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Coarse‐Grain Simulations of the R‐SNARE Fusion Protein in its Membrane Environment Detect Long‐Lived Conformational Sub‐States
Author(s) -
Durrieu MariePierre,
Bond Peter J.,
Sansom Mark S. P.,
Lavery Richard,
Baaden Marc
Publication year - 2009
Publication title -
chemphyschem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.016
H-Index - 140
eISSN - 1439-7641
pISSN - 1439-4235
DOI - 10.1002/cphc.200900216
Subject(s) - lipid bilayer fusion , snare complex , context (archaeology) , biophysics , lipid bilayer , microsecond , bilayer , fusion , chemistry , molecular dynamics , membrane , crystallography , chemical physics , biological system , physics , biology , biochemistry , computational chemistry , optics , paleontology , linguistics , philosophy
The detected conformational sub‐states of an R‐SNARE peptide inserted in a lipid bilayer (see figure) give insights into the membrane fusion mechanism. The simulations are in agreement with most experimental data on the SNARE system, but differ in some details that may have a functional interest. Comparing rat and yeast sequences shows some minor differences in their behaviour.Coarse‐grain molecular dynamics are used to look at conformational and dynamic aspects of an R‐SNARE peptide inserted in a lipid bilayer. This approach allows carrying out microsecond‐scale simulations which bring to light long‐lived conformational sub‐states potentially interesting in the context of the membrane fusion mechanism mediated by the SNARE proteins. We show that these coarse‐grain models are in agreement with most experimental data on the SNARE system, but differ in some details that may have a functional interest, most notably in the orientation of the soluble part of R‐SNARE that does not appear to be spontaneously accessible for SNARE complex formation. We also compare rat and yeast sequences of R‐SNARE and find some minor differences in their behavior.