Quantum mechanical and molecular dynamics simulations of ureases and Zn β-lactamases

被引:51
作者
Estiu, Guillermina
Suarez, Dimas
Merz, Kenneth M., Jr.
机构
[1] Univ Florida, Dept Chem, Quantum Theory Project, Gainesville, FL 32611 USA
[2] Univ Oviedo, Dept Quim Fis & Analit, E-33006 Oviedo, Spain
关键词
metallo-beta-lactamases; ureases; QM calculations; MD simulations; QM/MM;
D O I
10.1002/jcc.20411
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
Herein we briefly review theoretical contributions that have increased our understanding of the structure and function of metallo-beta-lactamases and ureases. Both are bimetallic metalloenzymes, with the former containing two zinc ions and the latter containing two nickel ions. We describe the use of several different methodologies, including quantum chemical calculations, molecular dynamic simulations, as well as mixed QM/MM approaches and how they have impacted our understanding of the structure and function of metallo-beta-lactamases and ureases. (c) 2006 Wiley Periodicals, Inc.
引用
收藏
页码:1240 / 1262
页数:23
相关论文
共 137 条
[1]   AB-INITIO ANALYSIS OF WATER-ASSISTED REACTION-MECHANISMS IN AMIDE HYDROLYSIS [J].
ANTONCZAK, S ;
RUIZLOPEZ, MF ;
RIVAIL, JL .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1994, 116 (09) :3912-3921
[2]   Complexes of thiomandelate and captopril mercaptocarboxylate inhibitors to metallo-β-lactamase by polarizable molecular mechanics.: Validation on model binding sites by quantum chemistry [J].
Antony, J ;
Piquemal, JP ;
Gresh, N .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2005, 26 (11) :1131-1147
[3]   Binding of D- and L-captopril inhibitors to metallo-β-lactamase studied by polarizable molecular mechanics and quantum mechanics [J].
Antony, J ;
Gresh, N ;
Olsen, L ;
Hemmingsen, L ;
Schofield, CJ ;
Bauer, R .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2002, 23 (13) :1281-1296
[4]   Theoretical study of base-catalyzed amide hydrolysis: Gas- and aqueous-phase hydrolysis of formamide [J].
Bakowies, D ;
Kollman, PA .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1999, 121 (24) :5712-5726
[5]   Decomposition of alkyl-substituted urea molecules at a hydroxide-bridged dinickel center [J].
Barrios, AM ;
Lippard, SJ .
INORGANIC CHEMISTRY, 2001, 40 (06) :1250-1255
[6]   Amide hydrolysis effected by a hydroxo-bridged dinickel(II) complex: Insights into the mechanism of urease [J].
Barrios, AM ;
Lippard, SJ .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1999, 121 (50) :11751-11757
[7]   Interaction of urea with a hydroxide-bridged dinuclear nickel center: An alternative model for the mechanism of urease [J].
Barrios, AM ;
Lippard, SJ .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2000, 122 (38) :9172-9177
[8]   How enzyme dynamics helps catalyze a reaction in atomic detail: A transition path sampling study [J].
Basner, JE ;
Schwartz, SD .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2005, 127 (40) :13822-13831
[9]   A new proposal for urease mechanism based on the crystal structures of the native and inhibited enzyme from Bacillus pasteurii:: why urea hydrolysis casts two nickels [J].
Benini, S ;
Rypniewski, WR ;
Wilson, KS ;
Miletti, S ;
Ciurli, S ;
Mangani, S .
STRUCTURE, 1999, 7 (02) :205-216
[10]   Crystallization and preliminary high-resolution X-ray diffraction analysis of native and β-mercaptoethanol-inhibited urease from Bacillus pasteurii [J].
Benini, S ;
Ciurli, S ;
Rypniewski, WR ;
Wilson, KS ;
Mangani, S .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1998, 54 :409-412