Integrative, dynamic structural biology at atomic resolution-it's about time

被引:183
作者
van den Bedem, Henry [1 ,2 ]
Fraser, James S. [3 ,4 ]
机构
[1] Stanford Univ, Stanford Synchrotron Radiat Lightsource, Joint Ctr Struct Genom, Menlo Pk, CA 94025 USA
[2] Stanford Univ, SLAC Natl Accelerator Lab, Div Biosci, Menlo Pk, CA USA
[3] Univ Calif San Francisco, Dept Bioengn & Therapeut Sci, San Francisco, CA 94143 USA
[4] Univ Calif San Francisco, Calif Inst Quantitat Biol, San Francisco, CA 94143 USA
基金
美国国家科学基金会; 美国国家卫生研究院;
关键词
SOLID-STATE NMR; X-RAY CRYSTALLOGRAPHY; RESIDUAL DIPOLAR COUPLINGS; NUCLEAR-MAGNETIC-RESONANCE; DIHYDROFOLATE-REDUCTASE CATALYSIS; PROTEIN CONFORMATIONAL ENSEMBLES; RESTRAINED MOLECULAR-DYNAMICS; SIDE-CHAIN DYNAMICS; CRYSTAL-STRUCTURES; ORDER PARAMETERS;
D O I
10.1038/nmeth.3324
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Biomolecules adopt a dynamic ensemble of conformations, each with the potential to interact with binding partners or perform the chemical reactions required for a multitude of cellular functions. Recent advances in X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy and other techniques are helping us realize the dream of seeing-in atomic detail-how different parts of biomolecules shift between functional substates using concerted motions. Integrative structural biology has advanced our understanding of the formation of large macromolecular complexes and how their components interact in assemblies by leveraging data from many low-resolution methods. Here, we review the growing opportunities for integrative, dynamic structural biology at the atomic scale, contending there is increasing synergistic potential between X-ray crystallography, NMR and computer simulations to reveal a structural basis for protein conformational dynamics at high resolution.
引用
收藏
页码:307 / 318
页数:12
相关论文
共 112 条
[1]   Structure of HIV-1 TAB RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulge [J].
AboulEla, F ;
Karn, J ;
Varani, G .
NUCLEIC ACIDS RESEARCH, 1996, 24 (20) :3974-3981
[2]   Optical measurements of long-range protein vibrations [J].
Acbas, Gheorghe ;
Niessen, Katherine A. ;
Snell, Edward H. ;
Markelz, A. G. .
NATURE COMMUNICATIONS, 2014, 5
[3]   Protein Side-Chain Dynamics As Observed by Solution- and Solid-State NMR Spectroscopy: A Similarity Revealed [J].
Agarwal, Vipin ;
Xue, Yi ;
Reif, Bernd ;
Skrynnikov, Nikolai R. .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2008, 130 (49) :16611-16621
[4]  
[Anonymous], 1986, NMR of proteins and nucleic acids
[5]   Recovering a Representative Conformational Ensemble from Underdetermined Macromolecular Structural Data [J].
Berlin, Konstantin ;
Castaneda, Carlos A. ;
Schneidman-Duhovny, Dina ;
Sali, Andrej ;
Nava-Tudela, Alfredo ;
Fushman, David .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2013, 135 (44) :16595-16609
[6]   Determination of protein structures consistent with NMR order parameters [J].
Best, RB ;
Vendruscolo, M .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2004, 126 (26) :8090-8091
[7]   Relation between native ensembles and experimental structures of proteins [J].
Best, Robert B. ;
Lindorff-Larsen, Kresten ;
DePristo, Mark A. ;
Vendruscolo, Michele .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (29) :10901-10906
[8]   Divergent evolution of protein conformational dynamics in dihydrofolate reductase [J].
Bhabha, Gira ;
Ekiert, Damian C. ;
Jennewein, Madeleine ;
Zmasek, Christian M. ;
Tuttle, Lisa M. ;
Kroon, Gerard ;
Dyson, H. Jane ;
Godzik, Adam ;
Wilson, Ian A. ;
Wright, Peter E. .
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 2013, 20 (11) :1243-U262
[9]   A Dynamic Knockout Reveals That Conformational Fluctuations Influence the Chemical Step of Enzyme Catalysis [J].
Bhabha, Gira ;
Lee, Jeeyeon ;
Ekiert, Damian C. ;
Gam, Jongsik ;
Wilson, Ian A. ;
Dyson, H. Jane ;
Benkovic, Stephen J. ;
Wright, Peter E. .
SCIENCE, 2011, 332 (6026) :234-238
[10]   The dynamic energy landscape of dihydrofolate reductase catalysis [J].
Boehr, David D. ;
McElheny, Dan ;
Dyson, H. Jane ;
Wright, Peter E. .
SCIENCE, 2006, 313 (5793) :1638-1642