eCheminfo InterAction Meeting Session, Philadelphia, 12 October 2005 (proceedings available through website)
Membranes & Ion Channels
co-chaired by Richard Pastor (FDA) and Michael Klein (University of Pennsylvania)
eCheminfo 2005 InterAction Meeting, 11-12 October 2005, Philadelphia, USA
Presenters & Discussion Leaders:
Exploring Rhodopsin Activation with Large Scale Molecular Dynamics, Mike Pitman (IBM)
Structure of Lipid Membranes and Improving the Head Group Force Field, Jeff Klauda (NIH)
Understanding membrane transport at full atomic resolution - Molecular dynamics simulations of lipid bilayers and membrane channels, Emad Tajkhorshid (Beckman Institute, University of Illinois at Urbana-Champaign)
Response of Lipid Bilayers and Monolayers to Trehalose: Molecular Dynamics in Constant Area and Surface Tension Ensembles, Richard Pastor (FDA)
Molecular Dynamics Simulations of Oligomeric Ion Channels within Lipid Bilayers, Preston Moore (USIP)
The five talks presented in this session span essential methodology on simple bilayers to forefront applications on complex membranes. Beginning with the simplest, Jeffrey Klauda (NIH) will describe developments in the CHARMM forcefield for lipid headgroups. The approach consists of high level ab initio quantum mechanical calculations on model compounds followed by molecular dynamics (MD) simulations of fully hydrated bilayers. Dr. Klauda will also present a simulation-based structural model for analyzing X-ray diffraction. The new model enables the direct determination of the elusive surface area per lipid from experiment. Richard Pastor (FDA) will present results from constant surface area and constant surface tension simulation of lipid bilayers and monolayers in the presence of trehalose, an important cell preservative. Comparison of monolayer pressure-area isotherms and bilayer elastic moduli with experiment provide a important validation of the CHARMM force field and lend insight into the action of trehalose. Building on his groundbreaking work on the water channel aquaporin, Emad Tajkhorshid (U. of Illinois at Urbana-Champaign) will describe recent simulations on related channels for transport of alcohols, oxygen and carbon dioxide. Michael Pitman (IBM) will describe remarkably long simulations on bilayers with rhodopsin made possible by the IBM Blue-Gene computer. Some membrane systems are too large to be simulated at the detailed all-atom level at present. Preston Moore (U of the Sciences in Philadelphia) will describe simulations of assembly of oligomeric ion channels using a coarse grained model.
Posters
All registrants and members are eligible to submit a Conference Poster. Attendees may view and discuss the Posters and leave messages for the authors on the Web site.
Poster Abstracts (of ca. 300 words) with Title, Institution, Authors and Contact Information should be submitted for consideration to echeminfo at douglasconnect.com Posters can be presented as HTML, pdf, Powerpoint or Word documents.
Existing invited seminars on membranes and ion channels currently available on eCheminfo:
Simulation of Nucleic Acid Transport Through Carbon Nanotube Membranes,
Gerhard Hummer (National Institutes of Health)
Emerging approaches to computation of peptide folding, electrified interfaces and drug binding for biomembrane systems, Tom Woolf (Johns Hopkins University, School of Medicine)
The Search for Trehalose's Function in Lipid Bilayers, Anna Skibinsky (Center for Biologics Evaluation & Research, FDA)
Structure, Function, Self-assembly and Origin of Simple Membrane Proteins, Andrew Pohorill (NASA Ames Research Center)
Complexes Between Lipids in Bilayers, Max Berkowitz (UNC)
Understanding the Unique Properties of Polyunsaturated Lipids, Scott Feller (Wabash College)
Computational Studies of Permeation and Selectivity of Membrane Channels, Emad Tajkhorshid (Beckman Institute, University of Illinois at Urbana-Champaign)
Membrane Simulation: Parameterisation and Application, Indira Chandrasekhar (Swiss Federal Institute of Technology Zurich)
