ArticleJournal of computer-aided molecular design2012
Replica exchange Monte-Carlo simulations of helix bundle membrane proteins: rotational parameters of helices.
Article in Journal of computer-aided molecular design, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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Who cites it
3 citing papers in PubMed.
- Exploring conformational states and helical packings in the P2X receptor transmembrane domain by molecular dynamics simulation.Journal of biological physics · 2018Article
- Computational prediction of kink properties of helices in membrane proteins.Journal of computer-aided molecular design · 2014Article
- Statistical analyses and computational prediction of helical kinks in membrane proteins.Journal of computer-aided molecular design · 2012Article
Corrections and comments
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Authors and funding
3 authors.
Funding
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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(α) 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.
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Registered trials
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