receptor: Everybody's moving"
11:15 am - 11:25 am Discussion
11:25 am - 11:50 am Floyd Romesburg (The Scripps Research Institute)
"The evolution of protein dynamics"
11:50 am - 12:00 pm Discussion
12:00 pm - 12:15 pm Ken Dill (University of California, San Francisco)
"Perspectives on heterogeneity in protein structure"
12:15 pm - 12:30 pm General Discussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session C
6:00 pmDinner
7:30 pm - 9:30 pmVisualization of Proteins in the Cell
A crucial achievement in our understanding of proteins in the cellular environment has been the development of tools that allow them to be visualized in the cell. This session will explore these tools and the challenges in their use and interpretation.
Discussion Leader: Enrico Gratton (University of California, Irvine)
7:30 pm - 8:00 pm Ahmet Yildiz (University of California, Berkeley)
"Observation of motor protein movement in vitro and in live cells"
8:00 pm - 8:10 pm Discussion
8:10 pm - 8:20 pm Mahesh Narayan (University Of Texas El Paso)
"A Jekyll and Hyde oxidoreductase chaperone in the ER: Implications for neurodegenerative disorders"
8:20 pm - 8:25 pm Discussion
8:25 pm - 8:55 pm Catherine Royer (University of Montpellier)
"Protein interactions and dynamics studied in live cells using fluorescence fluctuation approaches"
8:55 pm - 9:05 pm Discussion
9:05 pm - 9:15 pm Enrico Gratton (University of California, Irvine)
"Perspectives on, and challenges of, visualization of proteins in the cell"
9:15 pm - 9:30 pm General Discussion
THURSDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmStructural and Functional Proteomics
The field of proteomics has exploded in the post-genomic era and is ironically populated by many scientists from outside the field of traditional protein science. This session will explore the developments in structural genomics (high throughput structure determination) with those in the field of functional proteomics, where high throughput methods are used to analyze modify protein function in vivo.
Discussion Leader: Jane Richardson (Duke University)
9:00 am - 9:25 am Benjamin Cravatt (The Scripps Research Institute)
"Activity-based proteomics and its applications for enzyme and inhibitor discovery"
9:25 am - 9:35 am Discussion
9:35 am - 10:00 am Adam Godzik (The Burnham Institute)
"A three dimensional atomic-level view of the complete metabolic network of model organism, Thermotoga maritime"
10:00 am - 10:10 am Discussion
10:10 am - 10:25 am Oscar Millett (Parque Technogico De Vizcaya)
"Structural Basis for the Amino Acid Composition of Proteins from Halophilic Archea"
10:25 am - 10:35 am Discussion
10:35 am - 10:55 am Coffee Break
10:55 am - 11:10 am Thomas J. Magliery (Ohio State University)
"Information in Protein Sequences: Combinatorial and Statistical Protein Design"
11:10 am - 11:20 am Discussion
11:20 am - 11:45 am Patricia Babbitt (University of California, San Francisco)
"Protein similarity networks and the evolution of new enzyme functions"
11:45 am - 11:55 am Discussion
11:55 am - 12:15 pm Jane Richardson (Duke University)
"Perspectives on large scale structural and functional proteomics projects"
12:15 pm - 12:30 pm General Discussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session D
6:00 pmDinner
7:30 pm - 8:00 pmBusiness Meeting
(Nominations for the next Vice Chair; fill out conference evaluation forms; discuss future site & scheduling preferences; election of the next Vice Chair)
8:00 pm - 9:30 pmKeynote Talk
Discussion Leader: Terry Oas (Duke University)
8:00 pm - 8:10 pm Terry Oas (Duke University)
"Introductory remarks"
8:10 pm - 9:00 pm Carlos Bustamante (University of California, Berkeley)
"Single Molecule Studies of the Stepping and Subunit Coordination in a DNA-Packaging Ring ATPase"
9:00 pm - 9:30 pm General Discussion
FRIDAY
7:30 am - 8:30 amBreakfast
9:00 amDepart
Funding for this conference was made possible (in part) by 1 R13 GM087770-01 from NIGMS. The views expressed in written conference materials or publications and by speakers and moderators do not necessarily reflect the official policies of the Department of Health and Human Services; nor does mention by trade names, commercial practices, or organizations imply endorsement by the U.S. Government.