Literature DB >> 15519314

Computer simulations of membrane proteins.

Walter L Ash1, Marian R Zlomislic, Eliud O Oloo, D Peter Tieleman.   

Abstract

Computer simulations are rapidly becoming a standard tool to study the structure and dynamics of lipids and membrane proteins. Increasing computer capacity allows unbiased simulations of lipid and membrane-active peptides. With the increasing number of high-resolution structures of membrane proteins, which also enables homology modelling of more structures, a wide range of membrane proteins can now be simulated over time spans that capture essential biological processes. Longer time scales are accessible by special computational methods. We review recent progress in simulations of membrane proteins.

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Year:  2004        PMID: 15519314     DOI: 10.1016/j.bbamem.2004.04.012

Source DB:  PubMed          Journal:  Biochim Biophys Acta        ISSN: 0006-3002


  64 in total

1.  Transportation behavior of alkali ions through a cell membrane ion channel. A quantum chemical description of a simplified isolated model.

Authors:  Ferenc Billes; Ildikó Mohammed-Ziegler; Hans Mikosch
Journal:  J Mol Model       Date:  2012-02-22       Impact factor: 1.810

Review 2.  Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes.

Authors:  Jamie Parkin; Matthieu Chavent; Syma Khalid
Journal:  Biophys J       Date:  2015-08-04       Impact factor: 4.033

3.  Interfacial tryptophan residues: a role for the cation-pi effect?

Authors:  Frederic N R Petersen; Morten Ø Jensen; Claus H Nielsen
Journal:  Biophys J       Date:  2005-09-08       Impact factor: 4.033

4.  Spontaneous formation of detergent micelles around the outer membrane protein OmpX.

Authors:  Rainer A Böckmann; Amedeo Caflisch
Journal:  Biophys J       Date:  2005-03-04       Impact factor: 4.033

5.  Test of molecular dynamics force fields in gramicidin A.

Authors:  Turgut Bastug; Serdar Kuyucak
Journal:  Eur Biophys J       Date:  2005-02-12       Impact factor: 1.733

6.  Conformation and environment of channel-forming peptides: a simulation study.

Authors:  Jennifer M Johnston; Gabriel A Cook; John M Tomich; Mark S P Sansom
Journal:  Biophys J       Date:  2005-12-30       Impact factor: 4.033

7.  Ion transport through membrane-spanning nanopores studied by molecular dynamics simulations and continuum electrostatics calculations.

Authors:  Christine Peter; Gerhard Hummer
Journal:  Biophys J       Date:  2005-07-08       Impact factor: 4.033

8.  Membrane protein dynamics and detergent interactions within a crystal: a simulation study of OmpA.

Authors:  Peter J Bond; José D Faraldo-Gómez; Sundeep S Deol; Mark S P Sansom
Journal:  Proc Natl Acad Sci U S A       Date:  2006-06-09       Impact factor: 11.205

9.  Interaction between K+ channel gate modifier hanatoxin and lipid bilayer membranes analyzed by molecular dynamics simulation.

Authors:  Manami Nishizawa; Kazuhisa Nishizawa
Journal:  Eur Biophys J       Date:  2006-02-02       Impact factor: 1.733

10.  Conserved methionine dictates substrate preference in Nramp-family divalent metal transporters.

Authors:  Aaron T Bozzi; Lukas B Bane; Wilhelm A Weihofen; Anne L McCabe; Abhishek Singharoy; Christophe J Chipot; Klaus Schulten; Rachelle Gaudet
Journal:  Proc Natl Acad Sci U S A       Date:  2016-08-29       Impact factor: 11.205

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