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.
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February 2008
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Conference Article|
January 22 2008
Coarse-grained simulation: a high-throughput computational approach to membrane proteins
Mark S.P. Sansom;
Mark S.P. Sansom
1
1Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
1To whom correspondence should be addressed (email mark.sansom@bioch.ox.ac.uk).
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Kathryn A. Scott;
Kathryn A. Scott
2
1Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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Peter J. Bond
Peter J. Bond
1Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K.
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Publisher: Portland Press Ltd
Received:
August 28 2007
Online ISSN: 1470-8752
Print ISSN: 0300-5127
© The Authors Journal compilation © 2008 Biochemical Society
2008
Biochem Soc Trans (2008) 36 (1): 27–32.
Article history
Received:
August 28 2007
Citation
Mark S.P. Sansom, Kathryn A. Scott, Peter J. Bond; Coarse-grained simulation: a high-throughput computational approach to membrane proteins. Biochem Soc Trans 1 February 2008; 36 (1): 27–32. doi: https://doi.org/10.1042/BST0360027
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