Three-dimensional stress field around a membrane protein: atomistic and coarse-grained simulation analysis of gramicidin A.

ABSTRACT: Using both atomistic and coarse-grained (CG) models, we compute the three-dimensional stress field around a gramicidin A (gA) dimer in lipid bilayers that feature different degrees of negative hydrophobic mismatch. The general trends in the computed stress field are similar at the atomistic and CG levels, supporting the use of the CG model for analyzing the mechanical features of protein/lipid/water interfaces. The calculations reveal that the stress field near the protein-lipid interface exhibits a layered structure with both significant repulsive and attractive regions, with the magnitude of the stress reaching 1000 bar in certain regions. Analysis of density profiles and stress field distributions helps highlight the Trp residues at the protein/membrane/water interface as mechanical anc

SUBMITTER: Yoo J 

PROVIDER: S-EPMC3540266 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature