A theoretical view of protein dynamics

被引:84
作者
Orozco, Modesto [1 ,2 ,3 ]
机构
[1] Inst Res Biomed IRB Barcelona, Barcelona 08028, Spain
[2] Joint BSC GRG IRB Program Computat Biol, Barcelona, Spain
[3] Univ Barcelona, Fac Biol, Dept Biochem & Mol Biol, Barcelona, Spain
基金
欧洲研究理事会;
关键词
DISCRETE MOLECULAR-DYNAMICS; NORMAL-MODE ANALYSIS; RESIDUAL DIPOLAR COUPLINGS; ELASTIC NETWORK MODEL; COARSE-GRAINED MODELS; FAST-FOLDING PROTEINS; FORCE-FIELD; CONFORMATIONAL-CHANGE; BIOMOLECULAR SYSTEMS; MD SIMULATIONS;
D O I
10.1039/c3cs60474h
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
Proteins are fascinating supramolecular structures, which are able to recognize ligands transforming binding information into chemical signals. They can transfer information across the cell, can catalyse complex chemical reactions, and are able to transform energy into work with much more efficiency than any human engine. The unique abilities of proteins are tightly coupled with their dynamic properties, which are coded in a complex way in the sequence and carefully refined by evolution. Despite its importance, our experimental knowledge of protein dynamics is still rather limited, and mostly derived from theoretical calculations. I will review here, in a systematic way, the current state-of-the-art theoretical approaches to the study of protein dynamics, emphasizing the most recent advances, examples of use and the expected lines of development in the near future.
引用
收藏
页码:5051 / 5066
页数:16
相关论文
共 205 条
[1]  
Addock S. A., 2006, CHEM REV, V106, P1589
[2]   ESSENTIAL DYNAMICS OF PROTEINS [J].
AMADEI, A ;
LINSSEN, ABM ;
BERENDSEN, HJC .
PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1993, 17 (04) :412-425
[3]   Polarizable empirical force field for the primary and secondary alcohol series based on the classical drude model [J].
Anisimov, Victor M. ;
Vorobyov, Igor V. ;
Roux, Benoit ;
MacKerell, Alexander D., Jr. .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2007, 3 (06) :1927-1946
[4]  
[Anonymous], Reviews in Computational Chemistry
[5]  
[Anonymous], 2014, INTRO MARKOV STATE M
[6]  
Aponte-Santamaria C., 2012, P NATL ACAD SCI USA, V109, P44319
[7]   SIMULATION OF ENZYME-REACTIONS USING VALENCE-BOND FORCE-FIELDS AND OTHER HYBRID QUANTUM-CLASSICAL APPROACHES [J].
AQVIST, J ;
WARSHEL, A .
CHEMICAL REVIEWS, 1993, 93 (07) :2523-2544
[8]   Stability and dynamics of virus capsids described by coarse-grained modeling [J].
Arkhipov, Anton ;
Freddolino, Peter L. ;
Schulten, Klaus .
STRUCTURE, 2006, 14 (12) :1767-1777
[9]   Coarse-grained molecular dynamics simulations of a rotating bacterial flagellum [J].
Arkhipov, Anton ;
Freddolino, Peter L. ;
Imada, Katsumi ;
Namba, Keiichi ;
Schulten, Klaus .
BIOPHYSICAL JOURNAL, 2006, 91 (12) :4589-4597
[10]   Architecture and Membrane Interactions of the EGF Receptor [J].
Arkhipov, Anton ;
Shan, Yibing ;
Das, Rahul ;
Endres, Nicholas F. ;
Eastwood, Michael P. ;
Wemmer, David E. ;
Kuriyan, John ;
Shaw, David E. .
CELL, 2013, 152 (03) :557-569