Prediction of transmembrane helix configurations by replica-exchange simulations

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 second part of the method with the dimeric transmembrane domain of glycophorin A. The structure obtained from the prediction was in close agreement with the experimental data. (C) 2003 Elsevier B.V. All rights reserved.