Abstract
Molecular dynamics simulations were performed to understand the interactions of synthetic coiled-coil peptides (the shorter versions of SNARE proteins, called “E” and “K”) with lipid bilayers composed of DOPC, DOPE, and cholesterol at different molar ratios. Potentials of mean force (PMF) were calculated using the umbrella sampling method, showing the effect of the lipid type on the binding strength between peptides and bilayers. To understand the configurations and insertion of peptides into bilayer, we analyzed the helicity and tilt angles of peptides, the distance between peptide and bilayer, lateral diffusivity of lipids, and electrostatic and hydrophobic interactions between peptides and lipids, showing that K peptides retain their helicity and more deeply insert into the bilayer than do E peptides, which helps explain the experimentally proposed “the snorkeling effect”.
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