Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations.

ABSTRACT: The assembly of simple transmembrane helix homo-oligomers is studied by combining a generalized Born implicit membrane model with replica exchange molecular dynamics simulations to sample the conformational space of various oligomerization states and the native oligomeric conformation. Our approach is applied to predict the structures of transmembrane helices of three proteins--glycophorin A, the M2 proton channel, and phospholamban--using only peptide sequence and the native oligomerization state information. In every case, the methodology reproduces native conformations that are in good agreement with available experimental structural data. Thus, our method should be useful in the prediction of native structures of transmembrane domains of other peptides. When we ignore the experimental

SUBMITTER: Bu L 

PROVIDER: S-EPMC1779983 | biostudies-literature | 2007 Feb

REPOSITORIES: biostudies-literature