A Membrane Burial Potential with H-Bonds and Applications to Curved Membranes and Fast Simulations.

ABSTRACT: We use the statistics of a large and curated training set of transmembrane helical proteins to develop a knowledge-based potential that accounts for the dependence on both the depth of burial of the protein in the membrane and the degree of side-chain exposure. Additionally, the statistical potential includes depth-dependent energies for unsatisfied backbone hydrogen bond donors and acceptors, which are found to be relatively small, ∼2 RT. Our potential accurately places known proteins within the bilayer. The potential is applied to the mechanosensing MscL channel in membranes of varying thickness and curvature, as well as to the prediction of protein structure. The potential is incorporated into our new Upside molecular dynamics algorithm. Notably, we account for the exchange of protein-l

SUBMITTER: Wang Z 

PROVIDER: S-EPMC6303381 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature