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

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

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)363-374
Number of pages12
JournalJournal of Computer-Aided Molecular Design
Volume26
Issue number3
DOIs
Publication statusPublished - 2012 Mar 1

Keywords

  • Helix bundle membrane proteins
  • Molecular dynamics simulations
  • Monte-Carlo simulations
  • Structure prediction

ASJC Scopus subject areas

  • Drug Discovery
  • Computer Science Applications
  • Physical and Theoretical Chemistry

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