2003/09/14 by Hironori Kokubo, Yuko Okamoto · 27 citations
Biochemistry, Genetics and Molecular Biology · Chemistry · Mathematics · Physics and Astronomy · #Amino acid #Biochemistry #Biological system #Biology #Chemistry #Computer science #Crystallography #Domain (mathematical analysis) #Glycophorin #Helix (gastropod) #Lipid Membrane Structure and Behavior #Mathematics #Membrane #Physics #Protein Structure and Dynamics #Protein structure #Protein structure prediction #RNA and protein synthesis mechanisms #Replica #Statistical physics #Transmembrane domain #Transmembrane protein #cond-mat.stat-mech #q-bio.BM
paper · pdf · doi:10.1016/j.cplett.2003.10.153
published in Chemical Physics Letters 383(3-4), 397-402 (Elsevier BV) · 12 pages, 4 figures, (LaTeX)
arxiv created 2003/09/14 · openalex publication_date 2003/12/09 · arxiv updated 2009/12/01 · openalex created_date 2016/06/24 · openalex updated_date 2026/08/05
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.