Coarse-grain simulations of the R-SNARE fusion protein in its membrane environment detect long-lived conformational sub-states.
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.
Durrieu
Marie-Pierre
MP
Institut de Biologie Physico-Chimique, Laboratoire de Biochimie Théorique, CNRS UPR 9080, 13, rue Pierre et Marie Curie, F-75005 Paris, France.
Bond
Peter J
PJ
Sansom
Mark S P
MS
Lavery
Richard
R
Baaden
Marc
M
D000595:Amino Acid Sequence; D000818:Animals; D002462:Cell Membrane / Q000737:chemistry* / Q000378:metabolism; D008051:Lipid Bilayers / Q000737:chemistry / Q000378:metabolism; D008969:Molecular Sequence Data; D011487:Protein Conformation; D051381:Rats; D011993:Recombinant Fusion Proteins / Q000737:chemistry / Q000378:metabolism; D050600:SNARE Proteins / Q000737:chemistry* / Q000378:metabolism
D008051:Lipid Bilayers; D011993:Recombinant Fusion Proteins; D050600:SNARE Proteins