Using simulation to interpret experimental data in terms of protein conformational ensembles

被引:36
作者
Allison, Jane R. [1 ,2 ,3 ]
机构
[1] Massey Univ Auckland, Ctr Theoret Chem & Phys, Inst Nat & Math Sci, Auckland 0632, New Zealand
[2] Univ Canterbury, Biomol Interact Ctr, Private Bag 4800, Christchurch 8140, New Zealand
[3] Univ Auckland, Maurice Wilkins Ctr Mol Biodiscovery, Private Bag 92019, Auckland, New Zealand
关键词
MOLECULAR-DYNAMICS SIMULATIONS; RESIDUAL DIPOLAR COUPLINGS; NMR CHEMICAL-SHIFTS; AVERAGED STRUCTURAL RESTRAINTS; TENSOR-FREE METHOD; X-RAY-SCATTERING; STATISTICAL-MECHANICS; STRUCTURE REFINEMENT; GUIDED METADYNAMICS; CROSS-VALIDATION;
D O I
10.1016/j.sbi.2016.11.018
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
In their biological environment, proteins are dynamic molecules, necessitating an ensemble structural description. Molecular dynamics simulations and solution-state experiments provide complimentary information in the form of atomically detailed coordinates and averaged or distributions of structural properties or related quantities. Recently, increases in the temporal and spatial scale of conformational sampling and comparison of the more diverse conformational ensembles thus generated have revealed the importance of sampling rare events. Excitingly, new methods based on maximum entropy and Bayesian inference are promising to provide a statistically sound mechanism for combining experimental data with molecular dynamics simulations.
引用
收藏
页码:79 / 87
页数:9
相关论文
共 73 条
[41]   Structural Insights into the Calcium-Mediated Allosteric Transition in the C-Terminal Domain of Calmodulin from Nuclear Magnetic Resonance Measurements [J].
Kukic, Predrag ;
Lundstrom, Patrik ;
Camilloni, Carlo ;
Evenas, Johan ;
Akke, Mikael ;
Vendruscolo, Michele .
BIOCHEMISTRY, 2016, 55 (01) :19-28
[42]   Structure and Dynamics of the Integrin LFA-1 I-Domain in the Inactive State Underlie its Inside-Out/Outside-In Signaling and Allosteric Mechanisms [J].
Kukic, Predrag ;
Leung, Hoi Tik Alvin ;
Bemporad, Francesco ;
Aprile, Francesco A. ;
Kumita, Janet R. ;
De Simone, Alfonso ;
Camilloni, Carlo ;
Vendruscolo, Michele .
STRUCTURE, 2015, 23 (04) :745-753
[43]   Determination of the Individual Roles of the Linker Residues in the Interdomain Motions of Calmodulin Using NMR Chemical Shifts [J].
Kukic, Predrag ;
Camilloni, Carlo ;
Cavalli, Andrea ;
Vendruscolo, Michele .
JOURNAL OF MOLECULAR BIOLOGY, 2014, 426 (08) :1826-1838
[44]   Escaping free-energy minima [J].
Laio, A ;
Parrinello, M .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2002, 99 (20) :12562-12566
[45]   Simultaneous determination of protein structure and dynamics [J].
Lindorff-Larsen, K ;
Best, RB ;
DePristo, MA ;
Dobson, CM ;
Vendruscolo, M .
NATURE, 2005, 433 (7022) :128-132
[46]   Picosecond to Millisecond Structural Dynamics in Human Ubiquitin [J].
Lindorff-Larsen, Kresten ;
Maragakis, Paul ;
Piana, Stefano ;
Shaw, David E. .
JOURNAL OF PHYSICAL CHEMISTRY B, 2016, 120 (33) :8313-8320
[47]   Systematic Validation of Protein Force Fields against Experimental Data [J].
Lindorff-Larsen, Kresten ;
Maragakis, Paul ;
Piana, Stefano ;
Eastwood, Michael P. ;
Dror, Ron O. ;
Shaw, David E. .
PLOS ONE, 2012, 7 (02)
[48]   On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain order parameters [J].
O'Brien, Evan S. ;
Wand, A. Joshua ;
Sharp, Kim A. .
PROTEIN SCIENCE, 2016, 25 (06) :1156-1160
[49]   Molecular Dynamics of Biomolecules through Direct Analysis of Dipolar Couplings [J].
Olsson, Simon ;
Ekonomiuk, Dariusz ;
Sgrignani, Jacopo ;
Cavalli, Andrea .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2015, 137 (19) :6270-6278
[50]   Probabilistic Determination of Native State Ensembles of Proteins [J].
Olsson, Simon ;
Voegeli, Beat Rolf ;
Cavalli, Andrea ;
Boomsma, Wouter ;
Ferkinghoff-Borg, Jesper ;
Lindorff-Larsen, Kresten ;
Hamelryck, Thomas .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2014, 10 (08) :3484-3491