Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order "chain-of-replicas" methods

被引:33
作者
Cisneros, GA [1 ]
Liu, HY
Lu, ZY
Yang, WT
机构
[1] Duke Univ, Dept Chem, Durham, NC 27708 USA
[2] Univ Sci & Technol China, Sch Life Sci, Anhua 230026, Peoples R China
关键词
D O I
10.1063/1.1860560
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
A two-step procedure for the determination of reaction paths in enzyme systems is presented. This procedure combines. two chain-of-states methods: a quantum mechanical/molecular mechanical (QM/MM) implementation of the nudged elastic band (NEB) method and a second order parallel path optimizer method both recently developed in our laboratory. In the first step, a reaction path determination is performed with the NEB method, along with a restrained minimization procedure for the MM environment to obtain a first approximation to the reaction path. In the second step; the calculated path is refined with the parallel path optimizer method. By combining these two methods the reaction paths are determined accurately, and in addition, the number of path optimization iterations are significantly reduced. This procedure is tested by calculating both steps of the isomerization of 2-oxo-4-hexenedioate I by 4-oxalocrotonate, tautomerase, which have been previously determined by our group. The calculated paths agree with the previously reported results and we obtain a reduction of 45%-55% in the number of path optimization cycles. (c) 2005 American Institute of Physics.
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页数:7
相关论文
共 32 条
[21]   Determination of enzymatic reaction pathways using QM/MM methods [J].
Monard, G ;
Prat-Resina, X ;
González-Lafont, A ;
Lluch, JM .
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 2003, 93 (03) :229-244
[22]  
PONDER J, 1998, TINKER SOFTWARE TOOL
[23]   Energetics and dynamics of enzymatic reactions [J].
Villà, J ;
Warshel, A .
JOURNAL OF PHYSICAL CHEMISTRY B, 2001, 105 (33) :7887-7907
[24]  
Wang M.-T, IN PRESS
[25]   Molecular dynamics simulations of biological reactions [J].
Warshel, A .
ACCOUNTS OF CHEMICAL RESEARCH, 2002, 35 (06) :385-395
[26]  
WILLIAMS IH, 1982, J MOL STRUC-THEOCHEM, V6, P365, DOI 10.1016/0166-1280(82)80095-X
[27]   Exploring the quantum mechanical/molecular mechanical replica path method: a pathway optimization of the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase [J].
Woodcock, HL ;
Hodoscek, M ;
Sherwood, P ;
Lee, YS ;
Schaefer, HF ;
Brooks, BR .
THEORETICAL CHEMISTRY ACCOUNTS, 2003, 109 (03) :140-148
[28]   Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes [J].
Xie, L ;
Liu, HY ;
Yang, WT .
JOURNAL OF CHEMICAL PHYSICS, 2004, 120 (17) :8039-8052
[29]  
ZHANG Y, 2002, COMPUTATIONAL METHOD
[30]   A pseudobond approach to combining quantum mechanical and molecular mechanical methods [J].
Zhang, YK ;
Lee, TS ;
Yang, WT .
JOURNAL OF CHEMICAL PHYSICS, 1999, 110 (01) :46-54