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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.

Original publication

DOI

10.1002/cphc.200900216

Type

Journal article

Journal

Chemphyschem

Publication Date

13/07/2009

Volume

10

Pages

1548 - 1552

Keywords

Amino Acid Sequence, Animals, Cell Membrane, Lipid Bilayers, Molecular Sequence Data, Protein Conformation, Rats, Recombinant Fusion Proteins, SNARE Proteins