Structure refinement of membrane proteins via molecular dynamics simulations.

ABSTRACT: A refinement protocol based on physics-based techniques established for water soluble proteins is tested for membrane protein structures. Initial structures were generated by homology modeling and sampled via molecular dynamics simulations in explicit lipid bilayer and aqueous solvent systems. Snapshots from the simulations were selected based on scoring with either knowledge-based or implicit membrane-based scoring functions and averaged to obtain refined models. The protocol resulted in consistent and significant refinement of the membrane protein structures similar to the performance of refinement methods for soluble proteins. Refinement success was similar between sampling in the presence of lipid bilayers and aqueous solvent but the presence of lipid bilayers may benefit the improveme

SUBMITTER: Dutagaci B 

PROVIDER: S-EPMC6013386 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature