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This meeting took place in 2013
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Meeting Details
Structural Analysis of Supramolecular Assemblies by Hybrid Methods (C1)
Organizer(s) Andrej Sali, Brian T. Chait and David Baker
March 3 - March 7, 2013
Granlibakken Resort • Tahoe City, California USA
Abstract Deadline: November 5, 2012
Late Abstract Deadline: December 3, 2012
Scholarship Deadline: November 5, 2012
Early Registration Deadline: December 19, 2012
Supported by the Directors' Fund
CME Information
Summary of Meeting:
In order to understand the workings of a living cell, we need to know the structures and dynamics of individual biological macromolecules, their complexes and networks, organelles and whole cells, thus interfacing structural biology with cell biology, systems biology, proteomics, chemical biology and biophysics. The accuracy, precision, completeness and efficiency of structural characterization are maximized by hybrid or integrative approaches that combine data from multiple types of experimental methods through the use of computational analysis and modeling methods. These experimental methods include X-ray crystallography, NMR spectroscopy, electron microscopy, small angle X-ray scattering, mass spectrometry, chemical cross-linking, super-high resolution optical microscopy, optical microscopy and others. The goal of this meeting is to highlight the strengths and limitations of the current hybrid approaches as well as to identify promising new advances in experimental methods for collecting the data and computational methods for converting the data to models. Finally, hybrid approaches will be demonstrated by their applications to important and challenging biological problems, spanning a wide range of length and time scales, from atomic structures of individual proteins to low-resolution representations of whole cells.
CME Information
In order to understand the workings of a living cell, we need to know the structures and dynamics of individual biological macromolecules, their complexes and networks, organelles and whole cells, thus interfacing structural biology with cell biology, systems biology, proteomics, chemical biology and biophysics. The accuracy, precision, completeness and efficiency of structural characterization are maximized by hybrid or integrative approaches that combine data from multiple types of experimental methods through the use of computational analysis and modeling methods. These experimental methods include X-ray crystallography, NMR spectroscopy, electron microscopy, small angle X-ray scattering, mass spectrometry, chemical cross-linking, super-high resolution optical microscopy, optical microscopy and others. The goal of this meeting is to highlight the strengths and limitations of the current hybrid approaches as well as to identify promising new advances in experimental methods for collecting the data and computational methods for converting the data to models. Finally, hybrid approaches will be demonstrated by their applications to important and challenging biological problems, spanning a wide range of length and time scales, from atomic structures of individual proteins to low-resolution representations of whole cells.
Conference Program Print | View meeting in 12 hr (am/pm) time
SUNDAY, MARCH 3
08:00—09:00
Opening Remarks and Keynote Address
Meeting has ended...abstracts no longer viewable online. Purchase an Abstract Book from this meeting
*
Andrej Sali,
University of California, San Francisco, USA
*
David Baker,
University of Washington, USA
*
Brian T. Chait,
Rockefeller University, USA
Peter Walter,
HHMI/University of California, San Francisco, USA
The Unfolded Protein Response in Health and Disease
The Unfolded Protein Response in Health and Disease
09:00—12:00
Computation for Hybrid Approaches
Meeting has ended...abstracts no longer viewable online. Purchase an Abstract Book from this meeting
NOTE: This session will introduce major challenges in structural modeling of biological systems at different resolutions, from atomic to cellular, based on varied experimental datasets. Such challenges include representing the system, converting data into scoring functions, finding good scoring solutions, and analysing the results.
*
Ian A. Wilson,
The Scripps Research Institute, USA
Andrej Sali,
University of California, San Francisco, USA
Integrative Structure Determination of Macromolecular Assemblies
Integrative Structure Determination of Macromolecular Assemblies
David Baker,
University of Washington, USA
Computation of Protein Structures from Sparse NMR Data and Low Resolution X-Ray Data
Computation of Protein Structures from Sparse NMR Data and Low Resolution X-Ray Data
Nikolaos G. Sgourakis,
NIDDK, National Institutes of Health, USA
Short Talk: Advances in Structure Determination of Multimeric Protein Assemblies using NMR and cryoEM Data
Short Talk: Advances in Structure Determination of Multimeric Protein Assemblies using NMR and cryoEM Data
Gregory A. Voth,
University of Chicago, USA
Hybrid Multiscale Modeling of Biological Macromolecules and Macromolecular Assemblies
Hybrid Multiscale Modeling of Biological Macromolecules and Macromolecular Assemblies
Zaida (Zan) Luthey-Schulten,
University of Illinois at Urbana-Champaign, USA
Whole Cell Simulations
Whole Cell Simulations
17:00—19:00
Hybrid Approaches to Studying Dynamic Systems
Meeting has ended...abstracts no longer viewable online. Purchase an Abstract Book from this meeting
NOTE: This session will highlight successes and challenges in using hybrid methods to describe the dynamics of individual macromolecules and their assemblies. Presentations will motivate further method development by the needs of structural biologists interested in specific systems.
*
Alasdair C. Steven,
NIAMS, National Institutes of Health, USA
James R. Williamson,
The Scripps Research Institute, USA
Hybrid Methods for Study of Ribosome Assembly in Bacterial Cells
Hybrid Methods for Study of Ribosome Assembly in Bacterial Cells
Bo Huang,
University of California, San Francisco, USA
Dissecting Molecular Complex Architecture by Super-Resolution Microscopy
Dissecting Molecular Complex Architecture by Super-Resolution Microscopy
Timothy O. Street,
University of California, San Francisco, USA
Short Talk: The Mechanism of the Hsp90 Chaperonin Revealed by Hybrid Methods
Short Talk: The Mechanism of the Hsp90 Chaperonin Revealed by Hybrid Methods
Klaus J. Schulten,
University of Illinois at Urbana-Champaign, USA
Solving Large Structures by Molecular Dynamics Flexible Fitting
Solving Large Structures by Molecular Dynamics Flexible Fitting
08:00—11:15
Hybrid Approaches to Studying Macromolecular Structures
Meeting has ended...abstracts no longer viewable online. Purchase an Abstract Book from this meeting
NOTE: This session will highlight successes and challenges in using hybrid methods to describe the structures of individual macromolecules and their assemblies. Presentations will motivate further method development by the needs of structural biologists interested in specific systems.
*
David Baker,
University of Washington, USA
Holger Stark,
Max Planck Institute for Biophysical Chemistry, Germany
Combining Cryo-EM, X-Ray and MD Simulations to Study Dynamic Macromolecular Complexes
Combining Cryo-EM, X-Ray and MD Simulations to Study Dynamic Macromolecular Complexes
Alasdair C. Steven,
NIAMS, National Institutes of Health, USA
Novel Fold and Maturation Dynamics of a dsRNA Virus Capsid Protein
Novel Fold and Maturation Dynamics of a dsRNA Virus Capsid Protein
Eva Nogales,
University of California Berkeley, USA
Cryo-EM and Computation toward a Mechanistic Understanding of Microtubule Dynamic Instability
Cryo-EM and Computation toward a Mechanistic Understanding of Microtubule Dynamic Instability
Mary E. Matyskiela,
University of California, Berkeley, USA
Short Talk: Molecular Mechanisms of Substrate Degradation by the 26S Proteasome Revealed by CryoEM
Short Talk: Molecular Mechanisms of Substrate Degradation by the 26S Proteasome Revealed by CryoEM
Helen M. Berman,
Rutgers University, Center for Proteomics Research, USA
Short Talk: The Protein Model Portal – A Comprehensive Web Resource For Protein Structure Information
Short Talk: The Protein Model Portal – A Comprehensive Web Resource For Protein Structure Information
14:30—15:30
Panel 1: Key Issues in Measuring, Computing, Analyzing, Visualizing, Archiving, and Disseminating Hybrid Models
NOTE: The panel members will be asked to discuss their key issues in hybrid methods (e.g., key issues and challenges in collecting and interpreting structural data; hybrid model computation; reproducibility of computing hybrid models; representations for data and hybrid models; visualization of hybrid models; role of the PDB in hybrid models; role of journals / funding agencies in hybrid models). If useful conclusions emerge, they will be included in the commentary on the meeting to be published in the journal Structure.
*
Andrej Sali,
University of California, San Francisco, USA
Frank Alber,
University of Southern California, USA
David Baker,
University of Washington, USA
Alasdair C. Steven,
NIAMS, National Institutes of Health, USA
Gregory A. Voth,
University of Chicago, USA
Ian A. Wilson,
The Scripps Research Institute, USA
15:30—16:30
Panel 2: Reproducibility and Publishing of Hybrid Models
NOTE: The goal of the workshop panel is to present and discuss guidelines and principles for publishing reproducible hybrid-computational protocols and workflows. Current standards and practices for publishing complex hybrid-computational workflows are insufficient to ensure reproducibility of published findings and promote adoption and adaption of hybrid-computational methods among scientists. Authors, publishers, funders and developers each have an important role to play in helping ensure the reproducibility, widespread adoption and utility of hybrid-computational methods.
*
Andrew Morin,
Harvard Medical School, USA
Helen M. Berman,
Rutgers University, Center for Proteomics Research, USA
Ines Chen,
Nature Publishing Group, USA
Daniel Russel,
University of California, San Francisco, USA
Klaus J. Schulten,
University of Illinois at Urbana-Champaign, USA
17:00—19:15
Hybrid Approaches to Studying Cellular Organization
Meeting has ended...abstracts no longer viewable online. Purchase an Abstract Book from this meeting
NOTE: This session will highlight approaches, tools, successes and challenges in using hybrid methods to describe the organization of whole cells.
*
James R. Williamson,
The Scripps Research Institute, USA
Benjamin Geiger,
Weizmann Institute of Science, Israel
Supramolecular Structures Involved in the Scaffolding and Signaling Processes in Focal Adhesions
Supramolecular Structures Involved in the Scaffolding and Signaling Processes in Focal Adhesions
Graham Johnson,
University of California, San Francisco, USA
cellPack: A Virtual Mesoscope to Model and Visualize Structural Systems Biology
cellPack: A Virtual Mesoscope to Model and Visualize Structural Systems Biology
Wolfgang P. Baumeister,
Max Planck Institute of Biochemistry, Germany
Structure of the 26S Proteasome Holocomplex Determined by an Integrative Approach
Structure of the 26S Proteasome Holocomplex Determined by an Integrative Approach
08:00—11:15
Single Molecule Methods
Meeting has ended...abstracts no longer viewable online. Purchase an Abstract Book from this meeting
NOTE: This session will focus on computational and experimental methods for studying single molecules, to localize them in the cell, position them with respect to other structures in the cell, and in particular to describe their dynamics. The methods will be illustrated by their application to specific biological systems.
*
Eva Nogales,
University of California Berkeley, USA
Stefan W. Hell,
Max Planck Institute for Biophysical Chemistry, Germany
Nanoscopy with Focused Light
Nanoscopy with Focused Light
Joseph D. Puglisi,
Stanford University, USA
Hybrid Studies of the Ribosome Function
Hybrid Studies of the Ribosome Function
Scott C. Blanchard,
Weill Cornell Medical College, USA
Allosteric Control of the Ribosome by Small-Molecule Antibiotics
Allosteric Control of the Ribosome by Small-Molecule Antibiotics
Yujie Sun,
Biodynamic Optical Imaging Center, China
Allostery Revisited
Allostery Revisited
Alexander Leitner,
ETH Zurich, Switzerland
Short Talk: Generating Spatial Restraints with an Integrated Chemical Cross-Linking-Mass Spectrometry Platform and their Use in Hybrid Methods
Short Talk: Generating Spatial Restraints with an Integrated Chemical Cross-Linking-Mass Spectrometry Platform and their Use in Hybrid Methods
Robin E. Stanley,
NIDDK, National Institutes of Health, USA
Short Talk: Architecture of the Atg17 Complex as a Scaffold for Autophagosome Biogenesis
Short Talk: Architecture of the Atg17 Complex as a Scaffold for Autophagosome Biogenesis
14:30—16:30
Workshop: Software for Integrative Structure Determination
NOTE: This workshop will include brief tutorials of software packages useful in building hybrid models. The functionality and scope of the packages will be outlined.
*
Klaus J. Schulten,
University of Illinois at Urbana-Champaign, USA
Yifan Song,
University of Washington, USA
High-Resolution Comparative Modeling with RosettaCM
High-Resolution Comparative Modeling with RosettaCM
Robert Paul Rambo,
Lawrence Berkeley National Laboratory, USA
SAXS Suite at LBNL
SAXS Suite at LBNL
Daniel Russel,
University of California, San Francisco, USA
IMP
IMP
17:00—19:00
Latest Advances in Hybrid Methods
Meeting has ended...abstracts no longer viewable online. Purchase an Abstract Book from this meeting
NOTE: This session will present recent methodological advances in hybrid approaches as well as in individual methods for structure and dynamics characterization that can be incorporated into hybrid approaches.
*
Brian T. Chait,
Rockefeller University, USA
Mass Spectrometry and Proteomics for Hybrid Structure Determination
Mass Spectrometry and Proteomics for Hybrid Structure Determination
Carolyn A. Larabell,
University of California, San Francisco, USA
Correlated Fluorescence and X-Ray Tomography of Intact Cells
Correlated Fluorescence and X-Ray Tomography of Intact Cells
Yifan Cheng,
University of California, San Francisco, USA
Short Talk: A New Electron Counting CMOS Camera Enables Routine Near Atomic Resolution Single Particle cryoEM
Short Talk: A New Electron Counting CMOS Camera Enables Routine Near Atomic Resolution Single Particle cryoEM
Michael Nilges,
Institut Pasteur, France
Inferential Structure Determination from Hybrid Data
Inferential Structure Determination from Hybrid Data
19:00—19:15
Closing Remarks
Meeting has ended...abstracts no longer viewable online. Purchase an Abstract Book from this meeting
Andrej Sali,
University of California, San Francisco, USA
David Baker,
University of Washington, USA
Brian T. Chait,
Rockefeller University, USA
*Session Chair †Speaker invited, not yet responded.
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