Computational and theoretical advances in studies of intrinsically disordered proteins

被引:163
作者
Best, Robert B. [1 ]
机构
[1] NIDDK, Chem Phys Lab, NIH, Bethesda, MD 20892 USA
基金
美国国家卫生研究院;
关键词
MOLECULAR-DYNAMICS SIMULATIONS; FORCE-FIELD; ATOMISTIC SIMULATIONS; SEQUENCE DETERMINANTS; FOLDING SIMULATIONS; UNFOLDED PROTEINS; PHASE-SEPARATION; SPECTROSCOPY; OPTIMIZATION; ENSEMBLES;
D O I
10.1016/j.sbi.2017.01.006
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
Intrinsically disordered proteins (IDPs) are increasingly realized to play diverse biological roles, ranging from molecular signaling to the formation of membraneless organelles. Their high degree of disorder makes them more challenging to study using the techniques of conventional structural biology, because any observable will be averaged over a heterogeneous ensemble of structures. Molecular simulations and theory are therefore a natural complement to experiment for studying the structure, dynamics and function of IDPs. The diverse time and length scales relevant to the roles played by IDPs require flexibility in the techniques applied. Here, I summarize some of the developments in simulation and theory in recent years, which have been driven by the desire to better capture IDP properties at different time- and length-scales. I also provide an outlook for how methods can be improved in the future and emerging problems which may be addressed by theory and simulation.
引用
收藏
页码:147 / 154
页数:8
相关论文
共 74 条
[31]   Development of Multiscale Models for Complex Chemical Systems: From H+H2 to Biomolecules (Nobel Lecture) [J].
Karplus, Martin .
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 2014, 53 (38) :9992-10005
[32]   Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model [J].
Knott, Michael ;
Best, Robert B. .
JOURNAL OF CHEMICAL PHYSICS, 2014, 140 (17)
[33]   A Preformed Binding Interface in the Unbound Ensemble of an Intrinsically Disordered Protein: Evidence from Molecular Simulations [J].
Knott, Michael ;
Best, Robert B. .
PLOS COMPUTATIONAL BIOLOGY, 2012, 8 (07)
[34]   Prepaying the entropic cost for allosteric regulation in KIX [J].
Law, Sean M. ;
Gagnon, Jessica K. ;
Mapp, Anna K. ;
Brooks, Charles L., III .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2014, 111 (33) :12067-12072
[35]  
Lazaridis T, 1999, PROTEINS, V35, P133, DOI 10.1002/(SICI)1097-0134(19990501)35:2<133::AID-PROT1>3.0.CO
[36]  
2-N
[37]   Simulations disordered proteins and systems with conformational heterogeneity [J].
Levine, Zachary A. ;
Shea, Joan-Emma .
CURRENT OPINION IN STRUCTURAL BIOLOGY, 2017, 43 :95-103
[38]   Iterative Optimization of Molecular Mechanics Force Fields from NMR Data of Full-Length Proteins [J].
Li, Da-Wei ;
Brueschweiler, Rafael .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2011, 7 (06) :1773-1782
[39]   Sequence-Specific Polyampholyte Phase Separation in Membraneless Organelles [J].
Lin, Yi-Hsuan ;
Forman-Kay, Julie D. ;
Chan, Hue Sun .
PHYSICAL REVIEW LETTERS, 2016, 117 (17)
[40]   How Fast-Folding Proteins Fold [J].
Lindorff-Larsen, Kresten ;
Piana, Stefano ;
Dror, Ron O. ;
Shaw, David E. .
SCIENCE, 2011, 334 (6055) :517-520