-
1
-
-
0346726109
-
How enzymes work: analysis by modern rate theory and computer simulations
-
Garcia-Viloca M., Gao J., Karplus M., and Truhlar D.G. How enzymes work: analysis by modern rate theory and computer simulations. Science 303 (2004) 186-195
-
(2004)
Science
, vol.303
, pp. 186-195
-
-
Garcia-Viloca, M.1
Gao, J.2
Karplus, M.3
Truhlar, D.G.4
-
2
-
-
0027506191
-
Computer modelling of enzyme catalysed reaction mechanisms
-
Mulholland A.J., Grant G.H., and Richards W.G. Computer modelling of enzyme catalysed reaction mechanisms. Prot. Eng. 6 (1993) 133-147
-
(1993)
Prot. Eng.
, vol.6
, pp. 133-147
-
-
Mulholland, A.J.1
Grant, G.H.2
Richards, W.G.3
-
3
-
-
27144494583
-
Modelling enzyme reaction mechanisms, specificity and catalysis
-
Mulholland A.J. Modelling enzyme reaction mechanisms, specificity and catalysis. Drug Discov. Today 10 (2005) 1393-1402
-
(2005)
Drug Discov. Today
, vol.10
, pp. 1393-1402
-
-
Mulholland, A.J.1
-
4
-
-
0032568612
-
Computer simulations of enzyme catalysis: finding out what has been optimized by evolution
-
Warshel A., and Florián J. Computer simulations of enzyme catalysis: finding out what has been optimized by evolution. Proc. Natl. Acad. Sci. U.S.A. 95 (1998) 5950-5955
-
(1998)
Proc. Natl. Acad. Sci. U.S.A.
, vol.95
, pp. 5950-5955
-
-
Warshel, A.1
Florián, J.2
-
5
-
-
1842340659
-
Studies on the reaction mechanism of citrate synthase
-
C3-C3
-
Mulholland A.J., and Richards W.G. Studies on the reaction mechanism of citrate synthase. FASEB J. 10 (1996) C3-C3
-
(1996)
FASEB J.
, vol.10
-
-
Mulholland, A.J.1
Richards, W.G.2
-
6
-
-
0000776297
-
A model of the condensation step in the citrate synthase reaction
-
Mulholland A.J., and Richards W.G. A model of the condensation step in the citrate synthase reaction. J. Mol. Struct. (Theochem.) 427 (1998) 175-184
-
(1998)
J. Mol. Struct. (Theochem.)
, vol.427
, pp. 175-184
-
-
Mulholland, A.J.1
Richards, W.G.2
-
7
-
-
0038305457
-
Quantum chemical studies of radical-containing enzymes
-
Himo F., and Siegbahn P.E.M. Quantum chemical studies of radical-containing enzymes. Chem. Rev. 103 (2003) 2421-2456
-
(2003)
Chem. Rev.
, vol.103
, pp. 2421-2456
-
-
Himo, F.1
Siegbahn, P.E.M.2
-
8
-
-
4143088551
-
An efficient linear scaling method for ab initio calculation of electron density of proteins
-
Gao A.M., Zhang D.W., Zhang J.Z.H., and Zhang Y.K. An efficient linear scaling method for ab initio calculation of electron density of proteins. Chem. Phys. Lett. 394 (2004) 293-297
-
(2004)
Chem. Phys. Lett.
, vol.394
, pp. 293-297
-
-
Gao, A.M.1
Zhang, D.W.2
Zhang, J.Z.H.3
Zhang, Y.K.4
-
9
-
-
34547237228
-
A fragment energy assembler method for Hartree-Fock calculations of large molecules
-
Li W., Fang T., and Li S.H. A fragment energy assembler method for Hartree-Fock calculations of large molecules. J. Chem. Phys. (2006) 124
-
(2006)
J. Chem. Phys.
, pp. 124
-
-
Li, W.1
Fang, T.2
Li, S.H.3
-
10
-
-
22944470256
-
A new method for direct calculation of total energy of protein
-
He X., and Zhang J.Z.H. A new method for direct calculation of total energy of protein. J. Chem. Phys. (2005) 122
-
(2005)
J. Chem. Phys.
, pp. 122
-
-
He, X.1
Zhang, J.Z.H.2
-
11
-
-
12344294827
-
A quantum chemical method for rapid optimization of protein structures
-
Wada M., and Sakurai M. A quantum chemical method for rapid optimization of protein structures. J. Comp. Chem. 26 (2005) 160-168
-
(2005)
J. Comp. Chem.
, vol.26
, pp. 160-168
-
-
Wada, M.1
Sakurai, M.2
-
12
-
-
0001499720
-
Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method
-
Van Der Vaart A., Gogonea V., Dixon S.L., and Merz K.M. Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method. J. Comp. Chem. 21 (2000) 1494-1504
-
(2000)
J. Comp. Chem.
, vol.21
, pp. 1494-1504
-
-
Van Der Vaart, A.1
Gogonea, V.2
Dixon, S.L.3
Merz, K.M.4
-
13
-
-
0032097513
-
Quantum mechanical treatment of biological macromolecules in solution using linear-scaling electronic structure methods
-
York D.M., Lee T.S., and Yang W.T. Quantum mechanical treatment of biological macromolecules in solution using linear-scaling electronic structure methods. Phys. Rev. Lett. 80 (1998) 5011-5014
-
(1998)
Phys. Rev. Lett.
, vol.80
, pp. 5011-5014
-
-
York, D.M.1
Lee, T.S.2
Yang, W.T.3
-
14
-
-
84986513644
-
A combined quantum-mechanical and molecular mechanical potential for molecular-dynamics simulations
-
Field M.J., Bash P.A., and Karplus M. A combined quantum-mechanical and molecular mechanical potential for molecular-dynamics simulations. J. Comp. Chem. 11 (1990) 700-733
-
(1990)
J. Comp. Chem.
, vol.11
, pp. 700-733
-
-
Field, M.J.1
Bash, P.A.2
Karplus, M.3
-
15
-
-
21244497608
-
Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis
-
Friesner R.A., and Guallar V. Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis. Ann. Rev. Phys. Chem. 56 (2005) 389-427
-
(2005)
Ann. Rev. Phys. Chem.
, vol.56
, pp. 389-427
-
-
Friesner, R.A.1
Guallar, V.2
-
16
-
-
33845283509
-
Free-energy perturbation method for chemical-reactions in the condensed phase: a dynamical-approach based on a combined quantum and molecular mechanics potential
-
Bash P.A., Field M.J., and Karplus M. Free-energy perturbation method for chemical-reactions in the condensed phase: a dynamical-approach based on a combined quantum and molecular mechanics potential. J. Am. Chem. Soc. 109 (1987) 8092-8094
-
(1987)
J. Am. Chem. Soc.
, vol.109
, pp. 8092-8094
-
-
Bash, P.A.1
Field, M.J.2
Karplus, M.3
-
17
-
-
0003525155
-
-
John Wiley and Sons, New York
-
Brooks III C.L., Karplus M., and Pettitt B.M. Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics (1988), John Wiley and Sons, New York
-
(1988)
Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics
-
-
Brooks III, C.L.1
Karplus, M.2
Pettitt, B.M.3
-
18
-
-
33750478314
-
High-accuracy computation of reaction barriers in enzymes
-
Claeyssens F., Harvey J.N., Manby F.R., Mata R.A., Mulholland A.J., Ranaghan K.E., Schutz M., Thiel S., Thiel W., and Werner H.J. High-accuracy computation of reaction barriers in enzymes. Angew. Chem. Int. Ed. 45 (2006) 6856-6859
-
(2006)
Angew. Chem. Int. Ed.
, vol.45
, pp. 6856-6859
-
-
Claeyssens, F.1
Harvey, J.N.2
Manby, F.R.3
Mata, R.A.4
Mulholland, A.J.5
Ranaghan, K.E.6
Schutz, M.7
Thiel, S.8
Thiel, W.9
Werner, H.J.10
-
19
-
-
33750157202
-
Mechanisms of reaction in cytochrome P450: hydroxylation of camphor in P450cam
-
Zurek J., Foloppe N., Harvey J.N., and Mulholland A.J. Mechanisms of reaction in cytochrome P450: hydroxylation of camphor in P450cam. Org. Biomol. Chem. 4 (2006) 3931-3937
-
(2006)
Org. Biomol. Chem.
, vol.4
, pp. 3931-3937
-
-
Zurek, J.1
Foloppe, N.2
Harvey, J.N.3
Mulholland, A.J.4
-
20
-
-
0031033361
-
Acetyl-CoA enolization in citrate synthase: a quantum mechanical/molecular mechanical (QM/MM) study
-
Mulholland A.J., and Richards W.G. Acetyl-CoA enolization in citrate synthase: a quantum mechanical/molecular mechanical (QM/MM) study. Prot. Struct. Funct. Genet. 27 (1997) 9-25
-
(1997)
Prot. Struct. Funct. Genet.
, vol.27
, pp. 9-25
-
-
Mulholland, A.J.1
Richards, W.G.2
-
21
-
-
0026485965
-
Structure and mechanism of citrate synthase
-
Remington S.J. Structure and mechanism of citrate synthase. Curr. Top. Cell. Regul. 33 (1992) 209-229
-
(1992)
Curr. Top. Cell. Regul.
, vol.33
, pp. 209-229
-
-
Remington, S.J.1
-
22
-
-
0016647269
-
Enzymology of formation and breakdown of citrate
-
Srere P.A. Enzymology of formation and breakdown of citrate. Adv. Enzymol. RAMB 43 (1975) 57-101
-
(1975)
Adv. Enzymol. RAMB
, vol.43
, pp. 57-101
-
-
Srere, P.A.1
-
23
-
-
0024584420
-
Citrate synthase stabilizes the enethiolate of acetyldithio coenzyme-A
-
Wlassics I.D., and Anderson V.E. Citrate synthase stabilizes the enethiolate of acetyldithio coenzyme-A. Biochemistry 28 (1989) 1627-1633
-
(1989)
Biochemistry
, vol.28
, pp. 1627-1633
-
-
Wlassics, I.D.1
Anderson, V.E.2
-
24
-
-
0023727337
-
Malate synthase: proof of a stepwise claisen condensation using the double-isotope fractionation test
-
Clark J.D., O'Keefe S.J., and Knowles J.R. Malate synthase: proof of a stepwise claisen condensation using the double-isotope fractionation test. Biochemistry 27 (1988) 5961-5971
-
(1988)
Biochemistry
, vol.27
, pp. 5961-5971
-
-
Clark, J.D.1
O'Keefe, S.J.2
Knowles, J.R.3
-
25
-
-
0022425329
-
Evidence from C-13 NMR for polarization of the carbonyl of oxaloacetate in the active-site of citrate synthase
-
Kurz L.C., Ackerman J.J.H., and Drysdale G.R. Evidence from C-13 NMR for polarization of the carbonyl of oxaloacetate in the active-site of citrate synthase. Biochemistry 24 (1985) 452-457
-
(1985)
Biochemistry
, vol.24
, pp. 452-457
-
-
Kurz, L.C.1
Ackerman, J.J.H.2
Drysdale, G.R.3
-
26
-
-
0023248839
-
Evidence from Fourier-transform infrared-spectroscopy for polarization of the carbonyl of oxaloacetate in the active-site of citrate synthase
-
Kurz L.C., and Drysdale G.R. Evidence from Fourier-transform infrared-spectroscopy for polarization of the carbonyl of oxaloacetate in the active-site of citrate synthase. Biochemistry 26 (1987) 2623-2627
-
(1987)
Biochemistry
, vol.26
, pp. 2623-2627
-
-
Kurz, L.C.1
Drysdale, G.R.2
-
27
-
-
0025030707
-
Mutation of essential catalytic residues in pig citrate synthase
-
Alter G.M., Casazza J.P., Wang Z., Nemeth P., Srere P.A., and Evans C.T. Mutation of essential catalytic residues in pig citrate synthase. Biochemistry 29 (1990) 7557-7563
-
(1990)
Biochemistry
, vol.29
, pp. 7557-7563
-
-
Alter, G.M.1
Casazza, J.P.2
Wang, Z.3
Nemeth, P.4
Srere, P.A.5
Evans, C.T.6
-
28
-
-
0025214122
-
Proposed mechanism for the condensation reaction of citrate synthase: 1.9 Å structure of the ternary complex with oxaloacetate and carboxymethyl coenzyme-A
-
Karpusas M., Branchaud B., and Remington S.J. Proposed mechanism for the condensation reaction of citrate synthase: 1.9 Å structure of the ternary complex with oxaloacetate and carboxymethyl coenzyme-A. Biochemistry 29 (1990) 2213-2219
-
(1990)
Biochemistry
, vol.29
, pp. 2213-2219
-
-
Karpusas, M.1
Branchaud, B.2
Remington, S.J.3
-
29
-
-
0025923565
-
1.9 Å structures of ternary complexes of citrate synthase with d-malate and l-malate: mechanistic implications
-
Karpusas M., Holland D., and Remington S.J. 1.9 Å structures of ternary complexes of citrate synthase with d-malate and l-malate: mechanistic implications. Biochemistry 30 (1991) 6024-6031
-
(1991)
Biochemistry
, vol.30
, pp. 6024-6031
-
-
Karpusas, M.1
Holland, D.2
Remington, S.J.3
-
30
-
-
0029782417
-
Active site mutants of pig citrate synthase: effects of mutations on the enzyme catalytic and structural properties
-
Evans C.T., Kurz L.C., Remington S.J., and Srere P.A. Active site mutants of pig citrate synthase: effects of mutations on the enzyme catalytic and structural properties. Biochemistry 35 (1996) 10661-10672
-
(1996)
Biochemistry
, vol.35
, pp. 10661-10672
-
-
Evans, C.T.1
Kurz, L.C.2
Remington, S.J.3
Srere, P.A.4
-
31
-
-
0025636490
-
Citrate synthase from the thermophilic archaebacterium Thermoplasma acidophilum: cloning and sequencing of the gene
-
Sutherland K.J., Henneke C.M., Towner P., Hough D.W., and Danson M.J. Citrate synthase from the thermophilic archaebacterium Thermoplasma acidophilum: cloning and sequencing of the gene. Eur. J. Biochem. 194 (1990) 839-844
-
(1990)
Eur. J. Biochem.
, vol.194
, pp. 839-844
-
-
Sutherland, K.J.1
Henneke, C.M.2
Towner, P.3
Hough, D.W.4
Danson, M.J.5
-
32
-
-
0030741375
-
The crystal structure of citrate synthase from the hyperthermophilic archaeon Pyrococcus furiosus at 1.9 Ångstrom resolution
-
Russell R.J.M., Ferguson J.M.C., Hough D.W., Danson M.J., and Taylor G.L. The crystal structure of citrate synthase from the hyperthermophilic archaeon Pyrococcus furiosus at 1.9 Ångstrom resolution. Biochemistry 36 (1997) 9983-9994
-
(1997)
Biochemistry
, vol.36
, pp. 9983-9994
-
-
Russell, R.J.M.1
Ferguson, J.M.C.2
Hough, D.W.3
Danson, M.J.4
Taylor, G.L.5
-
33
-
-
0000841544
-
Mechanisms of citrate synthase and related enzymes (triose phosphate isomerase and mandelate racemase)
-
Remington S.J. Mechanisms of citrate synthase and related enzymes (triose phosphate isomerase and mandelate racemase). Curr. Opin. Struct. Biol. 2 (1992) 730-735
-
(1992)
Curr. Opin. Struct. Biol.
, vol.2
, pp. 730-735
-
-
Remington, S.J.1
-
34
-
-
0031127432
-
Understanding enzymic catalysis: the importance of short, strong hydrogen bonds
-
Gerlt J.A., Kreevoy M.M., Cleland W.W., and Frey P.A. Understanding enzymic catalysis: the importance of short, strong hydrogen bonds. Chem. Biol. 4 (1997) 259-267
-
(1997)
Chem. Biol.
, vol.4
, pp. 259-267
-
-
Gerlt, J.A.1
Kreevoy, M.M.2
Cleland, W.W.3
Frey, P.A.4
-
35
-
-
0028030684
-
Low-barrier hydrogen-bonds and enzymatic catalysis
-
Cleland W.W., and Kreevoy M.M. Low-barrier hydrogen-bonds and enzymatic catalysis. Science 264 (1994) 1887-1890
-
(1994)
Science
, vol.264
, pp. 1887-1890
-
-
Cleland, W.W.1
Kreevoy, M.M.2
-
36
-
-
0000397708
-
Unstable carbanions: general acid catalysis of the cleavage of 1-phenylcyclopropanol and 1-phenyl-2-arylcyclopropanol anions
-
Thibblin A., and Jencks W.P. Unstable carbanions: general acid catalysis of the cleavage of 1-phenylcyclopropanol and 1-phenyl-2-arylcyclopropanol anions. J. Am. Chem. Soc. 101 (1979) 4963-4973
-
(1979)
J. Am. Chem. Soc.
, vol.101
, pp. 4963-4973
-
-
Thibblin, A.1
Jencks, W.P.2
-
37
-
-
0027133903
-
An explanation for rapid enzyme-catalyzed proton abstraction from carbon acids: importance of late transition-states in concerted mechanisms
-
Gerlt J.A., and Gassman P.G. An explanation for rapid enzyme-catalyzed proton abstraction from carbon acids: importance of late transition-states in concerted mechanisms. J. Am. Chem. Soc. 115 (1993) 11552-11568
-
(1993)
J. Am. Chem. Soc.
, vol.115
, pp. 11552-11568
-
-
Gerlt, J.A.1
Gassman, P.G.2
-
38
-
-
0028817050
-
Do enzymes stabilize transition-states by electrostatic interactions or pK(a) balance: the case of triose phosphate isomerase (TIM)
-
Alagona G., Ghio C., and Kollman P.A. Do enzymes stabilize transition-states by electrostatic interactions or pK(a) balance: the case of triose phosphate isomerase (TIM). J. Am. Chem. Soc. 117 (1995) 9855-9862
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 9855-9862
-
-
Alagona, G.1
Ghio, C.2
Kollman, P.A.3
-
39
-
-
0030090490
-
Short strong hydrogen bonds: can they explain enzymic catalysis?
-
Guthrie J.P. Short strong hydrogen bonds: can they explain enzymic catalysis?. Chem. Biol. 3 (1996) 163-170
-
(1996)
Chem. Biol.
, vol.3
, pp. 163-170
-
-
Guthrie, J.P.1
-
40
-
-
0029040169
-
On low-barrier hydrogen-bonds and enzyme catalysis
-
Warshel A., Papazyan A., and Kollman P.A. On low-barrier hydrogen-bonds and enzyme catalysis. Science 269 (1995) 102-104
-
(1995)
Science
, vol.269
, pp. 102-104
-
-
Warshel, A.1
Papazyan, A.2
Kollman, P.A.3
-
41
-
-
0030462453
-
Energy considerations show that low-barrier hydrogen bonds do not offer a catalytic advantage over ordinary hydrogen bonds
-
Warshel A., and Papazyan A. Energy considerations show that low-barrier hydrogen bonds do not offer a catalytic advantage over ordinary hydrogen bonds. Proc. Natl. Acad. Sci. U.S.A. 93 (1996) 13665-13670
-
(1996)
Proc. Natl. Acad. Sci. U.S.A.
, vol.93
, pp. 13665-13670
-
-
Warshel, A.1
Papazyan, A.2
-
42
-
-
0028854341
-
The non-existence of specially stabilized hydrogen-bonds in enzymes
-
Scheiner S., and Kar T. The non-existence of specially stabilized hydrogen-bonds in enzymes. J. Am. Chem. Soc. 117 (1995) 6970-6975
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 6970-6975
-
-
Scheiner, S.1
Kar, T.2
-
43
-
-
0001020921
-
Modeling enzyme reaction intermediates and transition states: citrate synthase
-
Mulholland A.J., and Richards W.G. Modeling enzyme reaction intermediates and transition states: citrate synthase. J. Phys. Chem. B 102 (1998) 6635-6646
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 6635-6646
-
-
Mulholland, A.J.1
Richards, W.G.2
-
44
-
-
0344138003
-
-
Molecular Simulations Inc., San Diego, CA
-
Quanta96 (1996), Molecular Simulations Inc., San Diego, CA
-
(1996)
Quanta96
-
-
-
45
-
-
84986512474
-
CHARMM: a program for macromolecular energy, minimization, and dynamics calculations
-
Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., and Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4 (1983) 187-217
-
(1983)
J. Comp. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
46
-
-
84893169025
-
General atomic and molecular electronic-structure system
-
Schmidt M.W., Baldridge K.K., Boatz J.A., Elbert S.T., Gordon M.S., Jensen J.H., Koseki S., Matsunaga N., Nguyen K.A., Su S.J., Windus T.L., Dupuis M., and Montgomery J.A. General atomic and molecular electronic-structure system. J. Comp. Chem. 14 (1993) 1347-1363
-
(1993)
J. Comp. Chem.
, vol.14
, pp. 1347-1363
-
-
Schmidt, M.W.1
Baldridge, K.K.2
Boatz, J.A.3
Elbert, S.T.4
Gordon, M.S.5
Jensen, J.H.6
Koseki, S.7
Matsunaga, N.8
Nguyen, K.A.9
Su, S.J.10
Windus, T.L.11
Dupuis, M.12
Montgomery, J.A.13
-
47
-
-
0000218385
-
A hybrid QM-MM potential employing Hartree-Fock or density functional methods in the quantum region
-
Lyne P.D., Hodoscek M., and Karplus M. A hybrid QM-MM potential employing Hartree-Fock or density functional methods in the quantum region. J. Phys. Chem. A 103 (1999) 3462-3471
-
(1999)
J. Phys. Chem. A
, vol.103
, pp. 3462-3471
-
-
Lyne, P.D.1
Hodoscek, M.2
Karplus, M.3
-
48
-
-
0034716340
-
Ab initio QM/MM study of the citrate synthase mechanism. A low-barrier hydrogen bond is not involved
-
Mulholland A.J., Lyne P.D., and Karplus M. Ab initio QM/MM study of the citrate synthase mechanism. A low-barrier hydrogen bond is not involved. J. Am. Chem. Soc. 122 (2000) 534-535
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 534-535
-
-
Mulholland, A.J.1
Lyne, P.D.2
Karplus, M.3
-
49
-
-
0004133516
-
-
Gaussian Inc., Pittsburgh, PA
-
Gaussian94 (1995), Gaussian Inc., Pittsburgh, PA
-
(1995)
Gaussian94
-
-
-
50
-
-
33644930396
-
Ab initio studies of hydrogen-bonding of N-methylacetamide: structure, cooperativity, and internal rotational barriers
-
Guo H., and Karplus M. Ab initio studies of hydrogen-bonding of N-methylacetamide: structure, cooperativity, and internal rotational barriers. J. Phys. Chem. 96 (1992) 7273-7287
-
(1992)
J. Phys. Chem.
, vol.96
, pp. 7273-7287
-
-
Guo, H.1
Karplus, M.2
-
51
-
-
0031559456
-
Proton transfer and correlations between the C-O, O-H, N-H and O⋯N bond lengths in amine phenolates
-
Majerz I., Malarski Z., and Sobczyk L. Proton transfer and correlations between the C-O, O-H, N-H and O⋯N bond lengths in amine phenolates. Chem. Phys. Lett. 274 (1997) 361-364
-
(1997)
Chem. Phys. Lett.
, vol.274
, pp. 361-364
-
-
Majerz, I.1
Malarski, Z.2
Sobczyk, L.3
-
52
-
-
0000167881
-
Insights into chorismate mutase catalysis from a combined QM/MM simulation of the enzyme reaction
-
Lyne P.D., Mulholland A.J., and Richards W.G. Insights into chorismate mutase catalysis from a combined QM/MM simulation of the enzyme reaction. J. Am. Chem. Soc. 117 (1995) 11345-11350
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 11345-11350
-
-
Lyne, P.D.1
Mulholland, A.J.2
Richards, W.G.3
-
53
-
-
0027023534
-
Simulation analysis of triose phosphate isomerase: conformational transition and catalysis
-
Karplus M., Evanseck J.D., Joseph D., Bash P.A., and Field M.J. Simulation analysis of triose phosphate isomerase: conformational transition and catalysis. Farad. Discuss. 93 (1992) 239-248
-
(1992)
Farad. Discuss.
, vol.93
, pp. 239-248
-
-
Karplus, M.1
Evanseck, J.D.2
Joseph, D.3
Bash, P.A.4
Field, M.J.5
-
54
-
-
0025743628
-
Computer-simulation and analysis of the reaction pathway of triosephosphate isomerase
-
Bash P.A., Field M.J., Davenport R.C., Petsko G.A., Ringe D., and Karplus M. Computer-simulation and analysis of the reaction pathway of triosephosphate isomerase. Biochemistry 30 (1991) 5826-5832
-
(1991)
Biochemistry
, vol.30
, pp. 5826-5832
-
-
Bash, P.A.1
Field, M.J.2
Davenport, R.C.3
Petsko, G.A.4
Ringe, D.5
Karplus, M.6
-
55
-
-
84962339874
-
Hydrated proton clusters and solvent effects on the proton-transfer barrier: a density-functional study
-
Wei D.Q., and Salahub D.R. Hydrated proton clusters and solvent effects on the proton-transfer barrier: a density-functional study. J. Chem. Phys. 101 (1994) 7633-7642
-
(1994)
J. Chem. Phys.
, vol.101
, pp. 7633-7642
-
-
Wei, D.Q.1
Salahub, D.R.2
-
56
-
-
0012613807
-
The effect of ordered water on a short, strong (Speakman-Hadzi) hydrogen bond
-
Marimanikkuppam S.S., Lee I.S.H., Binder D.A., Young V.G., and Kreevoy M.M. The effect of ordered water on a short, strong (Speakman-Hadzi) hydrogen bond. Croatica Chemica Acta 69 (1996) 1661-1674
-
(1996)
Croatica Chemica Acta
, vol.69
, pp. 1661-1674
-
-
Marimanikkuppam, S.S.1
Lee, I.S.H.2
Binder, D.A.3
Young, V.G.4
Kreevoy, M.M.5
-
57
-
-
0000263008
-
Study of hydrogen bonding interactions relevant to biomolecular structure and function
-
Zheng Y.-J., and Merz Jr. K.M. Study of hydrogen bonding interactions relevant to biomolecular structure and function. J. Comp. Chem. 13 (1992) 1151-1169
-
(1992)
J. Comp. Chem.
, vol.13
, pp. 1151-1169
-
-
Zheng, Y.-J.1
Merz Jr., K.M.2
-
58
-
-
0029905014
-
The change in hydrogen bond strength accompanying charge rearrangement: implications for enzymatic catalysis
-
Shan S.O., and Herschlag D. The change in hydrogen bond strength accompanying charge rearrangement: implications for enzymatic catalysis. Proc. Natl. Acad. Sci. U.S.A. 93 (1996) 14474-14479
-
(1996)
Proc. Natl. Acad. Sci. U.S.A.
, vol.93
, pp. 14474-14479
-
-
Shan, S.O.1
Herschlag, D.2
-
59
-
-
10344265555
-
Differential transition-state stabilization in enzyme catalysis: quantum chemical analysis of interactions in the chorismate mutase reaction and prediction of the optimal catalytic field
-
Szefczyk B., Mulholland A.J., Ranaghan K.E., and Sokalski W.A. Differential transition-state stabilization in enzyme catalysis: quantum chemical analysis of interactions in the chorismate mutase reaction and prediction of the optimal catalytic field. J. Am. Chem. Soc. 126 (2004) 16148-16159
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 16148-16159
-
-
Szefczyk, B.1
Mulholland, A.J.2
Ranaghan, K.E.3
Sokalski, W.A.4
-
60
-
-
0017058392
-
Evolution of enzyme function and development of catalytic efficiency
-
Albery W.J., and Knowles J.R. Evolution of enzyme function and development of catalytic efficiency. Biochemistry 15 (1976) 5631-5640
-
(1976)
Biochemistry
, vol.15
, pp. 5631-5640
-
-
Albery, W.J.1
Knowles, J.R.2
-
61
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., and Klein M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79 (1983) 926-935
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
62
-
-
0015168208
-
Stereochemistry of Si-citrate synthase and ATP-citrate-lyase reactions
-
Lenz H., Buckel W., Wunderwa P., Biederma G., Buschmei V., Eggerer H., Cornfort J.W., Redmond J.W., and Mallaby R. Stereochemistry of Si-citrate synthase and ATP-citrate-lyase reactions. Eur. J. Biochem. 24 (1971) 207-215
-
(1971)
Eur. J. Biochem.
, vol.24
, pp. 207-215
-
-
Lenz, H.1
Buckel, W.2
Wunderwa, P.3
Biederma, G.4
Buschmei, V.5
Eggerer, H.6
Cornfort, J.W.7
Redmond, J.W.8
Mallaby, R.9
-
63
-
-
0000047442
-
Generation and stability of a simple thiol ester enolate in aqueous-solution
-
Amyes T.L., and Richard J.P. Generation and stability of a simple thiol ester enolate in aqueous-solution. J. Am. Chem. Soc. 114 (1992) 10297-10302
-
(1992)
J. Am. Chem. Soc.
, vol.114
, pp. 10297-10302
-
-
Amyes, T.L.1
Richard, J.P.2
-
64
-
-
0041111670
-
Kinetic studies on citrate-condensing enzyme
-
Kosicki G.W., and Srere P.A. Kinetic studies on citrate-condensing enzyme. J. Biol. Chem. 236 (1961) 2560-2565
-
(1961)
J. Biol. Chem.
, vol.236
, pp. 2560-2565
-
-
Kosicki, G.W.1
Srere, P.A.2
-
65
-
-
0025871717
-
Neutral imidazole is the electrophile in the reaction catalyzed by triosephosphate isomerase: structural origins and catalytic implications
-
Lodi P.J., and Knowles J.R. Neutral imidazole is the electrophile in the reaction catalyzed by triosephosphate isomerase: structural origins and catalytic implications. Biochemistry 30 (1991) 6948-6956
-
(1991)
Biochemistry
, vol.30
, pp. 6948-6956
-
-
Lodi, P.J.1
Knowles, J.R.2
-
66
-
-
33646371941
-
Low-barrier hydrogen bond hypothesis in the catalytic triad residue of serine proteases: correlation between structural rearrangement and chemical shifts in the acylation process
-
Ishida T. Low-barrier hydrogen bond hypothesis in the catalytic triad residue of serine proteases: correlation between structural rearrangement and chemical shifts in the acylation process. Biochemistry 45 (2006) 5413-5420
-
(2006)
Biochemistry
, vol.45
, pp. 5413-5420
-
-
Ishida, T.1
-
67
-
-
2442606719
-
The low barrier hydrogen bond (LBHB) proposal revisited: the case of the Asp...His pair in serine proteases
-
Schutz C.N., and Warshel A. The low barrier hydrogen bond (LBHB) proposal revisited: the case of the Asp...His pair in serine proteases. Prot. Struct. Funct. Bioinf. 55 (2004) 711-723
-
(2004)
Prot. Struct. Funct. Bioinf.
, vol.55
, pp. 711-723
-
-
Schutz, C.N.1
Warshel, A.2
-
68
-
-
0038613083
-
NMR chemical shifts in the low-pH form of alpha-chymotrypsin. A QM/MM and ONIOM-NMR study
-
Molina P.A., Sikorski R.S., and Jensen J.H. NMR chemical shifts in the low-pH form of alpha-chymotrypsin. A QM/MM and ONIOM-NMR study. Theor. Chem. Accounts 109 (2003) 100-107
-
(2003)
Theor. Chem. Accounts
, vol.109
, pp. 100-107
-
-
Molina, P.A.1
Sikorski, R.S.2
Jensen, J.H.3
-
69
-
-
0037899651
-
Computational study of the citrate synthase catalyzed deprotonation of acetyl-coenzyme A and fluoroacetyl-coenzyme A: demonstration of a layered quantum mechanical approach
-
Yang W., and Drueckhammer D.G. Computational study of the citrate synthase catalyzed deprotonation of acetyl-coenzyme A and fluoroacetyl-coenzyme A: demonstration of a layered quantum mechanical approach. J. Phys. Chem. B 107 (2003) 5986-5994
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 5986-5994
-
-
Yang, W.1
Drueckhammer, D.G.2
-
70
-
-
31144441067
-
ONIOM: a multi-layered integrated MO + MM method for geometry optimizations and single point energy predictions. A test for Diels-Alder reactions and Pt(P(t-Bu)3)2 + H2 oxidative addition
-
Svensson M., Humbel S., Froese R.D.J., Matsubara T., Sieber S., and Morokuma K. ONIOM: a multi-layered integrated MO + MM method for geometry optimizations and single point energy predictions. A test for Diels-Alder reactions and Pt(P(t-Bu)3)2 + H2 oxidative addition. J. Phys. Chem. 100 (1996) 19357-19363
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 19357-19363
-
-
Svensson, M.1
Humbel, S.2
Froese, R.D.J.3
Matsubara, T.4
Sieber, S.5
Morokuma, K.6
-
71
-
-
0038617502
-
Improved second-order Møller-Plesset perturbation theory by separate scaling of parallel- and antiparallel-spin pair correlation energies
-
Grimme S. Improved second-order Møller-Plesset perturbation theory by separate scaling of parallel- and antiparallel-spin pair correlation energies. J. Chem. Phys. 118 (2003) 9095-9102
-
(2003)
J. Chem. Phys.
, vol.118
, pp. 9095-9102
-
-
Grimme, S.1
-
72
-
-
3042588230
-
Hydrogen tunneling in quinoproteins
-
Masgrau L., Basran J., Hothi P., Sutcliffe M.J., and Scrutton N.S. Hydrogen tunneling in quinoproteins. Arch. Biochem. Biophys. 428 (2004) 41-51
-
(2004)
Arch. Biochem. Biophys.
, vol.428
, pp. 41-51
-
-
Masgrau, L.1
Basran, J.2
Hothi, P.3
Sutcliffe, M.J.4
Scrutton, N.S.5
-
73
-
-
33645801770
-
Atomic description of an enzyme reaction dominated by proton tunneling
-
Masgrau L., Roujeinikova A., Johannissen L.O., Hothi P., Basran J., Ranaghan K.E., Mulholland A.J., Sutcliffe M.J., Scrutton N.S., and Leys D. Atomic description of an enzyme reaction dominated by proton tunneling. Science 312 (2006) 237-241
-
(2006)
Science
, vol.312
, pp. 237-241
-
-
Masgrau, L.1
Roujeinikova, A.2
Johannissen, L.O.3
Hothi, P.4
Basran, J.5
Ranaghan, K.E.6
Mulholland, A.J.7
Sutcliffe, M.J.8
Scrutton, N.S.9
Leys, D.10
-
74
-
-
0010114887
-
Deuterium isotope rate effects with citrate-condensing enzyme
-
Kosicki G., and Srere Pa. Deuterium isotope rate effects with citrate-condensing enzyme. J. Biol. Chem. 236 (1961) 2566
-
(1961)
J. Biol. Chem.
, vol.236
, pp. 2566
-
-
Kosicki, G.1
Srere, Pa.2
-
75
-
-
1442277682
-
Computational modeling of the catalytic reaction in triosephosphate isomerase
-
Guallar V., Jacobson M., Mcdermott A., and Friesner R.A. Computational modeling of the catalytic reaction in triosephosphate isomerase. J. Mol. Biol. 337 (2004) 227-239
-
(2004)
J. Mol. Biol.
, vol.337
, pp. 227-239
-
-
Guallar, V.1
Jacobson, M.2
Mcdermott, A.3
Friesner, R.A.4
-
76
-
-
0028241778
-
A very short hydrogen bond provides only moderate stabilization of an enzyme-inhibitor complex of citrate synthase
-
Usher K.C., Remington S.J., Martin D.P., and Drueckhammer D.G. A very short hydrogen bond provides only moderate stabilization of an enzyme-inhibitor complex of citrate synthase. Biochemistry 33 (1994) 7753-7759
-
(1994)
Biochemistry
, vol.33
, pp. 7753-7759
-
-
Usher, K.C.1
Remington, S.J.2
Martin, D.P.3
Drueckhammer, D.G.4
-
77
-
-
0031179495
-
A low energy short hydrogen bond in very high resolution structures of protein receptor phosphate complexes
-
Wang Z.M., Luecke H., Yao N.H., and Quiocho F.A. A low energy short hydrogen bond in very high resolution structures of protein receptor phosphate complexes. Nat. Struct. Biol. 4 (1997) 519-522
-
(1997)
Nat. Struct. Biol.
, vol.4
, pp. 519-522
-
-
Wang, Z.M.1
Luecke, H.2
Yao, N.H.3
Quiocho, F.A.4
-
78
-
-
0000756814
-
The ionic hydrogen-bond and ion solvation. 5. OH...O-bonds: gas-phase solvation and clustering of alkoxide and carboxylate anions
-
Meot-Ner M., and Sieck L.W. The ionic hydrogen-bond and ion solvation. 5. OH...O-bonds: gas-phase solvation and clustering of alkoxide and carboxylate anions. J. Am. Chem. Soc. 108 (1986) 7525-7529
-
(1986)
J. Am. Chem. Soc.
, vol.108
, pp. 7525-7529
-
-
Meot-Ner, M.1
Sieck, L.W.2
-
79
-
-
0029926948
-
The energetics of hydrogen bonds in model systems: implications for enzymatic catalysis
-
Shan S.O., Loh S., and Herschlag D. The energetics of hydrogen bonds in model systems: implications for enzymatic catalysis. Science 272 (1996) 97-101
-
(1996)
Science
, vol.272
, pp. 97-101
-
-
Shan, S.O.1
Loh, S.2
Herschlag, D.3
-
80
-
-
4243810035
-
Simulation of enzyme-reactions using valence-bond force-fields and other hybrid quantum-classical approaches
-
Åqvist J., and Warshel A. Simulation of enzyme-reactions using valence-bond force-fields and other hybrid quantum-classical approaches. Chem. Rev. 93 (1993) 2523-2544
-
(1993)
Chem. Rev.
, vol.93
, pp. 2523-2544
-
-
Åqvist, J.1
Warshel, A.2
-
81
-
-
2642622572
-
Combined ab initio and free energy calculations to study reactions in enzymes and solution: amide hydrolysis in trypsin and aqueous solution
-
Stanton V., Peräkylä P., Bakowies D., and Kollman P.A. Combined ab initio and free energy calculations to study reactions in enzymes and solution: amide hydrolysis in trypsin and aqueous solution. J. Am. Chem. Soc. 120 (1998) 3448-3457
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 3448-3457
-
-
Stanton, V.1
Peräkylä, P.2
Bakowies, D.3
Kollman, P.A.4
-
82
-
-
0035155864
-
Elucidating the nature of enzyme catalysis utilizing a new twist on an old methodology: quantum mechanical-free energy calculations on chemical reactions in enzymes and in aqueous solution
-
Kollman P.A., Kuhn B., Donini O., Perakyla M., Stanton R., and Bakowies D. Elucidating the nature of enzyme catalysis utilizing a new twist on an old methodology: quantum mechanical-free energy calculations on chemical reactions in enzymes and in aqueous solution. Acc. Chem. Res. 34 (2001) 72-79
-
(2001)
Acc. Chem. Res.
, vol.34
, pp. 72-79
-
-
Kollman, P.A.1
Kuhn, B.2
Donini, O.3
Perakyla, M.4
Stanton, R.5
Bakowies, D.6
-
83
-
-
0034645570
-
QM-FE calculations of aliphatic hydrogen abstraction in citrate synthase and in solution: reproduction of the effect of enzyme catalysis and demonstration that an enolate rather than an enol is formed
-
Donini O., Darden T., and Kollman P.A. QM-FE calculations of aliphatic hydrogen abstraction in citrate synthase and in solution: reproduction of the effect of enzyme catalysis and demonstration that an enolate rather than an enol is formed. J. Am. Chem. Soc. 122 (2000) 12270-12280
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 12270-12280
-
-
Donini, O.1
Darden, T.2
Kollman, P.A.3
-
84
-
-
0020483375
-
Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 and 1. 7 Å resolution
-
Remington S., Wiegand G., and Huber R. Crystallographic refinement and atomic models of two different forms of citrate synthase at 2.7 and 1. 7 Å resolution. J. Mol. Biol. 158 (1982) 111-152
-
(1982)
J. Mol. Biol.
, vol.158
, pp. 111-152
-
-
Remington, S.1
Wiegand, G.2
Huber, R.3
-
85
-
-
33747151589
-
QM/MM modeling of compound I active species in cytochrome P450, cytochrome C peroxidase, and ascorbate peroxidase
-
Harvey J.N., Bathelt C.M., and Mulholland A.J. QM/MM modeling of compound I active species in cytochrome P450, cytochrome C peroxidase, and ascorbate peroxidase. J. Comp. Chem. 27 (2006) 1352-1362
-
(2006)
J. Comp. Chem.
, vol.27
, pp. 1352-1362
-
-
Harvey, J.N.1
Bathelt, C.M.2
Mulholland, A.J.3
-
86
-
-
3042691605
-
Hybrid QM/MM potentials of mean force with interpolated corrections
-
Ruiz-Pernia J.J., Silla E., Tunon I., Marti S., and Moliner V. Hybrid QM/MM potentials of mean force with interpolated corrections. J. Phys. Chem. B 108 (2004) 8427-8433
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 8427-8433
-
-
Ruiz-Pernia, J.J.1
Silla, E.2
Tunon, I.3
Marti, S.4
Moliner, V.5
-
87
-
-
0037151638
-
Quantum mechanical/molecular mechanical free energy simulations of the glutathione S-transferase (M1-1) reaction with phenanthrene 9.10-oxide
-
Ridder L.O., Rietjens I.M.C.M., Vervoort J., and Mulholland A.J. Quantum mechanical/molecular mechanical free energy simulations of the glutathione S-transferase (M1-1) reaction with phenanthrene 9.10-oxide. J. Am. Chem. Soc. 124 (2002) 9926-9936
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 9926-9936
-
-
Ridder, L.O.1
Rietjens, I.M.C.M.2
Vervoort, J.3
Mulholland, A.J.4
-
88
-
-
0035138648
-
A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method
-
Cui Q., Elstner M., Kaxiras E., Frauenheim T., and Karplus M. A QM/MM implementation of the self-consistent charge density functional tight binding (SCC-DFTB) method. J. Phys. Chem. B 105 (2001) 569-585
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 569-585
-
-
Cui, Q.1
Elstner, M.2
Kaxiras, E.3
Frauenheim, T.4
Karplus, M.5
-
89
-
-
84961974890
-
Hybrid ab initio QM/MM simulation of N-methylacetamide in aqueous solution
-
Gao J.L., and Freindorf M. Hybrid ab initio QM/MM simulation of N-methylacetamide in aqueous solution. J. Phys. Chem. A 101 (1997) 3182-3188
-
(1997)
J. Phys. Chem. A
, vol.101
, pp. 3182-3188
-
-
Gao, J.L.1
Freindorf, M.2
-
90
-
-
2642585833
-
Importance of Van der Waals interactions in QM/MM simulations
-
Riccardi D., Li G.H., and Cui Q. Importance of Van der Waals interactions in QM/MM simulations. J. Phys. Chem. B 108 (2004) 6467-6478
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 6467-6478
-
-
Riccardi, D.1
Li, G.H.2
Cui, Q.3
|