-
1
-
-
78651228986
-
Enzymes of the mevalonate pathway of isoprenoid biosynthesis
-
Miziorko, H. M. (2011) Enzymes of the mevalonate pathway of isoprenoid biosynthesis Arch. Biochem. Biophys. 505, 131-143
-
(2011)
Arch. Biochem. Biophys.
, vol.505
, pp. 131-143
-
-
Miziorko, H.M.1
-
2
-
-
38049034068
-
Pleiotropic effects of statin therapy: Molecular mechanisms and clinical results
-
Liao, J. K., Wang, C. Y., and Liu, P. Y. (2008) Pleiotropic effects of statin therapy: Molecular mechanisms and clinical results Trends Mol. Med. 14, 37-44
-
(2008)
Trends Mol. Med.
, vol.14
, pp. 37-44
-
-
Liao, J.K.1
Wang, C.Y.2
Liu, P.Y.3
-
3
-
-
79957440771
-
Specific inhibitions of annonaceous acetogenins on class II 3-hydroxy-3-methylglutaryl coenzyme A reductase from Streptococcus pneumoniae
-
Feng, L. L., Zhou, L., Sun, Y., Gui, J., Wang, X. F., Wu, P., Wan, J., Ren, Y. L., Qiu, S. X., Wei, X. Y., and Li, J. (2011) Specific inhibitions of annonaceous acetogenins on class II 3-hydroxy-3-methylglutaryl coenzyme A reductase from Streptococcus pneumoniae Bioorg. Med. Chem. 19, 3512-3519
-
(2011)
Bioorg. Med. Chem.
, vol.19
, pp. 3512-3519
-
-
Feng, L.L.1
Zhou, L.2
Sun, Y.3
Gui, J.4
Wang, X.F.5
Wu, P.6
Wan, J.7
Ren, Y.L.8
Qiu, S.X.9
Wei, X.Y.10
Li, J.11
-
4
-
-
2442661382
-
Inhibition of the Class II HMG-CoA reductase of Pseudomonas mevalonii
-
Hedl, M. and Rodwell, V. W. (2004) Inhibition of the Class II HMG-CoA reductase of Pseudomonas mevalonii Protein Sci. 13, 1693-1697
-
(2004)
Protein Sci.
, vol.13
, pp. 1693-1697
-
-
Hedl, M.1
Rodwell, V.W.2
-
5
-
-
84864203547
-
Structure-Based Design and Screen of Novel Inhibitors for Class II 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase from Streptococcus pneumoniae
-
Li, D., Gui, J., Li, Y., Feng, L., Han, X., Sun, Y., Sun, T., Chen, Z., Cao, Y., Zhang, Y., Zhou, L., Hu, X., Ren, Y., and Wan, J. (2012) Structure-Based Design and Screen of Novel Inhibitors for Class II 3-Hydroxy-3-methylglutaryl Coenzyme A Reductase from Streptococcus pneumoniae J. Chem. Inf. Model. 52, 1833-1841
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 1833-1841
-
-
Li, D.1
Gui, J.2
Li, Y.3
Feng, L.4
Han, X.5
Sun, Y.6
Sun, T.7
Chen, Z.8
Cao, Y.9
Zhang, Y.10
Zhou, L.11
Hu, X.12
Ren, Y.13
Wan, J.14
-
6
-
-
73349085890
-
Inhibitors of HMG-CoA Reductase: Current and Future Prospects
-
Medina-Franco, J. L., Singh, N., Tamariz, J., and Chamorro, G. (2009) Inhibitors of HMG-CoA Reductase: Current and Future Prospects Mini-Rev. Med. Chem. 9, 1272-1283
-
(2009)
Mini-Rev. Med. Chem.
, vol.9
, pp. 1272-1283
-
-
Medina-Franco, J.L.1
Singh, N.2
Tamariz, J.3
Chamorro, G.4
-
7
-
-
0038004785
-
Lovastatin and beyond: The history of the HMG-CoA reductase inhibitors
-
Tobert, J. A. (2003) Lovastatin and beyond: The history of the HMG-CoA reductase inhibitors Nat. Rev. Drug Discovery 2, 517-526
-
(2003)
Nat. Rev. Drug Discovery
, vol.2
, pp. 517-526
-
-
Tobert, J.A.1
-
8
-
-
79961118496
-
Regulation of HMG-CoA reductase in mammals and yeast
-
Burg, J. S. and Espenshade, P. J. (2011) Regulation of HMG-CoA reductase in mammals and yeast Prog. Lipid Res. 50, 403-410
-
(2011)
Prog. Lipid Res.
, vol.50
, pp. 403-410
-
-
Burg, J.S.1
Espenshade, P.J.2
-
9
-
-
0034161543
-
Crystal structure of the catalytic portion of human HMG-CoA reductase: Insights into regulation of activity and catalysis
-
Istvan, E. S., Palnitkar, M., Buchanan, S. K., and Deisenhofer, J. (2000) Crystal structure of the catalytic portion of human HMG-CoA reductase: Insights into regulation of activity and catalysis EMBO J. 19, 819-830
-
(2000)
EMBO J.
, vol.19
, pp. 819-830
-
-
Istvan, E.S.1
Palnitkar, M.2
Buchanan, S.K.3
Deisenhofer, J.4
-
10
-
-
0034672685
-
The structure of the catalytic portion of human HMG-CoA reductase
-
Istvan, E. S. and Deisenhofer, J. (2000) The structure of the catalytic portion of human HMG-CoA reductase Biochim. Biophys. Acta 1529, 9-18
-
(2000)
Biochim. Biophys. Acta
, vol.1529
, pp. 9-18
-
-
Istvan, E.S.1
Deisenhofer, J.2
-
11
-
-
0033595021
-
Substrate-induced closure of the flap domain in the ternary complex structures provides insights into the mechanism of catalysis by 3-hydroxy-3-methylglutaryl-CoA reductase
-
Tabernero, L., Bochar, D. A., Rodwell, V. W., and Stauffacher, C. V. (1999) Substrate-induced closure of the flap domain in the ternary complex structures provides insights into the mechanism of catalysis by 3-hydroxy-3-methylglutaryl-CoA reductase Proc. Natl. Acad. Sci. U.S.A. 96, 7167-7171
-
(1999)
Proc. Natl. Acad. Sci. U.S.A.
, vol.96
, pp. 7167-7171
-
-
Tabernero, L.1
Bochar, D.A.2
Rodwell, V.W.3
Stauffacher, C.V.4
-
12
-
-
0029066497
-
Crystal-Structure of Pseudomonas mevalonii HMG-CoA Reductase at 3.0 Å Resolution
-
Lawrence, C. M., Rodwell, V. W., and Stauffacher, C. V. (1995) Crystal-Structure of Pseudomonas mevalonii HMG-CoA Reductase at 3.0 Å Resolution Science 268, 1758-1762
-
(1995)
Science
, vol.268
, pp. 1758-1762
-
-
Lawrence, C.M.1
Rodwell, V.W.2
Stauffacher, C.V.3
-
13
-
-
2442658600
-
Substrate-Competetive Inhibition of Bacterial Mevalonate:Nicotinamide- Adenine Dinucleotide Oxidoreductase (acylating CoA)
-
Fimognari, G. M. and Rodwell, V. W. (1965) Substrate-Competetive Inhibition of Bacterial Mevalonate:Nicotinamide-Adenine Dinucleotide Oxidoreductase (acylating CoA) Biochemistry 4, 2086-2090
-
(1965)
Biochemistry
, vol.4
, pp. 2086-2090
-
-
Fimognari, G.M.1
Rodwell, V.W.2
-
14
-
-
0035693327
-
Bacterial and mammalian HMG-CoA reductases: Related enzymes with distinct architectures
-
Istvan, E. S. (2001) Bacterial and mammalian HMG-CoA reductases: Related enzymes with distinct architectures Curr. Opin. Struct. Biol. 11, 746-751
-
(2001)
Curr. Opin. Struct. Biol.
, vol.11
, pp. 746-751
-
-
Istvan, E.S.1
-
15
-
-
0032789945
-
Sequence comparisons reveal two classes of 3-hydroxy-3-methylglutaryl coenzyme A reductase
-
Bochar, D. A., Stauffacher, C. V., and Rodwell, V. W. (1999) Sequence comparisons reveal two classes of 3-hydroxy-3-methylglutaryl coenzyme A reductase Mol. Genet. Metab. 66, 122-127
-
(1999)
Mol. Genet. Metab.
, vol.66
, pp. 122-127
-
-
Bochar, D.A.1
Stauffacher, C.V.2
Rodwell, V.W.3
-
16
-
-
9544233649
-
Structural determinants of nucleotide coenzyme specificity in the distinctive dinucleotide binding fold of HMG-CoA reductase from Pseudomonas mevalonii
-
Friesen, J. A., Lawrence, C. M., Stauffacher, C. V., and Rodwell, V. W. (1996) Structural determinants of nucleotide coenzyme specificity in the distinctive dinucleotide binding fold of HMG-CoA reductase from Pseudomonas mevalonii Biochemistry 35, 11945-11950
-
(1996)
Biochemistry
, vol.35
, pp. 11945-11950
-
-
Friesen, J.A.1
Lawrence, C.M.2
Stauffacher, C.V.3
Rodwell, V.W.4
-
17
-
-
0015218609
-
Stereospecificity of the transfer of hydrogen from reduced nicotinamide adenine dinucleotide phosphate in each of the two reductive steps catalyzed by β-hydroxy-β-methylglutaryl coenzyme A reductase
-
Dugan, R. E. and Porter, J. W. (1971) Stereospecificity of the transfer of hydrogen from reduced nicotinamide adenine dinucleotide phosphate in each of the two reductive steps catalyzed by β-hydroxy-β-methylglutaryl coenzyme A reductase J. Biol. Chem. 246, 5361-5364
-
(1971)
J. Biol. Chem.
, vol.246
, pp. 5361-5364
-
-
Dugan, R.E.1
Porter, J.W.2
-
18
-
-
0015504915
-
The stereochemistry of hydrogen transfer from NADPH catalysed by 3-hydroxy-3-methylglutaryl-coenzyme A reductase from rat liver
-
Beedle, A. S., Munday, K. A., and Wilton, D. C. (1972) The stereochemistry of hydrogen transfer from NADPH catalysed by 3-hydroxy-3-methylglutaryl-coenzyme A reductase from rat liver Eur. J. Biochem. 28, 151-155
-
(1972)
Eur. J. Biochem.
, vol.28
, pp. 151-155
-
-
Beedle, A.S.1
Munday, K.A.2
Wilton, D.C.3
-
19
-
-
0014810958
-
A Probable Intermediate in Enzymic Reduction of 3-Hydroxy-3- Methylglutaryl Coenzyme-A
-
Retey, J., Stetten, E. V., Coy, U., and Lynen, F. (1970) A Probable Intermediate in Enzymic Reduction of 3-Hydroxy-3-Methylglutaryl Coenzyme-A Eur. J. Biochem. 15, 72-76
-
(1970)
Eur. J. Biochem.
, vol.15
, pp. 72-76
-
-
Retey, J.1
Stetten, E.V.2
Coy, U.3
Lynen, F.4
-
20
-
-
0015511285
-
The stereochemistry of the reduction of mevaldic acid-coenzyme A hemithioacetal by rat liver 3-hydroxy-3-methylglutaryl coenzyme A reductase
-
Beedle, A. S., Munday, K. A., and Wilton, D. C. (1972) The stereochemistry of the reduction of mevaldic acid-coenzyme A hemithioacetal by rat liver 3-hydroxy-3-methylglutaryl coenzyme A reductase FEBS Lett. 28, 13-15
-
(1972)
FEBS Lett.
, vol.28
, pp. 13-15
-
-
Beedle, A.S.1
Munday, K.A.2
Wilton, D.C.3
-
21
-
-
84872654421
-
Coenzyme A as Catalyst
-
submitted for publication
-
Steussy, C. N. C., Schmidt, T., Wrensford, L. V., Burgner, J. B., II, Rodwell, V. W., and Stauffacher, C. V. Coenzyme A as Catalyst. J. Biol. Chem., submitted for publication.
-
J. Biol. Chem.
-
-
Steussy, C.N.C.1
Schmidt, T.2
Wrensford, L.V.3
Burgner, I.I.J.B.4
Rodwell, V.W.5
Stauffacher, C.V.6
-
22
-
-
0024448563
-
Pseudomonas mevalonii 3-Hydroxy-3-Methylglutaryl-CoA Reductase: Characterization and Chemical Modification
-
Jordanstarck, T. C. and Rodwell, V. W. (1989) Pseudomonas mevalonii 3-Hydroxy-3-Methylglutaryl-CoA Reductase: Characterization and Chemical Modification J. Biol. Chem. 264, 17913-17918
-
(1989)
J. Biol. Chem.
, vol.264
, pp. 17913-17918
-
-
Jordanstarck, T.C.1
Rodwell, V.W.2
-
23
-
-
0000932365
-
Reduction of β-Hydroxy-β-methylglutaryl Coenzyme-A to Mevalonic Acid
-
Durr, I. F. and Rudney, H. (1960) Reduction of β-Hydroxy-β- methylglutaryl Coenzyme-A to Mevalonic Acid J. Biol. Chem. 235, 2572-2578
-
(1960)
J. Biol. Chem.
, vol.235
, pp. 2572-2578
-
-
Durr, I.F.1
Rudney, H.2
-
24
-
-
64549127462
-
Uber Die β-Hydroxy-β-Methyl-Glutaryl-Reduktase der Hefe: Zur Biosynthese der Terpene. 9
-
Knappe, J., Ringelmann, E., and Lynen, F. (1959) Uber Die β-Hydroxy-β-Methyl-Glutaryl-Reduktase Der Hefe: Zur Biosynthese Der Terpene. 9 Biochem. Z. 332, 195-213
-
(1959)
Biochem. Z.
, vol.332
, pp. 195-213
-
-
Knappe, J.1
Ringelmann, E.2
Lynen, F.3
-
25
-
-
0014939939
-
Purification and Properties of 3-Hydroxy-3-Methylglutaryl Coenzyme-A Reductase from Pseudomonas
-
Bensch, W. R. and Rodwell, V. W. (1970) Purification and Properties of 3-Hydroxy-3-Methylglutaryl Coenzyme-A Reductase from Pseudomonas J. Biol. Chem. 245, 3755-3762
-
(1970)
J. Biol. Chem.
, vol.245
, pp. 3755-3762
-
-
Bensch, W.R.1
Rodwell, V.W.2
-
26
-
-
0017104565
-
Kinetic analysis of the individual reductive steps catalyzed by β-hydroxy-β-methylglutaryl-coenzyme A reductase obtained from yeast
-
Qureshi, N., Dugan, R. E., Cleland, W. W., and Porter, J. W. (1976) Kinetic analysis of the individual reductive steps catalyzed by β-hydroxy-β-methylglutaryl-coenzyme A reductase obtained from yeast Biochemistry 15, 4191-4107
-
(1976)
Biochemistry
, vol.15
, pp. 4191-4107
-
-
Qureshi, N.1
Dugan, R.E.2
Cleland, W.W.3
Porter, J.W.4
-
28
-
-
0019883145
-
PH Properties and Chemical Mechanism of Action of 3-Hydroxy-3- methylglutaryl Coenzyme-A Reductase
-
Veloso, D., Cleland, W. W., and Porter, J. W. (1981) pH Properties and Chemical Mechanism of Action of 3-Hydroxy-3-methylglutaryl Coenzyme-A Reductase Biochemistry 20, 887-894
-
(1981)
Biochemistry
, vol.20
, pp. 887-894
-
-
Veloso, D.1
Cleland, W.W.2
Porter, J.W.3
-
29
-
-
0025685478
-
Identification of the Principal Catalytically Important Acidic Residue of 3-Hydroxy-3-methylglutaryl Coenzyme-A Reductase
-
Wang, Y. L., Darnay, B. G., and Rodwell, V. W. (1990) Identification of the Principal Catalytically Important Acidic Residue of 3-Hydroxy-3- methylglutaryl Coenzyme-A Reductase J. Biol. Chem. 265, 21634-21641
-
(1990)
J. Biol. Chem.
, vol.265
, pp. 21634-21641
-
-
Wang, Y.L.1
Darnay, B.G.2
Rodwell, V.W.3
-
30
-
-
0026683310
-
Identification of the Catalytically Important Histidine of 3-Hydroxy-3-methylglutaryl-Coenzyme-A Reductase
-
Darnay, B. G., Wang, Y. L., and Rodwell, V. W. (1992) Identification of the Catalytically Important Histidine of 3-Hydroxy-3-methylglutaryl-Coenzyme-A Reductase J. Biol. Chem. 267, 15064-15070
-
(1992)
J. Biol. Chem.
, vol.267
, pp. 15064-15070
-
-
Darnay, B.G.1
Wang, Y.L.2
Rodwell, V.W.3
-
31
-
-
0027339651
-
His(865) Is the Catalytically Important Histidyl Residue of Syrian-Hamster 3-Hydroxy-3-methylglutaryl-Coenzyme-A Reductase
-
Darnay, B. G. and Rodwell, V. W. (1993) His(865) Is the Catalytically Important Histidyl Residue of Syrian-Hamster 3-Hydroxy-3-methylglutaryl- Coenzyme-A Reductase J. Biol. Chem. 268, 8429-8435
-
(1993)
J. Biol. Chem.
, vol.268
, pp. 8429-8435
-
-
Darnay, B.G.1
Rodwell, V.W.2
-
32
-
-
0028365069
-
Catalysis by Syrian-Hamster 3-Hydroxy-3-methylglutaryl-Coenzyme-A Reductase: Proposed Roles of Histidine-865, Glutamate-558, and Aspartate-766
-
Frimpong, K. and Rodwell, V. W. (1994) Catalysis by Syrian-Hamster 3-Hydroxy-3-methylglutaryl-Coenzyme-A Reductase: Proposed Roles of Histidine-865, Glutamate-558, and Aspartate-766 J. Biol. Chem. 269, 11478-11483
-
(1994)
J. Biol. Chem.
, vol.269
, pp. 11478-11483
-
-
Frimpong, K.1
Rodwell, V.W.2
-
33
-
-
0029140384
-
Crystallization of HMG-CoA Reductase from Pseudomonas mevalonii
-
Lawrence, C. M., Chi, Y. I., Rodwell, V. W., and Stauffacher, C. V. (1995) Crystallization of HMG-CoA Reductase from Pseudomonas mevalonii Acta Crystallogr. D51, 386-389
-
(1995)
Acta Crystallogr.
, vol.51
, pp. 386-389
-
-
Lawrence, C.M.1
Chi, Y.I.2
Rodwell, V.W.3
Stauffacher, C.V.4
-
34
-
-
0033551436
-
Aminoethylcysteine can replace the function of the essential active site lysine of Pseudomonas mevalonii 3-hydroxy-3-methylglutaryl coenzyme A reductase
-
Bochar, D. A., Tabernero, L., Stauffacher, C. V., and Rodwell, V. W. (1999) Aminoethylcysteine can replace the function of the essential active site lysine of Pseudomonas mevalonii 3-hydroxy-3-methylglutaryl coenzyme A reductase Biochemistry 38, 8879-8883
-
(1999)
Biochemistry
, vol.38
, pp. 8879-8883
-
-
Bochar, D.A.1
Tabernero, L.2
Stauffacher, C.V.3
Rodwell, V.W.4
-
35
-
-
33748601471
-
Tunneling and dynamics in enzymatic hydride transfer
-
Nagel, Z. D. and Klinman, J. P. (2006) Tunneling and dynamics in enzymatic hydride transfer Chem. Rev. 106, 3095-3118
-
(2006)
Chem. Rev.
, vol.106
, pp. 3095-3118
-
-
Nagel, Z.D.1
Klinman, J.P.2
-
36
-
-
82455219011
-
Flexibility, Diversity, and Cooperativity: Pillars of Enzyme Catalysis
-
Hammes, G. G., Benkovic, S. J., and Hammes-Schiffer, S. (2011) Flexibility, Diversity, and Cooperativity: Pillars of Enzyme Catalysis Biochemistry 50, 10422-10430
-
(2011)
Biochemistry
, vol.50
, pp. 10422-10430
-
-
Hammes, G.G.1
Benkovic, S.J.2
Hammes-Schiffer, S.3
-
37
-
-
79958826524
-
Protein dynamics and enzyme catalysis: Insights from simulations
-
McGeagh, J. D., Ranaghan, K. E., and Mulholland, A. J. (2011) Protein dynamics and enzyme catalysis: Insights from simulations Biochim. Biophys. Acta 1814, 1077-1092
-
(2011)
Biochim. Biophys. Acta
, vol.1814
, pp. 1077-1092
-
-
McGeagh, J.D.1
Ranaghan, K.E.2
Mulholland, A.J.3
-
38
-
-
84857515422
-
Good vibrations in enzyme-catalysed reactions
-
Hay, S. and Scrutton, N. S. (2012) Good vibrations in enzyme-catalysed reactions Nat. Chem. 4, 161-168
-
(2012)
Nat. Chem.
, vol.4
, pp. 161-168
-
-
Hay, S.1
Scrutton, N.S.2
-
39
-
-
0034679001
-
Computational studies of the mechanism for proton and hydride transfer in liver alcohol dehydrogenase
-
Agarwal, P. K., Webb, S. P., and Hammes-Schiffer, S. (2000) Computational studies of the mechanism for proton and hydride transfer in liver alcohol dehydrogenase J. Am. Chem. Soc. 122, 4803-4812
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 4803-4812
-
-
Agarwal, P.K.1
Webb, S.P.2
Hammes-Schiffer, S.3
-
40
-
-
0037076062
-
A theoretical analysis of the proton and hydride transfer in liver alcohol dehydrogenase (LADH)
-
Cui, Q., Elstner, M., and Karplus, M. (2002) A theoretical analysis of the proton and hydride transfer in liver alcohol dehydrogenase (LADH) J. Phys. Chem. B 106, 2721-2740
-
(2002)
J. Phys. Chem. B
, vol.106
, pp. 2721-2740
-
-
Cui, Q.1
Elstner, M.2
Karplus, M.3
-
41
-
-
0029785756
-
Mechanism of aldehyde oxidation catalyzed by horse liver alcohol dehydrogenase
-
Olson, L. P., Luo, J., Almarsson, O., and Bruice, T. C. (1996) Mechanism of aldehyde oxidation catalyzed by horse liver alcohol dehydrogenase Biochemistry 35, 9782-9791
-
(1996)
Biochemistry
, vol.35
, pp. 9782-9791
-
-
Olson, L.P.1
Luo, J.2
Almarsson, O.3
Bruice, T.C.4
-
42
-
-
0034734365
-
Quantum dynamics of hydride transfer in enzyme catalysis
-
Allhambra, C., Corchado, J. C., Sanchez, M. L., Gao, J. L., and Truhlar, D. G. (2000) Quantum dynamics of hydride transfer in enzyme catalysis J. Am. Chem. Soc. 122, 8197-8203
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 8197-8203
-
-
Allhambra, C.1
Corchado, J.C.2
Sanchez, M.L.3
Gao, J.L.4
Truhlar, D.G.5
-
43
-
-
0001015978
-
+, NADH, and the pyrophosphate groups of nucleotides
-
+, NADH, and the pyrophosphate groups of nucleotides J. Comput. Chem. 18, 221-239
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 221-239
-
-
Pavelites, J.J.1
Gao, J.L.2
Bash, P.A.3
MacKerell, A.D.4
-
44
-
-
0037038533
-
Large and fast relaxations inside a protein: Calculation and measurement of reorganization energies in alcohol dehydrogenase
-
Klug, D. R., Walker, R. C., de Souza, M. M., Mercer, I. P., and Gould, I. R. (2002) Large and fast relaxations inside a protein: Calculation and measurement of reorganization energies in alcohol dehydrogenase J. Phys. Chem. B 106, 11658-11665
-
(2002)
J. Phys. Chem. B
, vol.106
, pp. 11658-11665
-
-
Klug, D.R.1
Walker, R.C.2
De Souza, M.M.3
Mercer, I.P.4
Gould, I.R.5
-
45
-
-
3042524904
-
A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: The RESP Model
-
Bayly, C. I., Cieplak, P., Cornell, W. D., and Kollman, P. A. (1993) A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: The RESP Model J. Phys. Chem. 97, 10269-10280
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 10269-10280
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.D.3
Kollman, P.A.4
-
46
-
-
0029633186
-
Amber, a Package of Computer-Programs for Applying Molecular Mechanics, Normal-Mode Analysis, Molecular-Dynamics and Free-Energy Calculations to Simulate the Structural and Energetic Properties of Molecules
-
Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., Cheatham, T. E., Debolt, S., Ferguson, D., Seibel, G., and Kollman, P. (1995) Amber, a Package of Computer-Programs for Applying Molecular Mechanics, Normal-Mode Analysis, Molecular-Dynamics and Free-Energy Calculations to Simulate the Structural and Energetic Properties of Molecules Comput. Phys. Commun. 91, 1-41
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 1-41
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.S.4
Cheatham, T.E.5
Debolt, S.6
Ferguson, D.7
Seibel, G.8
Kollman, P.9
-
47
-
-
0000730887
-
Application of the RESP methodology in the parametrization of organic solvents
-
Fox, T. and Kollman, P. A. (1998) Application of the RESP methodology in the parametrization of organic solvents J. Phys. Chem. B 102, 8070-8079
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 8070-8079
-
-
Fox, T.1
Kollman, P.A.2
-
49
-
-
33646794930
-
A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules
-
Myers, J., Grothaus, G., Narayanan, S., and Onufriev, A. (2006) A simple clustering algorithm can be accurate enough for use in calculations of pKs in macromolecules Proteins 63, 928-938
-
(2006)
Proteins
, vol.63
, pp. 928-938
-
-
Myers, J.1
Grothaus, G.2
Narayanan, S.3
Onufriev, A.4
-
50
-
-
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. (1983) Comparison of Simple Potential Functions for Simulating Liquid Water J. Chem. Phys. 79, 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
-
51
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
-
Duan, Y., Wu, C., Chowdhury, S., Lee, M. C., Xiong, G. M., Zhang, W., Yang, R., Cieplak, P., Luo, R., Lee, T., Caldwell, J., Wang, J. M., and Kollman, P. (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations J. Comput. Chem. 24, 1999-2012
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Chowdhury, S.3
Lee, M.C.4
Xiong, G.M.5
Zhang, W.6
Yang, R.7
Cieplak, P.8
Luo, R.9
Lee, T.10
Caldwell, J.11
Wang, J.M.12
Kollman, P.13
-
52
-
-
2942532422
-
Development and testing of a general Amber force field
-
Wang, J. M., Wolf, R. M., Caldwell, J. W., Kollman, P. A., and Case, D. A. (2004) Development and testing of a general Amber force field J. Comput. Chem. 25, 1157-1174
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1157-1174
-
-
Wang, J.M.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
53
-
-
33646940952
-
Numerical-Integration of Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of N-Alkanes
-
Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C. (1977) Numerical-Integration of Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of N-Alkanes J. Comput. Phys. 23, 327-341
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
54
-
-
84946450438
-
Algorithms for Macromolecular Dynamics and Constraint Dynamics
-
Vangunsteren, W. F. and Berendsen, H. J. C. (1977) Algorithms for Macromolecular Dynamics and Constraint Dynamics Mol. Phys. 34, 1311-1327
-
(1977)
Mol. Phys.
, vol.34
, pp. 1311-1327
-
-
Vangunsteren, W.F.1
Berendsen, H.J.C.2
-
55
-
-
33750587438
-
Molecular-Dynamics with Coupling to an External Bath
-
Berendsen, H. J. C., Postma, J. P. M., Vangunsteren, W. F., Dinola, A., and Haak, J. R. (1984) Molecular-Dynamics with Coupling to an External Bath J. Chem. Phys. 81, 3684-3690
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Vangunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
56
-
-
33645961739
-
A Smooth Particle Mesh Ewald Method
-
Essmann, U., Perera, L., Berkowitz, M. L., Darden, T., Lee, H., and Pedersen, L. G. (1995) A Smooth Particle Mesh Ewald Method J. Chem. Phys. 103, 8577-8593
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
57
-
-
0000577932
-
Accuracy and Efficiency of the Particle Mesh Ewald Method
-
Petersen, H. G. (1995) Accuracy and Efficiency of the Particle Mesh Ewald Method J. Chem. Phys. 103, 3668-3679
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 3668-3679
-
-
Petersen, H.G.1
-
58
-
-
0032253961
-
Theozymes and compuzymes: Theoretical models for biological catalysis
-
Tantillo, D. J., Chen, J. G., and Houk, K. N. (1998) Theozymes and compuzymes: Theoretical models for biological catalysis Curr. Opin. Chem. Biol. 2, 743-750
-
(1998)
Curr. Opin. Chem. Biol.
, vol.2
, pp. 743-750
-
-
Tantillo, D.J.1
Chen, J.G.2
Houk, K.N.3
-
59
-
-
34548445989
-
How similar are enzyme active site geometries derived from quantum mechanical theozymes to crystal structures of enzyme-inhibitor complexes? Implications for enzyme design
-
Dechancie, J., Clemente, F. R., Smith, A. J. T., Gunaydin, H., Zhao, Y. L., Zhang, X. Y., and Houk, N. (2007) How similar are enzyme active site geometries derived from quantum mechanical theozymes to crystal structures of enzyme-inhibitor complexes? Implications for enzyme design Protein Sci. 16, 1851-1866
-
(2007)
Protein Sci.
, vol.16
, pp. 1851-1866
-
-
Dechancie, J.1
Clemente, F.R.2
Smith, A.J.T.3
Gunaydin, H.4
Zhao, Y.L.5
Zhang, X.Y.6
Houk, N.7
-
60
-
-
43949083733
-
Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods
-
Hu, H. and Yang, W. T. (2008) Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods Annu. Rev. Phys. Chem. 59, 573-601
-
(2008)
Annu. Rev. Phys. Chem.
, vol.59
, pp. 573-601
-
-
Hu, H.1
Yang, W.T.2
-
61
-
-
0031209054
-
A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics
-
Cances, E., Mennucci, B., and Tomasi, J. (1997) A new integral equation formalism for the polarizable continuum model: Theoretical background and applications to isotropic and anisotropic dielectrics J. Chem. Phys. 107, 3032-3041
-
(1997)
J. Chem. Phys.
, vol.107
, pp. 3032-3041
-
-
Cances, E.1
Mennucci, B.2
Tomasi, J.3
-
62
-
-
84961979198
-
Continuum solvation models: A new approach to the problem of solute's charge distribution and cavity boundaries
-
Mennucci, B. and Tomasi, J. (1997) Continuum solvation models: A new approach to the problem of solute's charge distribution and cavity boundaries J. Chem. Phys. 106, 5151-5158
-
(1997)
J. Chem. Phys.
, vol.106
, pp. 5151-5158
-
-
Mennucci, B.1
Tomasi, J.2
-
63
-
-
0032502372
-
Ab initio study of ionic solutions by a polarizable continuum dielectric model
-
Cossi, M., Barone, V., Mennucci, B., and Tomasi, J. (1998) Ab initio study of ionic solutions by a polarizable continuum dielectric model Chem. Phys. Lett. 286, 253-260
-
(1998)
Chem. Phys. Lett.
, vol.286
, pp. 253-260
-
-
Cossi, M.1
Barone, V.2
Mennucci, B.3
Tomasi, J.4
-
64
-
-
0024086838
-
A Theoretical Study of the Dielectric Constant of Protein
-
Nakamura, H., Sakamoto, T., and Wada, A. (1988) A Theoretical Study of the Dielectric Constant of Protein Protein Eng. 2, 177-183
-
(1988)
Protein Eng.
, vol.2
, pp. 177-183
-
-
Nakamura, H.1
Sakamoto, T.2
Wada, A.3
-
65
-
-
0029174681
-
Stabilization of the Transition-State of the Chorismate-Prephenate Rearrangement: An Ab-Initio Study of Enzyme and Antibody Catalysis
-
Wiest, O. and Houk, K. N. (1995) Stabilization of the Transition-State of the Chorismate-Prephenate Rearrangement: An Ab-Initio Study of Enzyme and Antibody Catalysis J. Am. Chem. Soc. 117, 11628-11639
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 11628-11639
-
-
Wiest, O.1
Houk, K.N.2
-
66
-
-
0033515394
-
A new ONIOM implementation in Gaussian98. Part I. The calculation of energies, gradients, vibrational frequencies and electric field derivatives
-
Dapprich, S., Komaromi, I., Byun, K. S., Morokuma, K., and Frisch, M. J. (1999) A new ONIOM implementation in Gaussian98. Part I. The calculation of energies, gradients, vibrational frequencies and electric field derivatives THEOCHEM 461, 1-21
-
(1999)
THEOCHEM
, vol.461
, pp. 1-21
-
-
Dapprich, S.1
Komaromi, I.2
Byun, K.S.3
Morokuma, K.4
Frisch, M.J.5
-
67
-
-
33746381417
-
Combining quantum mechanics methods with molecular mechanics methods in ONIOM
-
Vreven, T., Byun, K. S., Komaromi, I., Dapprich, S., Montgomery, J. A., Morokuma, K., and Frisch, M. J. (2006) Combining quantum mechanics methods with molecular mechanics methods in ONIOM J. Chem. Theory Comput. 2, 815-826
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 815-826
-
-
Vreven, T.1
Byun, K.S.2
Komaromi, I.3
Dapprich, S.4
Montgomery, J.A.5
Morokuma, K.6
Frisch, M.J.7
-
68
-
-
70350062723
-
Matrix Metalloproteinase 2 Inhibition: Combined Quantum Mechanics and Molecular Mechanics Studies of the Inhibition Mechanism of (4- Phenoxyphenylsulfonyl)methylthiirane and Its Oxirane Analogue
-
Tao, P., Fisher, J. F., Shi, Q. C., Vreven, T., Mobashery, S., and Schlegel, H. B. (2009) Matrix Metalloproteinase 2 Inhibition: Combined Quantum Mechanics and Molecular Mechanics Studies of the Inhibition Mechanism of (4-Phenoxyphenylsulfonyl)methylthiirane and Its Oxirane Analogue Biochemistry 48, 9839-9847
-
(2009)
Biochemistry
, vol.48
, pp. 9839-9847
-
-
Tao, P.1
Fisher, J.F.2
Shi, Q.C.3
Vreven, T.4
Mobashery, S.5
Schlegel, H.B.6
-
69
-
-
33847805515
-
Chemical-Reaction Paths. 3. Ab-Initio Study of Nucleophilic Addition to a Carbonyl Group
-
Burgi, H. B., Lehn, J. M., and Wipff, G. (1974) Chemical-Reaction Paths. 3. Ab-Initio Study of Nucleophilic Addition to a Carbonyl Group J. Am. Chem. Soc. 96, 1956-1957
-
(1974)
J. Am. Chem. Soc.
, vol.96
, pp. 1956-1957
-
-
Burgi, H.B.1
Lehn, J.M.2
Wipff, G.3
-
70
-
-
0015505480
-
Role of Zinc in Horse Liver Alcohol-Dehydrogenase: Influence on Structure and Conformational Changes
-
Coleman, P. L., Weiner, H., and Iweibo, I. (1972) Role of Zinc in Horse Liver Alcohol-Dehydrogenase: Influence on Structure and Conformational Changes Biochemistry 11, 1010-1018
-
(1972)
Biochemistry
, vol.11
, pp. 1010-1018
-
-
Coleman, P.L.1
Weiner, H.2
Iweibo, I.3
-
71
-
-
0021383012
-
Electrostatic-Field Effects of Coenzymes on Ligand-Binding to Catalytic Zinc in Liver Alcohol-Dehydrogenase
-
Andersson, P., Kvassman, J., Olden, B., and Pettersson, G. (1984) Electrostatic-Field Effects of Coenzymes on Ligand-Binding to Catalytic Zinc in Liver Alcohol-Dehydrogenase Eur. J. Biochem. 138, 603-609
-
(1984)
Eur. J. Biochem.
, vol.138
, pp. 603-609
-
-
Andersson, P.1
Kvassman, J.2
Olden, B.3
Pettersson, G.4
-
72
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S. H., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., Donini, O., Cieplak, P., Srinivasan, J., Case, D. A., and Cheatham, T. E. (2000) Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models Acc. Chem. Res. 33, 889-897
-
(2000)
Acc. Chem. Res.
, vol.33
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.H.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
Donini, O.11
Cieplak, P.12
Srinivasan, J.13
Case, D.A.14
Cheatham, T.E.15
-
73
-
-
33748637571
-
Recent Advances in Free Energy Calculations with a Combination of Molecular Mechanics and Continuum Models
-
Wang, J. M., Hou, T. J., and Xu, X. J. (2006) Recent Advances in Free Energy Calculations with a Combination of Molecular Mechanics and Continuum Models Curr. Comput.-Aided Drug Des. 2, 287-306
-
(2006)
Curr. Comput.-Aided Drug Des.
, vol.2
, pp. 287-306
-
-
Wang, J.M.1
Hou, T.J.2
Xu, X.J.3
-
74
-
-
0030458903
-
Coenzyme A hemithioacetals as easily prepared inhibitors of CoA ester-utilizing enzymes
-
Schwartz, B., Vogel, K. W., and Drueckhammer, D. G. (1996) Coenzyme A hemithioacetals as easily prepared inhibitors of CoA ester-utilizing enzymes J. Org. Chem. 61, 9356-9361
-
(1996)
J. Org. Chem.
, vol.61
, pp. 9356-9361
-
-
Schwartz, B.1
Vogel, K.W.2
Drueckhammer, D.G.3
-
75
-
-
0021402042
-
Purification and Properties of Cinnamoyl-CoA Reductase and Cinnamyl Alcohol-Dehydrogenase from Poplar Stems (Populus-X-Euramericana)
-
Sarni, F., Grand, C., and Boudet, A. M. (1984) Purification and Properties of Cinnamoyl-CoA Reductase and Cinnamyl Alcohol-Dehydrogenase from Poplar Stems (Populus-X-Euramericana) Eur. J. Biochem. 139, 259-265
-
(1984)
Eur. J. Biochem.
, vol.139
, pp. 259-265
-
-
Sarni, F.1
Grand, C.2
Boudet, A.M.3
-
76
-
-
0028990098
-
Short-Chain Dehydrogenases Reductases (SDR)
-
Jornvall, H., Persson, B., Krook, M., Atrian, S., Gonzalezduarte, R., Jeffery, J., and Ghosh, D. (1995) Short-Chain Dehydrogenases Reductases (SDR) Biochemistry 34, 6003-6013
-
(1995)
Biochemistry
, vol.34
, pp. 6003-6013
-
-
Jornvall, H.1
Persson, B.2
Krook, M.3
Atrian, S.4
Gonzalezduarte, R.5
Jeffery, J.6
Ghosh, D.7
-
77
-
-
59149107301
-
The human short-chain dehydrogenase/reductase (SDR) superfamily: A bioinformatics summary
-
Bray, J. E., Marsden, B. D., and Oppermann, U. (2009) The human short-chain dehydrogenase/reductase (SDR) superfamily: A bioinformatics summary Chem.-Biol. Interact. 178, 99-109
-
(2009)
Chem.-Biol. Interact.
, vol.178
, pp. 99-109
-
-
Bray, J.E.1
Marsden, B.D.2
Oppermann, U.3
-
78
-
-
80855131585
-
A prokaryotic acyl-CoA reductase performing reduction of fatty acyl-CoA to fatty alcohol
-
Hofvander, P., Doan, T. T. P., and Hamberg, M. (2011) A prokaryotic acyl-CoA reductase performing reduction of fatty acyl-CoA to fatty alcohol FEBS Lett. 585, 3538-3543
-
(2011)
FEBS Lett.
, vol.585
, pp. 3538-3543
-
-
Hofvander, P.1
Doan, T.T.P.2
Hamberg, M.3
-
79
-
-
82455219013
-
Characterization of a Fatty Acyl-CoA Reductase from Marinobacter aquaeolei VT8: A Bacterial Enzyme Catalyzing the Reduction of Fatty Acyl-CoA to Fatty Alcohol
-
Willis, R. M., Wahlen, B. D., Seefeldt, L. C., and Barney, B. M. (2011) Characterization of a Fatty Acyl-CoA Reductase from Marinobacter aquaeolei VT8: A Bacterial Enzyme Catalyzing the Reduction of Fatty Acyl-CoA to Fatty Alcohol Biochemistry 50, 10550-10558
-
(2011)
Biochemistry
, vol.50
, pp. 10550-10558
-
-
Willis, R.M.1
Wahlen, B.D.2
Seefeldt, L.C.3
Barney, B.M.4
-
80
-
-
84865735120
-
Structural basis of biological nitrile reduction
-
Chikwana, V. M., Stec, B., Lee, B. W., de Crecy-Lagard, V., Iwata-Reuyl, D., and Swairjo, M. A. (2012) Structural basis of biological nitrile reduction J. Biol. Chem. 287, 30560-30570
-
(2012)
J. Biol. Chem.
, vol.287
, pp. 30560-30570
-
-
Chikwana, V.M.1
Stec, B.2
Lee, B.W.3
De Crecy-Lagard, V.4
Iwata-Reuyl, D.5
Swairjo, M.A.6
-
81
-
-
78049445153
-
High-resolution structure of the nitrile reductase QueF combined with molecular simulations provide insight into enzyme mechanism
-
Kim, Y., Zhou, M., Moy, S., Morales, J., Cunningham, M. A., and Joachimiak, A. (2010) High-resolution structure of the nitrile reductase QueF combined with molecular simulations provide insight into enzyme mechanism J. Mol. Biol. 404, 127-137
-
(2010)
J. Mol. Biol.
, vol.404
, pp. 127-137
-
-
Kim, Y.1
Zhou, M.2
Moy, S.3
Morales, J.4
Cunningham, M.A.5
Joachimiak, A.6
-
82
-
-
33748631825
-
Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: Logic, machinery, and mechanisms
-
Fischbach, M. A. and Walsh, C. T. (2006) Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: Logic, machinery, and mechanisms Chem. Rev. 106, 3468-3496
-
(2006)
Chem. Rev.
, vol.106
, pp. 3468-3496
-
-
Fischbach, M.A.1
Walsh, C.T.2
-
83
-
-
84859564582
-
Nonprocessive [2 + 2]e- off-loading reductase domains from mycobacterial nonribosomal peptide synthetases
-
Chhabra, A., Haque, A. S., Pal, R. K., Goyal, A., Rai, R., Joshi, S., Panjikar, S., Pasha, S., Sankaranarayanan, R., and Gokhale, R. S. (2012) Nonprocessive [2 + 2]e- off-loading reductase domains from mycobacterial nonribosomal peptide synthetases Proc. Natl. Acad. Sci. U.S.A. 109, 5681-5686
-
(2012)
Proc. Natl. Acad. Sci. U.S.A.
, vol.109
, pp. 5681-5686
-
-
Chhabra, A.1
Haque, A.S.2
Pal, R.K.3
Goyal, A.4
Rai, R.5
Joshi, S.6
Panjikar, S.7
Pasha, S.8
Sankaranarayanan, R.9
Gokhale, R.S.10
-
84
-
-
76249090018
-
PKS and NRPS release mechanisms
-
Du, L. and Lou, L. (2010) PKS and NRPS release mechanisms Nat. Prod. Rep. 27, 255-278
-
(2010)
Nat. Prod. Rep.
, vol.27
, pp. 255-278
-
-
Du, L.1
Lou, L.2
|