arXiv subjects

Hironori Kokubo

Publications and source records attributed to Hironori Kokubo.

2 recordsLinked to original sources

arXiv2014

Predictions of tertiary stuctures of $α$-helical membrane proteins by replica-exchange method with consideration of helix deformations

We propose an improved prediction method of the tertiary structures of $α$-helical membrane proteins based on the replica-exchange method by taking into account helix deformations. Our method allows wide applications because transmembrane helices of native membrane proteins are often distorted. In order to test the effectiveness of the present method, we applied it to the structure predictions of glycophorin A and phospholamban. The results were in accord with experiments.

q-bio.BM↗

arXiv2003

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 method with the dimeric transmembrane domain of glycophorin A. The structure obtained from the prediction was in close agreement with the experimental data.

cond-mat.stat-mech↗