BioSimGRID: Application to Analysis of Membrane Protein Simulations
Topic:  8E Molecular Dynamics ;  1H Membrane Proteins
Presentation Time: Tuesday, 4:45 p.m.
Mark S. P. Sansom, D.Phil.¹, Kaihsu Tai, PhD¹, Bing Wu, PhD¹, Syma Khalid, PhD¹, Marc Baaden, PhD².
¹University of Oxford, Oxford, United Kingdom, ²Institut de Biologie Physico-Chimique, Paris, France.
Presentation Number: 1877.01-Plat
BioSimGRID (www.biosimgrid.org) is a prototype distributed database for storage, interrogation, and analysis of MD simulation data. In this presentation, we describe the use of BioSimGRID to facilitate comparative analyses of membrane protein simulations. Comparative analyses of MD simulation data provide a valuable tool for assessment of the significance of MD simulation results, and to explore possible conserved patterns of dynamic behaviour shared by related proteins. Two areas of application to membrane proteins will be discussed. The first is a comparison of two distantly related enzymes. Outer-membrane phospholipase A (OMPLA) is a bacterial outer membrane enzyme involved in pathogenesis. Structural data show that it has a similar active site to that of acetylcholinesterase (AChE), a key enzyme in the nervous system. The structures of the two proteins are otherwise unrelated. Simulation trajectories of these two distantly related enzymes have been deposited in BioSimGrid. These trajectories were generated in different laboratories and using different simulation codes. The simulations are being analysed to compare the dynamics the active site sidechains of OMPLA and of AChE. It is hoped that this will provide insights into the relationship between sidechain dynamics and catalytic mechanism. The second application which will be discussed is the use of BioSimGRID to provide a database of simulations of bacterial outer membrane proteins, including OmpA and its homologues. Comparative analyses will focus on aspects of lipid-protein interactions revealed by such simulations.