Prediction of transmembrane helix configurations by replica-exchange simulations
Statistical Mechanics
2009-11-10 v1 Biomolecules
Abstract
We propose a method for predicting helical membrane protein structures by computer simulations. Our method consists of two parts. In the first part, amino-acid sequences of the transmembrane helix regions are obtained from one of existing WWW servers. In the second part, we perform a replica-exchange simulation of these transmembrane helices with some constraints and identify the predicted structure as the global-minimum-energy state. We have tested the method with the dimeric transmembrane domain of glycophorin A. The structure obtained from the prediction was in close agreement with the experimental data.
Keywords
Cite
@article{arxiv.cond-mat/0309338,
title = {Prediction of transmembrane helix configurations by replica-exchange simulations},
author = {Hironori Kokubo and Yuko Okamoto},
journal= {arXiv preprint arXiv:cond-mat/0309338},
year = {2009}
}
Comments
12 pages, 4 figures, (LaTeX)