Coupling of hydrogenic tunneling to active-site motion in the hydrogen radical transfer catalyzed by a coenzyme B12-dependent mutase

被引:57
作者
Dybala-Defratyka, Agnieszka
Paneth, Piotr
Banerjee, Ruma
Truhlar, Donald G.
机构
[1] Tech Univ Lodz, Dept Chem, Inst Appl Radiat Chem, PL-90924 Lodz, Poland
[2] Univ Nebraska, Dept Biochem, Lincoln, NE 68588 USA
[3] Univ Minnesota, Dept Chem, Minneapolis, MN 55455 USA
[4] Univ Minnesota, Inst Supercomp, Minneapolis, MN 55455 USA
关键词
enzyme kinetics; kinetic isotope effects; quantum dynamics; molecular modeling; ensemble-averaged variational transition state theory;
D O I
10.1073/pnas.0702188104
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Hydrogen transfer reactions catalyzed by coenzyme B-12-dependent methylmalonyl-CoA mutase have very large kinetic isotope effects, indicating that they proceed by a highly quantal tunneling mechanism. We explain the kinetic isotope effect by using a combined quantum mechanical/molecular mechanical potential and semiclassical quantum dynamics calculations. Multidimensional tunneling increases the magnitude of the calculated intrinsic hydrogen kinetic isotope effect by a factor of 3.6 from 14 to 51, in excellent agreement with experimental results. These calculations confirm that tunneling contributions can be large enough to explain even a kinetic isotope effect > 50, not because the barrier is unusually thin but because corner-cutting tunneling decreases the distance over which the system tunnels without a comparable increase in either the effective potential barrier or the effective mass for tunneling.
引用
收藏
页码:10774 / 10779
页数:6
相关论文
共 52 条
[1]   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
[2]  
ALHAMBRA C, 1999, CHARMMRATE
[3]   Radical carbon skeleton rearrangements:: Catalysis by coenzyme B12-dependent mutases [J].
Banerjee, R .
CHEMICAL REVIEWS, 2003, 103 (06) :2083-2094
[4]  
BANERJEE R, 2007, HYDROGEN TRANSFER RE, V4, P1473
[5]   Quantum catalysis in B12-dependent methylmalonyl-CoA mutase:: experimental and computational insights [J].
Banerjee, Ruma ;
Dybala-Defratyka, Agnieszka ;
Paneth, Piotr .
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 2006, 361 (1472) :1333-1339
[6]   CHARMM - A PROGRAM FOR MACROMOLECULAR ENERGY, MINIMIZATION, AND DYNAMICS CALCULATIONS [J].
BROOKS, BR ;
BRUCCOLERI, RE ;
OLAFSON, BD ;
STATES, DJ ;
SWAMINATHAN, S ;
KARPLUS, M .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1983, 4 (02) :187-217
[7]   ACTIVE-SITE DYNAMICS IN PROTEIN MOLECULES - A STOCHASTIC BOUNDARY MOLECULAR-DYNAMICS APPROACH [J].
BROOKS, CL ;
BRUNGER, A ;
KARPLUS, M .
BIOPOLYMERS, 1985, 24 (05) :843-865
[8]   Stabilisation of methylene radicals by cob(II)alamin in coenzyme B12 denendent mutases [J].
Buckel, W ;
Kratky, C ;
Golding, BT .
CHEMISTRY-A EUROPEAN JOURNAL, 2006, 12 (02) :352-362
[9]   Evidence for quantum mechanical tunneling in the coupled cobalt-carbon bond homolysis-substrate radical generation reaction catalyzed by methylmalonyl-CoA mutase [J].
Chowdhury, S ;
Banerjee, R .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2000, 122 (22) :5417-5418
[10]   Thermodynamic and kinetic characterization of Co-C bond homolysis catalyzed by coenzyme B12-dependent methylmalonyl-CoA mutase [J].
Chowdhury, S ;
Banerjee, R .
BIOCHEMISTRY, 2000, 39 (27) :7998-8006