Replica exchange Monte-Carlo simulations of helix bundle membrane proteins: Rotational parameters of helices

H. H. Wu, C. C. Chen, C. M. Chen*

*此作品的通信作者

研究成果: 雜誌貢獻期刊論文同行評審

6 引文 斯高帕斯(Scopus)

摘要

We propose a united-residue model of membrane proteins to investigate the structures of helix bundle membrane proteins (HBMPs) using coarse-grained (CG) replica exchange Monte-Carlo (REMC) simulations. To demonstrate the method, it is used to identify the ground state of HBMPs in a CG model, including bacteriorhodopsin (BR), halorhodopsin (HR), and their subdomains. The rotational parameters of transmembrane helices (TMHs) are extracted directly from the simulations, which can be compared with their experimental measurements from site-directed dichroism. In particular, the effects of amphiphilic interaction among the surfaces of TMHs on the rotational angles of helices are discussed. The proposed CG model gives a reasonably good structure prediction of HBMPs, as well as a clear physical picture for the packing, tilting, orientation, and rotation of TMHs. The root mean square deviation (RMSD) in coordinates of C a atoms of the ground state CG structure from the X-ray structure is 5.03 Å for BR and 6.70 Å for HR. The final structure of HBMPs is obtained from the all-atom molecular dynamics simulations by refining the predicted CG structure, whose RMSD is 4.38 Å for BR and 5.70 Å for HR.

原文英語
頁(從 - 到)363-374
頁數12
期刊Journal of Computer-Aided Molecular Design
26
發行號3
DOIs
出版狀態已發佈 - 2012 三月 1

ASJC Scopus subject areas

  • 藥物發現
  • 電腦科學應用
  • 物理與理論化學

指紋

深入研究「Replica exchange Monte-Carlo simulations of helix bundle membrane proteins: Rotational parameters of helices」主題。共同形成了獨特的指紋。

引用此