Quantum mechanical methods for enzyme kinetics

被引:652
作者
Gao, JL
Truhlar, DG
机构
[1] Univ Minnesota, Dept Chem, Minneapolis, MN 55455 USA
[2] Univ Minnesota, Inst Supercomp, Minneapolis, MN 55455 USA
关键词
catalysis; dynamics; free energy; potential of mean force; QM/MM; rate constant; tunneling; variational transition state theory;
D O I
10.1146/annurev.physchem.53.091301.150114
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
This review discusses methods for the incorporation of quantum mechanical effects into enzyme kinetics simulations in which the enzyme is an explicit part of the model. We emphasize three aspects: (a) use of quantum mechanical electronic structure methods such as molecular orbital theory and density functional theory, usually in conjunction with molecular mechanics; (b) treating vibrational motions quantum mechanically, either in an instantaneous harmonic approximation, or by path integrals, or by a three-dimensional wave function coupled to classical nuclear motion; (c) incorporation of multidimensional tunneling approximations into reaction rate calculations.
引用
收藏
页码:467 / 505
页数:39
相关论文
共 299 条
[1]   Computational studies of the mechanism for proton and hydride transfer in liver alcohol dehydrogenase [J].
Agarwal, PK ;
Webb, SP ;
Hammes-Schiffer, S .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2000, 122 (19) :4803-4812
[2]   Molecular mechanics for chemical reactions: A standard strategy for using multiconfiguration molecular mechanics for variational transition state theory with optimized multidimensional tunneling [J].
Albu, TV ;
Corchado, JC ;
Truhlar, DG .
JOURNAL OF PHYSICAL CHEMISTRY A, 2001, 105 (37) :8465-8487
[3]   Canonical variational theory for enzyme kinetics with the protein mean force and multidimensional quantum mechanical tunneling dynamics.: Theory and application to liver alcohol dehydrogenase [J].
Alhambra, C ;
Corchado, J ;
Sánchez, ML ;
Garcia-Viloca, M ;
Gao, J ;
Truhlar, DG .
JOURNAL OF PHYSICAL CHEMISTRY B, 2001, 105 (45) :11326-11340
[4]   Quantum mechanical dynamical effects in an enzyme-catalyzed proton transfer reaction [J].
Alhambra, C ;
Gao, JL ;
Corchado, JC ;
Villà, J ;
Truhlar, DG .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1999, 121 (10) :2253-2258
[5]   Walden-inversion-enforced transition-state stabilization in a protein tyrosine phosphatase [J].
Alhambra, C ;
Wu, L ;
Zhang, ZY ;
Gao, JL .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1998, 120 (16) :3858-3866
[6]   Quantum mechanical tunneling in methylamine dehydrogenase [J].
Alhambra, C ;
Sánchez, ML ;
Corchado, J ;
Gao, JL ;
Truhlar, DG .
CHEMICAL PHYSICS LETTERS, 2001, 347 (4-6) :512-518
[7]   Quantum dynamics of hydride transfer in enzyme catalysis [J].
Alhambra, C ;
Corchado, JC ;
Sánchez, ML ;
Gao, JL ;
Truhlar, DG .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2000, 122 (34) :8197-8203
[8]  
ALHAMBRA C, 1998, ACS SYM SER, V712, P35
[9]  
ALHAMBRA C, IN PRESS
[10]   VALIDITY OF TIME-DEPENDENT SELF-CONSISTENT-FIELD (TDSCF) APPROXIMATIONS FOR UNIMOLECULAR DYNAMICS - A TEST FOR PHOTODISSOCIATION OF THE XE-HI CLUSTER [J].
ALIMI, R ;
GERBER, RB ;
HAMMERICH, AD ;
KOSLOFF, R ;
RATNER, MA .
JOURNAL OF CHEMICAL PHYSICS, 1990, 93 (09) :6484-6490