Coarse-grained simulation: a high-throughput computational approach to membrane proteins.
An understanding of the interactions of membrane proteins with a lipid bilayer environment is central to relating their structure to their function and stability. A high-throughput approach to prediction of membrane protein interactions with a lipid bilayer based on coarse-grained Molecular Dynamics simulations is described. This method has been used to develop a database of CG simulations (coarse-grained simulations) of membrane proteins (http://sbcb.bioch.ox.ac.uk/cgdb). Comparison of CG simulations and AT simulations (atomistic simulations) of lactose permease reveals good agreement between the two methods in terms of predicted lipid headgroup contacts. Both CG and AT simulations predict considerable local bilayer deformation by the voltage sensor domain of the potassium channel KvAP.
Sansom
Mark S P
MS
Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K. mark.sansom@bioch.ox.ac.uk
Scott
Kathryn A
KA
Bond
Peter J
PJ
D003198:Computer Simulation; D008051:Lipid Bilayers / Q000737:chemistry; D008565:Membrane Proteins / Q000737:chemistry*; D026901:Membrane Transport Proteins / Q000737:chemistry; D008958:Models, Molecular; D015221:Potassium Channels / Q000737:chemistry
D008051:Lipid Bilayers; D008565:Membrane Proteins; D026901:Membrane Transport Proteins; D015221:Potassium Channels; C021499:lactose permease