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Computational Aspects - Biomolecular NMR
Gordon Research Conference

Dates

May 22-27, 2011

Location

Renaissance Tuscany Il Ciocco
Lucca (Barga), Italy

Organizers

Chair:
Stephan Grzesiek

Vice Chair:
James H. Prestegard

Meeting Description

The Gordon Research Conference on Computational Aspects of Biomolecular NMR provides a unique forum to present newly emerging computational and experimental methods that will drive NMR applications to ever more complex and challenging biomolecular systems. Nuclear Magnetic Resonance (NMR) spectroscopy is one of the most powerful biophysical techniques for studying biomolecules. Progress in NMR to probe hitherto inaccessible aspects of biomolecular behavior has regularly resulted directly from advances in computational methodology that unravel more of the rich information content of NMR data and provide faster and more accurate analysis tools. This includes the computation of chemical shifts and scalar couplings by quantum-chemical methods, the heuristic analysis of experimental databases to derive correlations between NMR observables and biomolecular behavior, the design of new data acquisition and processing schemes, novel methods for accelerated and automated structure determination, computational approaches to interpret spin relaxation and dipolar couplings, computational approaches to integrate NMR data with complementary data (SAXS, ion mobility MS, X-ray crystallography) that enable the study of larger and more complex systems, and NMR data analysis in Systems Biology. Computation thus represents a major driving force enabling NMR to advance and continually enhance our ability to understand specific aspects of biomolecular function.

The conference will focus on the most recent developments in the field, with sessions and discussions devoted to some of the most exciting and topical aspects of biomolecular NMR, animated by world leaders in the respective sub-fields. While the conference is centered on computational aspects of biomolecular NMR, the applications are at the intersection between biology, chemistry, bioinformatics, and physics. The conference thus provides an ideal platform for an interdisciplinary exchange of ideas. The assembly of a prominent speaker list along with the small format of the conference will provide unique opportunities for graduate students and postdocs for discussions of their research with leaders in the field. Extensive poster sessions will be held to facilitate this process. Moreover, we have reserved a number of time slots for posters that will be upgraded to oral presentations with the idea to give young scientists an opportunity to present their work.

Contributors

Meeting Program

SUNDAY
4:00 pm - 8:00 pmArrival and Check-in (Check-in Desk Closed 6:00 pm - 7:45 pm)
5:00 pmWelcome Mixer
6:00 pmDinner
7:30 pm - 7:50 pmWelcome / Introductory Comments by GRC Site Staff and Chair
7:50 pm - 9:30 pmPerspectives for NMR and Computation in Structural Biology
Discussion Leader: Stephan Grzesiek (University of Basel)
7:50 pm - 8:30 pm Lyndon Emsley (Ecole Normale Superieure de Lyon)
"Protein NMR Crystallography"
8:30 pm - 8:40 pm Discussion
8:40 pm - 9:20 pm Michele Parrinello (ETH Zurich)
"The well-tempered ensemble"
9:20 pm - 9:30 pm Discussion
MONDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmNew Efficient Avenues for Structure Determination
Discussion Leader: Lewis Kay (University of Toronto)
9:00 am - 9:25 am Ad Bax (National Institutes of Health)
"Chemical shifts, SAXS, and dipolar couplings: how can they help?"
9:25 am - 9:35 am Discussion
9:35 am - 10:00 am Michele Vendruscolo (University of Cambridge)
"Determination of the Dynamics of Proteins Using Residual Dipolar Couplings"
10:00 am - 10:10 am Discussion
10:10 am - 10:40 am Coffee Break / Group Photo
10:40 am - 11:05 am Alexandre Bonvin (Utrecht University)
"Structural biology on the GRID: the tale of the WeNMR virtual research community"
11:05 am - 11:15 am Discussion
11:15 am - 11:40 am David Wishart (University of Alberta)
"Advances in Predicting Chemical Shifts from Structure and Structure from Chemical Shifts"
11:40 am - 11:50 am Discussion
11:50 am - 12:15 pm Jens Meiler (Vanderbilt University)
"De novo membrane protein folding from sparse NMR data"
12:15 pm - 12:25 pm Discussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 5:30 pmPoster Session I
5:30 pm - 7:30 pmAdvances in Speed and Sensitivity of Data Acquisition
Discussion Leader: Jeff Hoch (University of Connecticut)
5:30 pm - 5:55 pm Thomas Prisner (Goethe University Frankfurt)
"Dynamic Nuclear Polarization at High Magnetic Fields in the Liquid State"
5:55 pm - 6:05 pm Discussion
6:05 pm - 6:30 pm Guy Montelione (Rutgers University)
"Assessment of Protein NMR Structures Determined by Automated and Manual Analysis Methods"
6:30 pm - 6:40 pm Discussion
6:40 pm - 6:50 pm Eriks Kupce (Agilent Techmologies)
"Compressive Sensing with Multiple Receivers in NMR Spectroscopy"
6:50 pm - 6:55 pm Discussion
6:55 pm - 7:20 pm Lucio Frydman (Weizmann Institute of Science)
"Novel RF Strategies For a Faster and More Efficient Acquisition of Multidimensional NMR Spectra"
7:20 pm - 7:30 pm Discussion
8:00 pmDinner
TUESDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmComputer Simulations of Biomolecular Structure and Dynamics
Discussion Leader: Art Palmer (Columbia University)
9:00 am - 9:25 am Valerie Daggett (University of Washington)
"Dynameomics: Motion, entropy, and NMR order parameters"
9:25 am - 9:35 am Discussion
9:35 am - 10:00 am Kresten Lindorff-Larsen (D.E. Shaw Research)
"Testing and improving force fields for long-timescale MD simulations"
10:00 am - 10:10 am Discussion
10:10 am - 10:30 am Coffee Break
10:30 am - 10:55 am Rafael Brueschweiler (Florida State University)
"From NMR Parameters to Boltzmann Ensembles"
10:55 am - 11:05 am Discussion
11:05 am - 11:30 am David Case (Rutgers University)
"New Analyses of Chemical Shifts and Anisotropies in Proteins and Nucleic Acids"
11:30 am - 11:40 am Discussion
11:40 am - 12:05 pm Martin Blackledge (CEA/CNRS/UJF Grenoble)
"Developing a Quantitative Understanding of Functional Disorder in Proteins"
12:05 pm - 12:15 pm Discussion
12:15 pm - 12:25 pm Tanja Kortemme (UCSF)
"Robotics-inspired approaches to modeling protein conformations and designing functional interactions"
12:25 pm - 12:30 pm Discussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 5:30 pmPoster Session II
5:30 pm - 7:30 pmStructure and Dynamics in the Solid State
Discussion Leader: Lyndon Emsley (Ecole Normale Superieure de Lyon)
5:30 pm - 5:55 pm Mei Hong (Iowa State University)
"Structure and dynamics of the influenza M2 proton channel by solid-state NMR"
5:55 pm - 6:05 pm Discussion
6:05 pm - 6:30 pm Beat Meier (ETH Zurich)
"Amyloids and Prions as seen by Solid-State NMR"
6:30 pm - 6:40 pm Discussion
6:40 pm - 7:05 pm Bernd Reif (Technische Universität München)
"Quantification of dynamics in rotating solids using perdeuterated proteins"
7:05 pm - 7:15 pm Discussion
7:15 pm - 7:25 pm Robert Tycko (National Institutes of Health)
"Incorporating Novel Torsion Angle Constraints into Solid State NMR Structures"
7:25 pm - 7:30 pm Discussion
8:00 pmDinner
WEDNESDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmNew Approaches to Detect Biomolecular Dynamics
Discussion Leader: Peter Wright (The Scripps Research Institute)
9:00 am - 9:25 am Lewis Kay (University of Toronto)
"Seeing the invisible by solution NMR spectroscopy"
9:25 am - 9:35 am Discussion
9:35 am - 10:00 am Art Palmer (Columbia University)
"Protein dynamics from experiment and simulation"
10:00 am - 10:10 am Discussion
10:10 am - 10:30 am Coffee Break
10:30 am - 10:55 am Marius Clore (National Institutes of Health)
"Hybrid structure determination methods, paramagnetic relaxation and differential relaxation"
10:55 am - 11:05 am Discussion
11:05 am - 11:30 am Gabriele Varani (University of Washington)
"Intermediate motions in RNA from solid state and solution NMR"
11:30 am - 11:40 am Discussion
11:40 am - 12:05 pm Hashim Al-Hashimi (University of Michigan)
"Transient Hoogsteen Base-Pairs in Canonical Duplex DNA"
12:05 pm - 12:15 pm Discussion
12:15 pm - 12:25 pm Nicolai Skrynnikov (Purdue University)
"Toward a comprehensive model of protein disorder: long MD simulations validated through experimental data"
12:25 pm - 12:30 pm Discussion
12:30 pmLunch
1:30 pm - 5:30 pmFree Time / Optional Activities: Excursion to Lucca; Mountain hiking
4:00 pm - 5:30 pmPoster Session III (Optional)
5:30 pm - 7:30 pmQuantifying Structure and Dynamics of Disordered Protein States
Discussion Leader: Martin Blackledge (CEA/CNRS/UJF Lyon)
5:30 pm - 5:50 pm Peter Wright (The Scripps Research Institute)
"Folding and binding of intrinsically disordered proteins"
5:50 pm - 6:00 pm Discussion
6:00 pm - 6:20 pm Julie Forman-Kay (University of Toronto)
"ENSEMBLE characterization of intrinsically disordered proteins and their dynamic complexes"
6:20 pm - 6:30 pm Discussion
6:30 pm - 6:50 pm Markus Zweckstetter (Max-Planck-Institut für biophysikalische Chemie)
"Folding and Misfolding of Tau"
6:50 pm - 7:00 pm Discussion
7:00 pm - 7:20 pm Jane Dyson (The Scripps Research Institute)
"Examining unstructured and partly structured proteins by NMR"
7:20 pm - 7:30 pm Discussion
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 pmDinner
THURSDAY
7:30 am - 8:30 amBreakfast
9:00 am - 12:30 pmCombining NMR with Complementary Techniques
Discussion Leader: Jim Prestegard (University of Georgia)
9:00 am - 9:25 am Jill Trewhella (University of Sydney)
"Combining SAXS and NMR data for improved structure determination: requirements for accurate and reliable scattering data"
9:25 am - 9:35 am Discussion
9:35 am - 10:00 am Justin Benesch (University of Oxford)
"Integrating NMR with Ion-Mobility Mass Spectrometry: Monitoring Structural Dynamics on the Secondary to Quaternary Levels"
10:00 am - 10:10 am Discussion
10:10 am - 10:30 am Coffee Break
10:30 am - 10:55 am Ben Schuler (University of Zurich)
"Single molecule spectroscopy of protein folding dynamics"
10:55 am - 11:05 am Discussion
11:05 am - 11:30 am Claudio Luchinat (University of Florence)
"Computational aspects of paramagnetism-based NMR"
11:30 am - 11:40 am Discussion
11:40 am - 12:05 pm Marcellus Ubbink (Leiden University)
"Structure and dynamics of protein complexes from paramagnetic NMR and modeling"
12:05 pm - 12:15 pm Discussion
12:15 pm - 12:25 pm Frans Mulder (University of Groningen)
"Protein 'random coil' chemical shifts derived from intrinsically disordered proteins"
12:25 pm - 12:30 pm Discussion
12:30 pmLunch
1:30 pm - 4:00 pmFree Time
4:00 pm - 5:30 pmPoster Session III
5:30 pm - 7:30 pmNMR Detection of Biomolecular Function in Complex Systems
Discussion Leader: Jane Dyson (The Scripps Research Institute)
5:30 pm - 5:55 pm Masahiro Shirakawa (Kyoto University)
"Mechanics of cells and intracellular macromolecules measured by magnetic resonance"
5:55 pm - 6:05 pm Discussion
6:05 pm - 6:30 pm Phil Selenko (FMP Berlin)
"Looking at proteins inside live cells with NMR spectroscopy"
6:30 pm - 6:40 pm Discussion
6:40 pm - 7:05 pm Jerome Boisbouvier (CEA/CNRS/UJF Grenoble)
"Towards Real-Time NMR Studies of Biological Machineries"
7:05 pm - 7:15 pm Discussion
7:15 pm - 7:25 pm Remco Sprangers (Max-Planck-Institut for Developmental Biology)
"Insights into the mechanism of the 250 kDa exosome complex"
7:25 pm - 7:30 pm Discussion
8:00 pmDinner
10:00 pm Disco Night
FRIDAY
7:30 am - 8:30 amBreakfast
9:00 amDeparture

Funding for this conference was made possible (in part) by 1 R13 GM097959-01 from the National Institute of General Medical Sciences. 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.
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