Computer simulations of membrane proteins

被引：196

作者：

Ash, WL ^{[1
]}

Zlomislic, MR ^{[1
]}

Oloo, EO ^{[1
]}

Tieleman, DP ^{[1
]}

机构：

[1] Univ Calgary, Dept Biol Sci, Calgary, AB T2N 1N4, Canada

来源：

BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES | 2004年 / 1666卷 / 1-2期

基金：

加拿大健康研究院;

关键词：

molecular dynamics simulation; ion channel; helix-helix interaction; antimicrobial peptide; bilayer structure; outer membrane protein; aquaporin;

D O I：

10.1016/j.bbamem.2004.04.012

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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 highresolution 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. (C) 2004 Elsevier B.V. All rights reserved.

引用

页码：158 / 189

页数：32

共 335 条

[1] STRUCTURE AT 2.8-ANGSTROM RESOLUTION OF F1-ATPASE FROM BOVINE HEART-MITOCHONDRIA [J].

ABRAHAMS, JP ;

LESLIE, AGW ;

LUTTER, R ;

WALKER, JE .

NATURE, 1994, 370 (6491) :621-628

[2]

Adams PD, 1996, PROTEINS, V26, P257, DOI 10.1002/(SICI)1097-0134(199611)26:3<257::AID-PROT2>3.3.CO

[3]

2-O

[4] Insights into the molecular mechanism of rotation in the Fo sector of ATP synthase [J].

Aksimentiev, A ;

Balabin, IA ;

Fillingame, RH ;

Schulten, K .

BIOPHYSICAL JOURNAL, 2004, 86 (03) :1332-1344

[5] Structural studies on rhodopsin [J].

Albert, AD ;

Yeagle, PL .

BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 2002, 1565 (02) :183-195

[6] Molecular dynamics simulations of pentapeptides at interfaces:: Salt bridge and cation-π interactions [J].

Aliste, MP ;

MacCallum, JL ;

Tieleman, DP .

BIOCHEMISTRY, 2003, 42 (30) :8976-8987

[7] Energetics of ion conduction through the gramicidin channel [J].

Allen, TW ;

Andersen, OS ;

Roux, B .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (01) :117-122

[8] Structure of gramicidin A in a lipid bilayer environment determined using molecular dynamics simulations and solid-state NMR data [J].

Allen, TW ;

Andersen, OS ;

Roux, B .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2003, 125 (32) :9868-9877

[9] Gramicidin A channel as a test ground for molecular dynamics force fields [J].

Allen, TW ;

Bastug, T ;

Kuyucak, S ;

Chung, SH .

BIOPHYSICAL JOURNAL, 2003, 84 (04) :2159-2168

[10] Methodological issues in lipid bilayer simulations [J].

Anézo, C ;

de Vries, AH ;

Höltje, HD ;

Tieleman, DP ;

Marrink, SJ .

JOURNAL OF PHYSICAL CHEMISTRY B, 2003, 107 (35) :9424-9433

← 1 2 3 4 5 6 7 8 9 10 →