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Conference Program
 
Biopolymers
June 8-13, 2008
Salve Regina University
Newport, RI

Biopolymers (proteins, RNA, DNA) are central to most biological processes, including those relevant to human health such as signaling pathways, metabolism, and gene expression. They are implicated in many human diseases, are usually targets of therapeutic drugs and are becoming increasingly used as therapeutic agents themselves. The 2008 Biopolymers GRC will explore recent advances and future trends in understanding the structure, stability, dynamics, and interactions of biopolymers, as well as the impact of these fundamental physico-chemical properties on cellular processes. Biopolymers GRC is uniquely poised to foster multidisciplinary and interdisciplinary connections between chemistry, chemical engineering, physics and biology. This meeting of scientists working in the areas of experimental and theoretical understanding of biopolymers allows the results and ideas to be exchanged, compared, discussed, and synthesized.


Contributors

SUNDAY
2:00 pm - 11:00 pmArrival and Check-in
6:00 pmDinner
7:30 pm - 7:40 pmWelcome / Introductory Comments by GRC Site Staff
7:40 pm - 9:30 pm KEYNOTE LECTURES
Discussion Leader: Joan-Emma Shea (University of California Santa Barbara)
7:40 pm - 8:30 pmAngela Gronenborn (University of Pittsburg)
"Structural Basis of Signaling & Gene Regulation by NMR Spectroscopy"
8:30 pm - 8:40 pm Discussion
8:40 pm - 9:30 pmJosé Onuchic (University of California San Diego)
"The Energy Landscape for Protein Folding and Function"
9:15 pm - 9:30 pm Discussion
MONDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pm DYNAMIC PROPERTIES OF BIOPOLYMERS
9:00 am - 9:05 amDiscussion Leader: Patrick Loria (Yale University)
"Introduction to the session"
9:05 am - 9:30 amPatrick Loria (Yale University)
"NMR studies of the relation between enzyme motions and catalytic activity"
9:30 am - 9:40 am Discussion
9:40 am - 10:05 amDavid Fushman (University of Maryland)
"Structure, dynamics, and interactions in multidomain proteins: polyubiquitin as a test case"
10:05 am - 10:15 am Discussion
10:15 am - 10:45 am Coffee Break
10:45 am - 11:10 amChunyu Wang (Rensselaer Polytechnic Institute)
"Dynamics of Amyloid beta-peptide"
11:10 am - 11:20 am Discussion
11:20 am - 11:45 amDon Jacobs (University of North Carolina - Charlotte)
"Quantifying stability and flexibility in proteins using constraint theory"
11:45 am - 11:55 am Discussion
11:55 am - 12:20 pmPatrick Wintrode (Case Western University)
"Exploring the link between folding, dynamics and metastability in human serpins"
12:20 pm - 12:25 pm Discussion
12:25 pm - 12:30 pmPatrick Loria (Yale University)
"Concluding Remarks"
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session
6:00 pmDinner
7:30 pm - 9:30 pm SMALL NUCLEIC ACIDS
7:30 pm - 7:35 pmDiscussion Leader: Andrew Feig (Wayne State University)
"Introduction to the session"
7:35 pm - 7:55 pmAndrew Feig (Wayne State University)
"Progression from kissing interactions to strand displacement: Biophysical analysis of RNA structural rearrangements that mediate post-transcriptional gene regulation"
7:55 pm - 8:00 pm Discussion
8:00 pm - 8:20 pmPan TX Li (SUNY Albany)
"Mechanical unfolding of single RNA kissing complexes"
8:20 pm - 8:30 pm Discussion
8:30 pm - 8:50 pmTianbing Xia (University of Texas, Dallas)
"Probing RNA Conformational Complexity and Dynamics by Femtosecond Time-Resolved Spectroscopy"
8:50 pm - 8:55 pm Discussion
8:55 pm - 9:15 pmLuis Marky (University of Nebraska Medical Center)
"Targeting DNA Intramolecular Complexes with Complementary Strands"
9:15 pm - 9:25 pm Discussion
9:25 pm - 9:30 pmAndrew Feig (Wayne State University)
"Concluding Remarks"
TUESDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pm ELECTROSTATIC INTERACTIONS IN BIOPOLYMERS
9:00 am - 9:05 amDiscussion Leader: Bertrand Garcia-Moreno (Johns Hopkins University)
"Introduction to the session"
9:05 am - 9:30 amBertrand Garcia-Moreno (Johns Hopkins University)
"The unusual properties of internal ionizable groups in proteins"
9:30 am - 9:40 am Discussion
9:40 am - 10:05 amMarilyn Gunner (City College of New York)
"Motifs proteins use to modify their electrostatic environments and techniques for recognizing them"
10:05 am - 10:15 am Discussion
10:15 am - 10:45 am Coffee Break / Group Photo
10:45 am - 11:10 amHuan-Xiang Zhou (Florida State University)
"Electrostatic interactions in unfolded, folded, and transition states and in native and transient complexes of proteins"
11:10 am - 11:20 am Discussion
11:20 am - 11:45 amEmil Alexov (Clemson University)
"Electrostatic Effects Induced by Protein-Protein Association"
11:45 am - 11:55 am Discussion
11:55 am - 12:20 pmNathan Baker (Washington University St. Louis)
"Solvation forces on protein and nucleic acid systems: from atomistic to continuum models"
12:20 pm - 12:25 pm Discussion
12:25 pm - 12:30 pmBertrand Garcia-Moreno (Johns Hopkins University)
"Concluding Remarks"
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session
6:00 pmDinner
7:30 pm - 9:30 pm PROTEIN-NUCLEIC ACID INTERACTIONS
7:30 pm - 7:35 pmDiscussion Leader: Dorothy Beckett (University of Maryland)
"Introduction to the session"
7:35 pm - 7:55 pmDorothy Beckett (University of Maryland)
"Equilibrium and Kinetic Control in a Transcriptional Regulatory Circuit"
7:55 pm - 8:00 pm Discussion
8:00 pm - 8:20 pmJonathan Widom (Northwestern University)
"Nucleosome DNA sequence preferences"
8:20 pm - 8:30 pm Discussion
8:30 pm - 8:50 pmDorothy Erie (University of North Carolina, Chapel Hill)
"AFM and single molecule fluorescence studies of DNA mismatch repair"
8:50 pm - 8:55 pm Discussion
8:55 pm - 9:15 pmWlodek Bujalowski (University of Texas Medical Branch)
"Hexameric Helicases: Protein - Nucleic Acid and Protein-Protein Interactions"
9:15 pm - 9:25 pm Discussion
9:25 pm - 9:30 pmDorothy Beckett (University of Maryland)
"Concluding Remarks"
WEDNESDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pm RIBOSOMES AND CO-TRANSLATIONAL PROTEIN FOLDING
9:00 am - 9:05 amDiscussion Leader: Harry Noller (University of California Santa Cruz)
"Introduction to the session"
9:05 am - 9:30 amHarry Noller (University of California Santa Cruz)
"Ribosome Structure and Dynamics"
9:30 am - 9:40 am Discussion
9:40 am - 10:05 amCarol Deutsch (University of Pennsylvania)
"Tunnel Vision"
10:05 am - 10:15 am Discussion
10:15 am - 10:45 am Coffee Break
10:45 am - 11:10 amKevin Sanbonmatsu (Los Alamos National Lab)
"Ribosome dynamics: large-scale simulations of tRNA movement through the ribosome"
11:10 am - 11:20 am Discussion
11:20 am - 11:45 amRuben Gonzalez (Affiliation)
"Coupling of ribosome and tRNA conformational dynamics during translation elongation"
11:45 am - 11:55 am Discussion
11:55 am - 12:20 pmPaola Fucini (Max Plank Institute)
"Structure and dynamics of a ribosome-bound nascent chain by NMR spectroscopy"
12:20 pm - 12:25 pm Discussion
12:25 pm - 12:30 pmHarry Noller (University of California Santa Cruz)
"Concluding Remarks"
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session
6:00 pmDinner
7:30 pm - 9:30 pm BIOPOLYMERS AT HIGH PRESSURE
7:30 pm - 7:35 pmDiscussion Leader: Cathy Royer (University of Montpellier)
"Introduction to the session"
7:35 pm - 7:55 pmCathy Royer (University of Montpellier)
"Volumetric properties of proteins and the role of solvent in conformational dynamics"
7:55 pm - 8:00 pm Discussion
8:00 pm - 8:20 pmAngel Garcia (Rensselaer Polytechnic Institute)
"Simulations of the pressure driven folding/unfolding of biomolecules"
8:20 pm - 8:30 pm Discussion
8:30 pm - 8:50 pmKazuyuki Akasaka (Kinki University)
"The unique role of variable-pressure NMR spectroscopy in protein dynamic studies"
8:50 pm - 8:55 pm Discussion
8:55 pm - 9:15 pmDoug Clark (University of California Berkeley)
"Adapting to a Life of Stress: Why Do Some Enzymes Work Best Under Pressure?"
9:15 pm - 9:25 pm Discussion
9:25 pm - 9:30 pmCathy Royer (University of Montpellier)
"Concluding Remarks"
THURSDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pm PROTEIN FOLDING AND DESIGN
9:00 am - 9:05 amDiscussion Leader: Rohit Pappu (Washington University St. Louis)
"Introduction to the session"
9:05 am - 9:30 amValerie Daggett (University of Washington)
"Dynameomics"
9:30 am - 9:40 am Discussion
9:40 am - 10:05 amTracy Handel (University of California San Diego)
"Chemokine:Receptor Structural and Functional Dynamics. Can it Get More Complex?"
10:05 am - 10:15 am Discussion
10:15 am - 10:45 am Coffee Break
10:45 am - 11:10 amDoug Barrick (Johns Hopkins University)
"Folding of Ankyrin Repeat Proteins"
11:10 am - 11:20 am Discussion
11:20 am - 11:45 amLynne Regan (Yale University)
"Natural and engineered activities of TPR modules"
11:45 am - 11:55 am Discussion
11:55 am - 12:20 pmBrian Kuhlman (University of North Carolina Chapel Hill)
"Computer-based Design of Protein Structures and Interfaces"
12:20 pm - 12:25 pm Discussion
12:25 pm - 12:30 pmRohit Pappu (Washington University St. Louis)
"Concluding Remarks"
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 6:00 pmPoster Session
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 pm BIOPOLYMERS "IN VIVO"
7:30 pm - 7:35 pmDiscussion Leader: Michael Hecht (Princeton University)
"Introduction to the session"
7:35 pm - 8:00 pmAdrian Elcock (University of Iowa)
"Molecular Simulations of Intracellular Environments and Events"
8:00 pm - 8:10 pm Discussion
8:10 pm - 8:35 pmGerard C. L. Wong (University of Illinois Urbana)
"Interactions between cell penetrating peptides and membranes"
8:35 pm - 8:45 pm Discussion
8:45 pm - 9:10 pmRohit Pappu (Washington University St. Louis)
"The how and why of polyglutamine aggregation"
9:10 pm - 9:20 pm Discussion
9:20 pm - 9:30 pmGeorge Makhatadze (RPI)and Lois Pollack (Cornell)
"Concluding Remarks"
FRIDAY
7:30 am - 8:30 amBreakfast
9:00 amDeparture

Funding for this conference was made possible (in part) by 1 R13GM084482-01 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 not mention trade names, commercial practices, or organizations imply endorsement by the U.S. Government.

 
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