Protein dynamics simulations from nanoseconds to microseconds

被引:53
作者
Doniach, S [1 ]
Eastman, P
机构
[1] Stanford Univ, Dept Phys, Stanford, CA 94305 USA
[2] Stanford Univ, Dept Appl Phys, Stanford, CA 94305 USA
关键词
D O I
10.1016/S0959-440X(99)80022-0
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
There have been a number of advances in atomic resolution simulations of biomolecules during the past few years. These have arisen partly from improvements to computer power and partly from algorithmic improvements. There have also been advances in measuring time-dependent fluctuations in proteins using NMR spectroscopy, revealing the importance of fluctuations in the microsecond to millisecond time range. Progress has also been made in measuring how far the simulations are able to represent the accessible phase space that is available to the protein in its native state, in solution, at room temperature. Another area of development is the simulation of protein unfolding at atomic resolution.
引用
收藏
页码:157 / 163
页数:7
相关论文
共 49 条
[21]  
EASTMAN P, 1999, IN PRESS J CHEM PHYS
[22]   Can protein unfolding simulate protein folding? [J].
Finkelstein, AV .
PROTEIN ENGINEERING, 1997, 10 (08) :843-845
[23]   Flexibility and function in HIV protease: Dynamics of the HIV-1 protease bound to the asymmetric inhibitor kynostatin 272 (KNI-272) [J].
Freedberg, DI ;
Wang, YX ;
Stahl, SJ ;
Kaufman, JD ;
Wingfield, PT ;
Kiso, Y ;
Torchia, DA .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1998, 120 (31) :7916-7923
[24]   GENERALIZED VERLET ALGORITHM FOR EFFICIENT MOLECULAR DYNAMICS SIMULATIONS WITH LONG-RANGE INTERACTIONS [J].
Grubmueller, H. ;
Heller, H. ;
Windemuth, A. ;
Schulten, K. .
MOLECULAR SIMULATION, 1991, 6 (1-3) :121-142
[25]  
Grubmüller H, 1998, J COMPUT CHEM, V19, P1534, DOI 10.1002/(SICI)1096-987X(199810)19:13<1534::AID-JCC10>3.0.CO
[26]  
2-I
[27]  
Hess B, 1997, J COMPUT CHEM, V18, P1463, DOI 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO
[28]  
2-H
[29]   SWARM-MD: Searching conformational space by cooperative molecular dynamics [J].
Huber, T ;
van Gunsteren, WF .
JOURNAL OF PHYSICAL CHEMISTRY A, 1998, 102 (29) :5937-5943
[30]   The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of proteins [J].
Hummer, G ;
Garde, S ;
García, AE ;
Paulaitis, ME ;
Pratt, LR .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (04) :1552-1555