Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles

被引：81

作者：

Bryn Fenwick, R. ^{[1
]}

Esteban-Martin, Santi ^{[1
]}

Salvatella, Xavier ^{[1
,2
]}

机构：

[1] IRB Barcelona, Inst Biomed Res, Joint BSC IRB Res Programme Computat Biol, Barcelona 08028, Spain

[2] ICREA, Barcelona, Spain

来源：

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS | 2011年 / 40卷 / 12期

关键词：

Dynamic ensembles; NMR; Conformational selection; Induced fit; Allostery; MOLECULAR-DYNAMICS SIMULATIONS; RESIDUAL DIPOLAR COUPLINGS; NUCLEAR-MAGNETIC-RESONANCE; SMALL ALPHA/BETA PROTEIN; LONG-RANGE ORDER; INDUCED-FIT; ADENYLATE KINASE; CORRELATED MOTIONS; SCALAR COUPLINGS; BACTERIOPHAGE-T4; LYSOZYME;

D O I：

10.1007/s00249-011-0754-8

中图分类号：

Q6 [生物物理学];

学科分类号：

071011 ;

摘要：

We review the role conformational ensembles can play in the analysis of biomolecular dynamics, molecular recognition, and allostery. We introduce currently available methods for generating ensembles of biomolecules and illustrate their application with relevant examples from the literature. We show how, for binding, conformational ensembles provide a way of distinguishing the competing models of induced fit and conformational selection. For allostery we review the classic models and show how conformational ensembles can play a role in unravelling the intricate pathways of communication that enable allostery to occur. Finally, we discuss the limitations of conformational ensembles and highlight some potential applications for the future.

引用

页码：1339 / 1355

页数：17

共 146 条

[1] Network of coupled promoting motions in enzyme catalysis [J].

Agarwal, PK ;

Billeter, SR ;

Rajagopalan, PTR ;

Benkovic, SJ ;

Hammes-Schiffer, S .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (05) :2794-2799

[2] Molecular Dynamics Simulations Show That Conformational Selection Governs the Binding Preferences of Imatinib for Several Tyrosine Kinases [J].

Aleksandrov, Alexey ;

Simonson, Thomas .

JOURNAL OF BIOLOGICAL CHEMISTRY, 2010, 285 (18) :13807-13815

[3] CARBON-13 FOURIER TRANFORM NUCLEAR MAGNETIC RESONANCE .3. CONFORMATION AND SEGMENTAL MOTION OF NATIVE AND DENATURED RIBONUCLEASE-A IN SOLUTION - APPLICATION OF NATURAL-ABUNDANCE CARBON-13 PARTIALLY RELAXED FOURIER TRANSFORM NUCLEAR MAGNETIC RESONANCE [J].

ALLERHAN.A ;

DODDRELL, D ;

GLUSHKO, U ;

COCHRAN, DW ;

WENKERT, E ;

LAWSON, PJ ;

GURD, FRN .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1971, 93 (02) :544-+

[4] A Method to Explore Protein Side Chain Conformational Variability Using Experimental Data [J].

Allison, Jane R. ;

van Gunsteren, Wilfred F. .

CHEMPHYSCHEM, 2009, 10 (18) :3213-3228

[5] Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism [J].

Arora, Karunesh ;

Brooks, Charles L., III .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (47) :18496-18501

[6] Global Dynamics of Proteins: Bridging Between Structure and Function [J].

Bahar, Ivet ;

Lezon, Timothy R. ;

Yang, Lee-Wei ;

Eyal, Eran .

ANNUAL REVIEW OF BIOPHYSICS, VOL 39, 2010, 39 :23-42

[7] Zipping and Unzipping of Adenylate Kinase: Atomistic Insights into the Ensemble of Open ⇆ Closed Transitions [J].

Beckstein, Oliver ;

Denning, Elizabeth J. ;

Perilla, Juan R. ;

Woolf, Thomas B. .

JOURNAL OF MOLECULAR BIOLOGY, 2009, 394 (01) :160-176

[8] Defining long-range order and local disorder in native α-synuclein using residual dipolar couplings [J].

Bernadó, P ;

Bertoncini, CW ;

Griesinger, C ;

Zweckstetter, M ;

Blackledge, M .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2005, 127 (51) :17968-17969

[9] Structure and Dynamics of Ribosomal Protein L12: An Ensemble Model Based on SAXS and NMR Relaxation [J].

Bernado, Pau ;

Modig, Kristofer ;

Grela, Przemyslaw ;

Svergun, Dmitri I. ;

Tchorzewski, Marek ;

Pons, Miquel ;

Akke, Mikael .

BIOPHYSICAL JOURNAL, 2010, 98 (10) :2374-2382

[10] A Self-Consistent Description of the Conformational Behavior of Chemically Denatured Proteins from NMR and Small Angle Scattering [J].

Bernado, Pau ;

Blackledge, Martin .

BIOPHYSICAL JOURNAL, 2009, 97 (10) :2839-2845

← 1 2 3 4 5 6 7 8 9 10 →