Home LiteratureArticle Details
PMID: 22463457 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

Transmembrane helix assembly by window exchange umbrella sampling.

Physical review letters ·Vol. 108 ·No. 10 ·2012-03-09 ·Pages 108102

Park S, Kim T, Im W

Abstract

A method of window exchange umbrella sampling molecular dynamics simulation is employed for transmembrane helix assembly. An analytical expression for the average acceptance probability between neighboring windows is derived and combined with the first passage time optimization method to predetermine a parameter set in an optimal range. With the parameter set, the method provides a substantially more efficient sampling of helix-helix interfaces together with the potential of mean force along the helix-helix distance of a transmembrane helix-dimer model, compared to the umbrella sampling method.

MeSH Terms
Amino Acid Sequence Cell Membrane/chemistry Computer Simulation Dimyristoylphosphatidylcholine/chemistry Hydrophobic and Hydrophilic Interactions Lipid Bilayers/chemistry Membrane Potentials Membrane Proteins/chemistry Models, Chemical Molecular Sequence Data Protein Structure, Secondary
Chemicals
Lipid Bilayers Membrane Proteins Dimyristoylphosphatidylcholine
Authors & Affiliations
3 authors, click to expand affiliations / ORCID
Park Soohyung
Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, 2030 Becker Drive, Lawrence, Kansas 66047, USA.
Kim Taehoon
Im Wonpil
References (21)
21 references, click to expand
  1. Efficient, multiple-range random walk algorithm to calculate the density of states.
    Phys Rev Lett. 2001 Mar 5;86(10):2050-3 PMID: 11289852
  2. Interhelical hydrogen bonding drives strong interactions in membrane proteins.
    Nat Struct Biol. 2000 Feb;7(2):154-60 PMID: 10655619
  3. Novel free energy calculations to explore mechanisms and energetics of membrane protein structure and function.
    J Comput Chem. 2009 Aug;30(11):1622-33 PMID: 19496166
  4. In silico screening of mutational effects on transmembrane helix dimerization: insights from rigid-body docking and molecular dynamics simulations.
    J Phys Chem B. 2007 Aug 2;111(30):9114-24 PMID: 17602582
  5. Implementation and application of helix-helix distance and crossing angle restraint potentials.
    J Comput Chem. 2007 Feb;28(3):669-80 PMID: 17195157
  6. Helix to helix packing in proteins.
    J Mol Biol. 1981 Jan 5;145(1):215-50 PMID: 7265198
  7. MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.
    J Mol Graph Model. 2004 May;22(5):377-95 PMID: 15099834
  8. Optimized explicit-solvent replica exchange molecular dynamics from scratch.
    J Phys Chem B. 2008 Aug 28;112(34):10386-7 PMID: 18671362
  9. Asparagine-mediated self-association of a model transmembrane helix.
    Nat Struct Biol. 2000 Feb;7(2):161-6 PMID: 10655620
  10. Role of hydrogen bonding and helix-lipid interactions in transmembrane helix association.
    J Am Chem Soc. 2008 May 21;130(20):6456-62 PMID: 18422318
  11. Transmembrane helix tilting: insights from calculating the potential of mean force.
    Phys Rev Lett. 2008 Jan 11;100(1):018103 PMID: 18232823
  12. Overcoming barriers to membrane protein structure determination.
    Nat Biotechnol. 2011 Apr;29(4):335-40 PMID: 21478852
  13. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil.
    Science. 1991 Oct 25;254(5031):539-44 PMID: 1948029
  14. Equilibrium sampling in biomolecular simulations.
    Annu Rev Biophys. 2011;40:41-62 PMID: 21370970
  15. Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems.
    Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20227-32 PMID: 19075242
  16. Effective energy function for proteins in lipid membranes.
    Proteins. 2003 Aug 1;52(2):176-92 PMID: 12833542
  17. Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin.
    BMC Biol. 2009 Aug 13;7:50 PMID: 19678920
  18. Generalized ensemble and tempering simulations: a unified view.
    Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Feb;75(2 Pt 2):026109 PMID: 17358396
  19. CHARMM: the biomolecular simulation program.
    J Comput Chem. 2009 Jul 30;30(10):1545-614 PMID: 19444816
  20. Replica Monte Carlo simulation of spin glasses.
    Phys Rev Lett. 1986 Nov 24;57(21):2607-2609 PMID: 10033814
  21. Insights into the recognition and association of transmembrane alpha-helices. The free energy of alpha-helix dimerization in glycophorin A.
    J Am Chem Soc. 2005 Jun 15;127(23):8478-84 PMID: 15941282
Article Info
Journal
Physical review letters
Abbr.
Phys Rev Lett
ISSN
1079-7114
DOI
10.1103/PhysRevLett.108.108102
Published
2012-03-09
Epub
2012-00-08
Pages
108102
Language
English
Region
United States
NLM ID
0401141
PMCID
PMC3657132
Subset
IM
Grants
NIGMS NIH HHS · R01 GM092950 · United States
NIGMS NIH HHS · R01-GM092950 · United States
External Links
PubMed source DOI: 10.1103/PhysRevLett.108.108102 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2