Technical aspects of quantum chemical modeling of enzymatic reactions: the case of phosphotriesterase

被引：62

作者：

Chen, Shi-Lu ^{[1
,2
]}

Fang, Wei-Hai ^{[2
]}

Himo, Fahmi ^{[1
]}

机构：

[1] Royal Inst Technol, Sch Biotechnol, Dept Theoret Chem, S-10691 Stockholm, Sweden

[2] Beijing Normal Univ, Coll Chem, Beijing 100875, Peoples R China

来源：

THEORETICAL CHEMISTRY ACCOUNTS | 2008年 / 120卷 / 4-6期

关键词：

D O I：

10.1007/s00214-008-0430-y

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：

Quantum chemical methods are today a powerful tool in the study of enzymatic reaction mechanisms. In this paper we evaluate the adequacy of some of the technical approximations frequently used in the modeling of enzyme reactions with high level methods. These include the choice of basis set for geometry optimizations and energy evaluation, the choice of dielectric constant to model the enzyme surrounding, and the effects of locking the centers of truncation. As a test case, we choose the phosphotriesterase enzyme, which is a binuclear zinc enzyme that catalyzes the hydrolysis of organophosphate triesters.

引用

页码：515 / 522

页数：8

共 44 条

[1] Mechanism for the hydrolysis of organophosphates by the bacterial phosphotriesterase [J].

Aubert, SD ;

Li, YC ;

Raushel, FM .

BIOCHEMISTRY, 2004, 43 (19) :5707-5715

[2] Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model [J].

Barone, V ;

Cossi, M .

JOURNAL OF PHYSICAL CHEMISTRY A, 1998, 102 (11) :1995-2001

[3] DENSITY-FUNCTIONAL THERMOCHEMISTRY .3. THE ROLE OF EXACT EXCHANGE [J].

BECKE, AD .

JOURNAL OF CHEMICAL PHYSICS, 1993, 98 (07) :5648-5652

[4] High resolution X-ray structures of different metal-substituted forms of phosphotriesterase from Pseudomonas diminuta [J].

Benning, MM ;

Shim, H ;

Raushel, FM ;

Holden, HM .

BIOCHEMISTRY, 2001, 40 (09) :2712-2722

[5] A quantum chemical approach to the study of reaction mechanisms of redox-active metalloenzymes [J].

Blomberg, MRA ;

Siegbahn, PEM .

JOURNAL OF PHYSICAL CHEMISTRY B, 2001, 105 (39) :9375-9386

[6] Biochemical characterization and crystallographic structure of an Escherichia coli protein from the phosphotriesterase gene family [J].

Buchbinder, JL ;

Stephenson, RC ;

Dresser, MJ ;

Pitera, JW ;

Scanlan, TS ;

Fletterick, RJ .

BIOCHEMISTRY, 1998, 37 (15) :5096-5106

[7] Second-order Moller-Plesset analytical derivatives for the polarizable continuum model using the relaxed density approach [J].

Cammi, R ;

Mennucci, B ;

Tomasi, J .

JOURNAL OF PHYSICAL CHEMISTRY A, 1999, 103 (45) :9100-9108

[8] Dehydration of ribonucleotides catalyzed by ribonucleotide reductase: The role of the enzyme [J].

Cerqueira, NMFSA ;

Fernandes, PA ;

Eriksson, LA ;

Ramos, MJ .

BIOPHYSICAL JOURNAL, 2006, 90 (06) :2109-2119

[9] Enzyme ribonucleotide reductase: Unraveling an enigmatic paradigm of enzyme inhibition by furanone derivatives [J].

Cerqueira, Nuno M. F. S. A. ;

Fernandes, Pedro A. ;

Ramos, Maria J. .

JOURNAL OF PHYSICAL CHEMISTRY B, 2006, 110 (42) :21272-21281

[10] ANTIFERROMAGNETIC COUPLING IN THE BINUCLEAR METAL CLUSTER OF MANGANESE-SUBSTITUTED PHOSPHOTRIESTERASE [J].

CHAE, MY ;

OMBURO, GA ;

LINDAHL, PA ;

RAUSHEL, FM .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1993, 115 (25) :12173-12174

← 1 2 3 4 5 →