-
1
-
-
0018077228
-
Arginine deiminase from Mycoplasma arthritidis
-
Smith, D. W.; Ganaway, R. L.; Fahrney, D. E. Arginine deiminase from Mycoplasma arthritidis J. Biol. Chem. 1978, 253, 6016
-
(1978)
J. Biol. Chem.
, vol.253
, pp. 6016
-
-
Smith, D.W.1
Ganaway, R.L.2
Fahrney, D.E.3
-
2
-
-
0014027490
-
The generation of energy by the arginine dihydrolase pathway in Mycoplasma hominis 07
-
Schimke, R. T.; Berlin, C. M.; Sweeney, E. W.; Carroll, W. R. The generation of energy by the arginine dihydrolase pathway in Mycoplasma hominis 07 J. Biol. Chem. 1966, 241, 2228
-
(1966)
J. Biol. Chem.
, vol.241
, pp. 2228
-
-
Schimke, R.T.1
Berlin, C.M.2
Sweeney, E.W.3
Carroll, W.R.4
-
3
-
-
0026518513
-
The pathway of arginine catabolism in Giardia intestinalis
-
Schofield, P. J.; Edwards, M. R.; Matthews, J.; Wilson, J. R. The pathway of arginine catabolism in Giardia intestinalis Mol. Biochem. Parasitol. 1992, 51, 29-36
-
(1992)
Mol. Biochem. Parasitol.
, vol.51
, pp. 29-36
-
-
Schofield, P.J.1
Edwards, M.R.2
Matthews, J.3
Wilson, J.R.4
-
4
-
-
0036435297
-
Evolution of arginine deiminase (ADI) pathway genes
-
Zuniga, M.; Perez, G.; Gonzalez-Candelas, F. Evolution of arginine deiminase (ADI) pathway genes Mol. Phylogenet. Evol. 2002, 25, 429
-
(2002)
Mol. Phylogenet. Evol.
, vol.25
, pp. 429
-
-
Zuniga, M.1
Perez, G.2
Gonzalez-Candelas, F.3
-
5
-
-
0032549032
-
Cloning and expression of a prokaryotic enzyme, arginine deiminase, from a primitive eukaryote Giardia intestinalis
-
Knodler, L. A.; Sekyere, E. O.; Stewart, T. S.; Schofield, P. J.; Edwards, M. R. Cloning and expression of a prokaryotic enzyme, arginine deiminase, from a primitive eukaryote Giardia intestinalis J. Biol. Chem. 1998, 273, 4470
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 4470
-
-
Knodler, L.A.1
Sekyere, E.O.2
Stewart, T.S.3
Schofield, P.J.4
Edwards, M.R.5
-
6
-
-
0037563766
-
Identification of immunoreactive proteins during acute human giardiasis
-
Palm, J. E. D.; Weiland, M. E.-L.; Griffiths, W. J.; Ljungstrom, I.; Svard, S. G. Identification of immunoreactive proteins during acute human giardiasis J. Infect. Dis. 2003, 187, 1849
-
(2003)
J. Infect. Dis.
, vol.187
, pp. 1849
-
-
Palm, J.E.D.1
Weiland, M.E.-L.2
Griffiths, W.J.3
Ljungstrom, I.4
Svard, S.G.5
-
7
-
-
28244478071
-
Inhibition of dimethylargine dimethylaminohyrolase (DDAH) and arginine deiminase (ADI) by pentafluorophenyl (PFP) sulfonates
-
Vallance, P.; Bush, H. D.; Mok, B. J.; Hurtado-Guerrero, R.; Gill, H.; Rossiter, S.; Wilden, J. D.; Caddick, S. Inhibition of dimethylargine dimethylaminohyrolase (DDAH) and arginine deiminase (ADI) by pentafluorophenyl (PFP) sulfonates Chem. Commun. 2005, 5563-5565
-
(2005)
Chem. Commun.
, pp. 5563-5565
-
-
Vallance, P.1
Bush, H.D.2
Mok, B.J.3
Hurtado-Guerrero, R.4
Gill, H.5
Rossiter, S.6
Wilden, J.D.7
Caddick, S.8
-
8
-
-
28444435875
-
L-canavanine is a time-controlled mechanism-based inhibitor of pseudomonas aeruginosa arginine deiminase
-
DOI 10.1021/ja056226p
-
Lu, X.; Li, L.; Feng, X.; Wu, Y.; Dunaway-Mariano, D.; Engen, J. R.; Mariano, P. S. L-Canavanine is a time-controlled mechanism-based inhibitor of Pseudomonas aeruginosa arginine deiminase J. Am. Chem. Soc. 2005, 127, 16412-16413 (Pubitemid 41740389)
-
(2005)
Journal of the American Chemical Society
, vol.127
, Issue.47
, pp. 16412-16413
-
-
Lu, X.1
Li, L.2
Feng, X.3
Wu, Y.4
Dunaway-Mariano, D.5
Engen, J.R.6
Mariano, P.S.7
-
9
-
-
39049108427
-
Inactivation of microbial arginine deiminases by L-canavaine
-
Li, L.; Li, Z.; Chen, D.; Lu, X.; Feng, X.; Wright, E. C.; Solberg, N. O.; Dunaway-Mariano, D.; Mariano, P. S.; Galkin, A.; Kulakova, L.; Herzberg, O.; Green-Church, K. B.; Zhang, L. Inactivation of microbial arginine deiminases by L-canavaine J. Am. Chem. Soc. 2008, 130, 1918
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 1918
-
-
Li, L.1
Li, Z.2
Chen, D.3
Lu, X.4
Feng, X.5
Wright, E.C.6
Solberg, N.O.7
Dunaway-Mariano, D.8
Mariano, P.S.9
Galkin, A.10
Kulakova, L.11
Herzberg, O.12
Green-Church, K.B.13
Zhang, L.14
-
10
-
-
0342748603
-
Arginine deiminase inhibits proliferation of human leukemia cells more potently than asparaginase by inducing cell cycle arrest and apoptosis
-
Gong, H.; Zolzer, F.; von Recklinghausen, G.; Havers, W.; Schweigerer, L. Arginine deiminase inhibits proliferation of human leukemia cells more potently than asparaginase by inducing cell cycle arrest and apoptosis Leukemia 1999, 14, 826
-
(1999)
Leukemia
, vol.14
, pp. 826
-
-
Gong, H.1
Zolzer, F.2
Von Recklinghausen, G.3
Havers, W.4
Schweigerer, L.5
-
11
-
-
8344258040
-
Controlling cancer by restricting arginine availability-arginine- catabolizing enzymes as anticancer agents
-
Wheatley, D. N. Controlling cancer by restricting arginine availability-arginine-catabolizing enzymes as anticancer agents Anti-Cancer Drugs 2004, 15, 825
-
(2004)
Anti-Cancer Drugs
, vol.15
, pp. 825
-
-
Wheatley, D.N.1
-
12
-
-
0035424604
-
A noval superfamily of enzymes that catalyze the modification of guandino group
-
Shirai, H.; Blundell, T. L.; Mizuguchi, K. A noval superfamily of enzymes that catalyze the modification of guandino group Trends Biochem. Sci. 2001, 26 (8) 465
-
(2001)
Trends Biochem. Sci.
, vol.26
, Issue.8
, pp. 465
-
-
Shirai, H.1
Blundell, T.L.2
Mizuguchi, K.3
-
13
-
-
77956063280
-
Mechanistic similarity and diversity among the guanidine-modifying members of the pentein superfamily
-
Linsky, T.; Fast, W. Mechanistic similarity and diversity among the guanidine-modifying members of the pentein superfamily Biochim. Biophys. Acta 2010, 1804, 1943-1953
-
(2010)
Biochim. Biophys. Acta
, vol.1804
, pp. 1943-1953
-
-
Linsky, T.1
Fast, W.2
-
14
-
-
0033214074
-
Identification of two human dimethylarginine dimethylaminohydrolases with distinct tissue distributions and homology with microbial arginine deiminases
-
Leiper, J. M.; Maria, J. S.; Chubb, A.; MacAllister, R. J.; Charles, I. G.; Whitley, G. S. J.; Vallance, P. Identification of two human dimethylarginine dimethylaminohydrolases with distinct tissue distributions and homology with microbial arginine deiminases Biochem. J. 1999, 343, 209
-
(1999)
Biochem. J.
, vol.343
, pp. 209
-
-
Leiper, J.M.1
Maria, J.S.2
Chubb, A.3
MacAllister, R.J.4
Charles, I.G.5
Whitley, G.S.J.6
Vallance, P.7
-
15
-
-
0032864893
-
Identification of microbial dimethylarginine dimethylaminohydrolase enzymes [1]
-
DOI 10.1046/j.1365-2958.1999.01580.x
-
Santa Maria, J.; Vallance, P.; Charles, I. G.; Leiper, J. M. Identification of microbial dimethylarginine dimethylaminohydrolase enzymes Mol. Microbiol. 1999, 33, 1278-1279 (Pubitemid 29433632)
-
(1999)
Molecular Microbiology
, vol.33
, Issue.6
, pp. 1278-1279
-
-
Maria, J.S.1
Vallance, P.2
Charles, I.G.3
Leiper, J.M.4
-
16
-
-
23244447251
-
Kinetic characterization of protein arginine deiminase 4: A transcriptional corepressor implicated in the onset and progression of rheumatoid arthritis
-
DOI 10.1021/bi050292m
-
Kearney, P. L.; Bhatia, M.; Jones, N. G.; Yuan, L.; Glascock, M. C.; Catchings, K. L.; Yamada, M.; Thompson, P. R. Kinetic characterization of protein arginine deiminase 4: A transcriptional corepressor implicated in the onset and progression of rheumetoid arthritis Biochemistry 2005, 44, 10570-10582 (Pubitemid 41098234)
-
(2005)
Biochemistry
, vol.44
, Issue.31
, pp. 10570-10582
-
-
Kearney, P.L.1
Bhatia, M.2
Jones, N.G.3
Yuan, L.4
Glascock, M.C.5
Catchings, K.L.6
Yamada, M.7
Thompson, P.R.8
-
17
-
-
0036883907
-
Blocking NO synthesis: How, where, and why?
-
Vallance, P.; Leiper, J. Blocking NO synthesis: how, where, and why? Nat. Rev. Drug Discovery 2002, 1, 939
-
(2002)
Nat. Rev. Drug Discovery
, vol.1
, pp. 939
-
-
Vallance, P.1
Leiper, J.2
-
18
-
-
36849001753
-
Inhibition of human dimethylarginine dimethylaminohydrolase-1 by S-nitroso-L-homocysteine and hydrogen peroxide: Analysis, quantification, and implications for hyperhomocysteinemia
-
DOI 10.1074/jbc.M707231200
-
Hong, L.; Fast, W. Inhibition of human dimethylarginine dimethylamionhydrolase-1 by S-nitroso-L-homocysteine and hydrogen peroxide: Analysis, quantification, and implications for hyperhomocysteinemia J. Biol. Chem. 2007, 282, 34684-34692 (Pubitemid 350232428)
-
(2007)
Journal of Biological Chemistry
, vol.282
, Issue.48
, pp. 34684-34692
-
-
Hong, L.1
Fast, W.2
-
19
-
-
0242720407
-
PAD, a growing family of ctirullinating enzymes: Genes, features, and involvment in disease
-
Vossenaar, E. R.; Zenderman, A. J. W.; van Venrooij, W. J.; Pruijn, G. J. M. PAD, a growing family of ctirullinating enzymes: genes, features, and involvment in disease BioEssays 2003, 25, 1106
-
(2003)
BioEssays
, vol.25
, pp. 1106
-
-
Vossenaar, E.R.1
Zenderman, A.J.W.2
Van Venrooij, W.J.3
Pruijn, G.J.M.4
-
20
-
-
5044228483
-
Human PAD4 regulates histone arginine methylation levels via demethylimination
-
DOI 10.1126/science.1101400
-
Wang, Y.; Wysocka, J.; Sayegh, J.; Lee, Y.-H.; Perlin, J. R.; Leonelli, L.; Sonbuchner, L. S.; McDonald, C. H.; Cook, R. G.; Dou, Y.; Roeder, R. G.; Clarke, S.; Stallcup, M. R.; Allis, C. D.; Coonrod, S. A. Human PAD4 regulates histone arginine methylation levels via demethylimination Science 2004, 306, 279-283 (Pubitemid 39336873)
-
(2004)
Science
, vol.306
, Issue.5694
, pp. 279-283
-
-
Wang, Y.1
Wysocka, J.2
Sayegh, J.3
Lee, Y.-H.4
Pertin, J.R.5
Leonelli, L.6
Sonbuchner, L.S.7
McDonald, C.H.8
Cook, R.G.9
Dou, Y.10
Roeder, R.G.11
Clarke, S.12
Stallcup, M.R.13
Allis, C.D.14
Coonrod, S.A.15
-
21
-
-
33751001725
-
Histone citrullination by protein arginine deiminase: Is arginine methylation a green light or a roadblock
-
Thompson, P. R.; Fast, W. Histone citrullination by protein arginine deiminase: Is arginine methylation a green light or a roadblock ACS Chem. Biol. 2006, 1, 433
-
(2006)
ACS Chem. Biol.
, vol.1
, pp. 433
-
-
Thompson, P.R.1
Fast, W.2
-
22
-
-
0034885255
-
Structural insights into the hydrolysis of cellular nitric oxide synthase inhibitors by dimenthylaminohydrolase
-
Murray-Rust, J.; Leiper, J.; McAlister, M.; Phelan, J.; Tilley, S.; Maria, J. S.; Valance, P.; McDonald, N. Structural insights into the hydrolysis of cellular nitric oxide synthase inhibitors by dimenthylaminohydrolase Nat. Struct. Biol. 2001, 8, 679
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 679
-
-
Murray-Rust, J.1
Leiper, J.2
McAlister, M.3
Phelan, J.4
Tilley, S.5
Maria, J.S.6
Valance, P.7
McDonald, N.8
-
23
-
-
3543004695
-
2+-induced activation of human PAD4
-
2+-induced activation of human PAD4 Nat. Struct. Mol. Biol. 2004, 11, 777
-
(2004)
Nat. Struct. Mol. Biol.
, vol.11
, pp. 777
-
-
Arita, K.1
Hashimoto, H.2
Shimizu, T.3
Nakashima, K.4
Yamada, M.5
Sato, M.6
-
24
-
-
1842450302
-
Crystal structures of arginine deiminase with covalent reaction intermediates; Implications for catalytic mechanism
-
Das, K.; Butler, G. H.; Kwiatkowski, V.; Clark, A. D., Jr.; Yadav, P.; Arnold, E. Crystal structures of arginine deiminase with covalent reaction intermediates; implications for catalytic mechanism Structure 2004, 12, 657
-
(2004)
Structure
, vol.12
, pp. 657
-
-
Das, K.1
Butler, G.H.2
Kwiatkowski, V.3
Clark Jr., A.D.4
Yadav, P.5
Arnold, E.6
-
25
-
-
1842639583
-
Structural Insight into Arginine Degradation by Arginine Deiminase, An Antibacterial and Parasite Drug Target
-
DOI 10.1074/jbc.M313410200
-
Galkin, A.; Kulakova, L.; Sarikaya, E.; Lim, K.; Howard, A.; Herzberg, O. Structural insight into arginine degradation by arginine deiminase, an antibacterial and parasite drug target J. Biol. Chem. 2004, 279, 14001-14008 (Pubitemid 38468934)
-
(2004)
Journal of Biological Chemistry
, vol.279
, Issue.14
, pp. 14001-14008
-
-
Galkin, A.1
Kulakova, L.2
Sarikaya, E.3
Lim, K.4
Howard, A.5
Herzberg, O.6
-
26
-
-
26644450503
-
Crystal structures representing the Michaelis complex and the thiouronium reaction intermediate of Pseudomonas aeruginosa arginine deiminase
-
DOI 10.1074/jbc.M505471200
-
Galkin, A.; Lu, X.; Dunaway-Mariano, D.; Herzberg, O. Crystal structures representing the Michaelis complex and thiouronium reaction intermediate of Pseudomonas aeruginosa arginine deiminase J. Biol. Chem. 2005, 280, 34080-34087 (Pubitemid 41443131)
-
(2005)
Journal of Biological Chemistry
, vol.280
, Issue.40
, pp. 34080-34087
-
-
Galkin, A.1
Lu, X.2
Dunaway-Mariano, D.3
Herzberg, O.4
-
27
-
-
33646348152
-
Structure of the Mammalian NOS Regulator Dimethylarginine Dimethylaminohydrolase: A Basis for the Design of Specific Inhibitors
-
DOI 10.1016/j.str.2006.03.006, PII S0969212606001717
-
Frey, D.; Braun, O.; Briand, C.; Vasak, M.; Grutter, M. G. Structure of the mammalian NOS regulator dimethylarginine dimethylaminohydrolase: A basis for the design of specific inhibitors Struct. 2006, 14 (5) 901-911 (Pubitemid 43674095)
-
(2006)
Structure
, vol.14
, Issue.5
, pp. 901-911
-
-
Frey, D.1
Braun, O.2
Briand, C.3
Vasak, M.4
Grutter, M.G.5
-
28
-
-
2342449187
-
Arginine deiminase uses an active-site cysteine in nucleophilic catalysis of L-arginine hydrolysis
-
Lu, X.; Galkin, A.; Herzberg, O.; Dunaway-Mariano, D. Arginine deiminase uses an active-site cysteine in nucleophilic catalysis of L-arginine hydrolysis J. Am. Chem. Soc. 2004, 126, 5374
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 5374
-
-
Lu, X.1
Galkin, A.2
Herzberg, O.3
Dunaway-Mariano, D.4
-
29
-
-
31544455800
-
Kinetic analysis of Pseudomonas aeruginosa arginine deiminase mutants and alternate substrates provides insight into structural determinants of function
-
DOI 10.1021/bi051591e
-
Lu, X.; Li, L.; Wu, R.; Feng, X.; Yang, H.; Wang, C.; Guo, H.; Galkin, A.; Herzberg, G.; Mariano, P. S.; Martin, B. M.; Dunaway-Mariano, D. Kinetic analysis of Pseudomonas aeruginosa arginine deiminase mutants and alternate substrates provides insight into structural determinants of function Biochemistry 2006, 45, 1162-1172 (Pubitemid 43167183)
-
(2006)
Biochemistry
, vol.45
, Issue.4
, pp. 1162-1172
-
-
Lu, X.1
Li, L.2
Wu, R.3
Feng, X.4
Li, Z.5
Yang, H.6
Wang, C.7
Guo, H.8
Galkin, A.9
Herzberg, O.10
Mariano, P.S.11
Martin, B.M.12
Dunaway-Mariano, D.13
-
30
-
-
33846250027
-
Insight into the catalytic mechanism of arginine deiminase: Functional studies on the crucial sites
-
DOI 10.1002/prot.21235
-
Wei, Y.; Zhou, H.; Sun, Y.; He, Y.; Luo, Y. Insight into the catalytic mechanism of arginine deiminase: functional studies on the crucial sites Proteins 2007, 66, 740-750 (Pubitemid 46106778)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.66
, Issue.3
, pp. 740-750
-
-
Wei, Y.1
Zhou, H.2
Sun, Y.3
He, Y.4
Luo, Y.5
-
31
-
-
42349110120
-
The electrostatic driving force for nucleophilic catalysis in L-arginine deiminase: A combined experimental and theoretical study
-
DOI 10.1021/bi7023496
-
Li, L.; Li, Z.; Wang, C.; Xu, D.; Mariano, P. S.; Guo, H.; Dunaway-Mariano, D. The electrostatic driving force for nucleophilic catalysis in L-arginine deiminase: A combined experimental and theoretical study Biochemistry 2008, 47, 4721-4732 (Pubitemid 351555493)
-
(2008)
Biochemistry
, vol.47
, Issue.16
, pp. 4721-4732
-
-
Li, L.1
Li, Z.2
Wang, C.3
Xu, D.4
Mariano, P.S.5
Guo, H.6
Dunaway-Mariano, D.7
-
32
-
-
18244386728
-
Characterization of a transient covalent adduct formed during dimethylarginine dimethylaminohydrolase catalysis
-
DOI 10.1021/bi047407r
-
Stone, E. M.; Person, M. D.; Costello, N. J.; Fast, W. Characterization of a transient covalent adduct formed during dimethylarginine dimethylaminohydrolase catalysis Biochemistry 2005, 44, 7069-7078 (Pubitemid 40632424)
-
(2005)
Biochemistry
, vol.44
, Issue.18
, pp. 7069-7078
-
-
Stone, E.M.1
Person, M.D.2
Costello, N.J.3
Fast, W.4
-
33
-
-
33646371495
-
Substrate-assisted cysteine deprotonation in the mechanism of dimethylargininase (DDAH) from Pseudomonas aeruginosa
-
DOI 10.1021/bi052595m
-
Stone, E. M.; Costello, A. L.; Tierney, D. L.; Fast, W. Substrate-assisted cysteine deprotonation in the mechanism of dimethylargininase (DDAH) from Pseudomonas aeruginosa Biochemistry 2006, 45, 5618-5630 (Pubitemid 43673192)
-
(2006)
Biochemistry
, vol.45
, Issue.17
, pp. 5618-5630
-
-
Stone, E.M.1
Costello, A.L.2
Tierney, D.L.3
Fast, W.4
-
34
-
-
34249877154
-
Protein arginine deiminase 4: Evidence for a reverse protonation mechanism
-
Knuckley, B.; Bhatia, M.; Thompson, P. R. Protein arginine deiminase 4: Evidence for a reverse protonation mechanism Biochemistry 2007, 46, 6578
-
(2007)
Biochemistry
, vol.46
, pp. 6578
-
-
Knuckley, B.1
Bhatia, M.2
Thompson, P.R.3
-
35
-
-
34147140531
-
Cysteine proteases
-
Sinnot, M., Ed.; Academic Press: San Diego, CA
-
Brockelhust, K.; Watts, A. B.; Patel, M.; Verma, C.; Thomas, E. W. Cysteine proteases. In Comprehensive Biological Catalysis; Sinnot, M., Ed.; Academic Press: San Diego, CA, 1998; Vol. 1.
-
(1998)
Comprehensive Biological Catalysis
, vol.1
-
-
Brockelhust, K.1
Watts, A.B.2
Patel, M.3
Verma, C.4
Thomas, E.W.5
Sinnot, M.6
-
36
-
-
34147183761
-
Molecular dynamics and density functional studies of substrate binding and catalysis of arginine deiminase
-
Wang, C.; Xu, D.; Zhang, L.; Xie, D.; Guo, H. Molecular dynamics and density functional studies of substrate binding and catalysis of arginine deiminase J. Phys. Chem. B 2007, 111, 3267
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 3267
-
-
Wang, C.1
Xu, D.2
Zhang, L.3
Xie, D.4
Guo, H.5
-
37
-
-
0017100947
-
Theoretical studies of enzymatic reactions: Dielectric, electrostatic and steric stabilization of carbonium ion in the reaction of lysozyme
-
Warshel, A.; Levitt, M. Theoretical studies of enzymatic reactions: Dielectric, electrostatic and steric stabilization of carbonium ion in the reaction of lysozyme J. Mol. Biol. 1976, 103, 227-249
-
(1976)
J. Mol. Biol.
, vol.103
, pp. 227-249
-
-
Warshel, A.1
Levitt, M.2
-
38
-
-
0001491955
-
Hybrid quantum and molecular mechanical simulations: An alternative avenue to solvent effects in organic chemistry
-
Gao, J. Hybrid quantum and molecular mechanical simulations: An alternative avenue to solvent effects in organic chemistry Acc. Chem. Res. 1996, 29, 298-305 (Pubitemid 126641084)
-
(1996)
Accounts of Chemical Research
, vol.29
, Issue.6
, pp. 298-305
-
-
Gao, J.1
-
39
-
-
84962422584
-
Catalysis and specificity in enzymes: A study of triosephophate isomerase and comparison with methyl glyoxal synthase
-
Cui, Q.; Karplus, M. Catalysis and specificity in enzymes: a study of triosephophate isomerase and comparison with methyl glyoxal synthase Adv. Protein Chem. 2003, 66, 315
-
(2003)
Adv. Protein Chem.
, vol.66
, pp. 315
-
-
Cui, Q.1
Karplus, M.2
-
40
-
-
33748263629
-
Pseudobond ab initio QM/MM approach and its applications to enzyme reactions
-
DOI 10.1007/s00214-005-0008-x
-
Zhang, Y. Pseudobond ab initio QM/MM approach and its applications to enzyme reactions Theor. Chem. Acc. 2006, 116, 43-50 (Pubitemid 44318414)
-
(2006)
Theoretical Chemistry Accounts
, vol.116
, Issue.1-3
, pp. 43-50
-
-
Zhang, Y.1
-
41
-
-
43949083733
-
Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods
-
DOI 10.1146/annurev.physchem.59.032607.093618
-
Hu, H.; Yang, W. Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods Annu. Rev. Phys. Chem. 2008, 59, 573-601 (Pubitemid 351703398)
-
(2008)
Annual Review of Physical Chemistry
, vol.59
, pp. 573-601
-
-
Hu, H.1
Yang, W.2
-
42
-
-
60349127442
-
QM/MM methods for biomolecular systems
-
Senn, H. M.; Thiel, W. QM/MM methods for biomolecular systems Angew. Chem., Int. Ed. 2009, 48, 1198-1229
-
(2009)
Angew. Chem., Int. Ed.
, vol.48
, pp. 1198-1229
-
-
Senn, H.M.1
Thiel, W.2
-
43
-
-
77949868796
-
Investigation of enzyme-catalyzed reactions iwth combined quantum mechanical/molecular mechanical (QM/MM) methods
-
Ranaghan, K. E.; Mulholland, A. J. Investigation of enzyme-catalyzed reactions iwth combined quantum mechanical/molecular mechanical (QM/MM) methods Int. Rev. Phys. Chem. 2010, 29, 65-133
-
(2010)
Int. Rev. Phys. Chem.
, vol.29
, pp. 65-133
-
-
Ranaghan, K.E.1
Mulholland, A.J.2
-
44
-
-
0038016725
-
Influence of structural fluctuation on enzyme reaction barriers in combined quantum mechanical/molecular mechanical studies
-
Zhang, Y.; Kua, J.; McCammon, J. A. Influence of structural fluctuation on enzyme reaction barriers in combined quantum mechanical/molecular mechanical studies J. Phys. Chem. B 2003, 107, 4459-4463
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 4459-4463
-
-
Zhang, Y.1
Kua, J.2
McCammon, J.A.3
-
45
-
-
0041876227
-
Computer simulations of enzyme catalysis: Methods, progress, and insights
-
DOI 10.1146/annurev.biophys.32.110601.141807
-
Warshel, A. Computer simulations of enzyme catalysis: methods, progress, and insights Annu. Rev. Biophys. Biomol. Struct. 2003, 32, 425-443 (Pubitemid 37056236)
-
(2003)
Annual Review of Biophysics and Biomolecular Structure
, vol.32
, pp. 425-443
-
-
Warshel, A.1
-
46
-
-
70349266325
-
Active site cysteine is protonated in the PAD4 Michaelis complex: Evidence from Born-Oppenheimer ab initio QM/MM molecular dynamics simulations
-
Ke, Z.; Zhou, Y.; Hu, P.; Wang, S.; Xie, D.; Zhang, Y. Active site cysteine is protonated in the PAD4 Michaelis complex: Evidence from Born-Oppenheimer ab initio QM/MM molecular dynamics simulations J. Phys. Chem. B 2009, 113, 12750-12758
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 12750-12758
-
-
Ke, Z.1
Zhou, Y.2
Hu, P.3
Wang, S.4
Xie, D.5
Zhang, Y.6
-
47
-
-
73349112879
-
Born-Oppenheimer ab initio QM/MM molecular dynamics simulations of the hydrolysis reaction catalyzed by protein arginine deiminase 4
-
Ke, Z.; Wang, S.; Xie, D.; Zhang, Y. Born-Oppenheimer ab initio QM/MM molecular dynamics simulations of the hydrolysis reaction catalyzed by protein arginine deiminase 4 J. Phys. Chem. B 2009, 113, 16705-16710
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 16705-16710
-
-
Ke, Z.1
Wang, S.2
Xie, D.3
Zhang, Y.4
-
48
-
-
58049201323
-
-
University of California: San Francisco, CA.
-
Case, D. A.; Darden, T.; Cheatham, I., T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Crowley, M.; Walker, R. C.; Zhang, W.; Merz, J., K. M.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossvary, I.; Wong, K. F.; Paesani, F.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Kollman, P. A. Amber 10; University of California: San Francisco, CA, 2008.
-
(2008)
Amber 10
-
-
Case, D.A.1
Darden, T.2
Cheatham, I..T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Crowley, M.8
Walker, R.C.9
Zhang, W.10
Merz, J..K.M.11
Wang, B.12
Hayik, S.13
Roitberg, A.14
Seabra, G.15
Kolossvary, I.16
Wong, K.F.17
Paesani, F.18
Wu, X.19
Brozell, S.R.20
Steinbrecher, T.21
Gohlke, H.22
Yang, L.23
Tan, C.24
Mongan, J.25
Hornak, V.26
Cui, G.27
Mathews, D.H.28
Seetin, M.G.29
Sagui, C.30
Babin, V.31
Kollman, P.A.32
more..
-
49
-
-
0029011701
-
A second generation force field for the simulation of protein, nucleic acids, and organic molecules
-
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, J. K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A second generation force field for the simulation of protein, nucleic acids, and organic molecules J. Am. Chem. Soc. 1995, 117, 5179
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, J.K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
50
-
-
33748518255
-
Comparison of multiple amber force fields and development of improved protein backbone parameters
-
DOI 10.1002/prot.21123
-
Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of multiple Amber force fields and development of improved protein backbone parameters Proteins 2006, 65, 712-725 (Pubitemid 44583220)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.65
, Issue.3
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
51
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 1983, 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
-
52
-
-
33846823909
-
Particle mesh Ewald: An NlogN method for Ewald sums in large systems
-
Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: an NlogN method for Ewald sums in large systems J. Chem. Phys. 1993, 98, 10089-10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
53
-
-
33645961739
-
A smooth particle mesh Ewald method
-
Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. A smooth particle mesh Ewald method J. Chem. Phys. 1995, 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.6
-
54
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comput. Phys. 1977, 23, 327-341
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.3
-
55
-
-
0001582558
-
A pseudobond approach to combining quantum mechanical and molecular mechanical methods
-
Zhang, Y.; Lee, T.; Yang, W. A pseudobond approach to combining quantum mechanical and molecular mechanical methods J. Chem. Phys. 1999, 110, 46
-
(1999)
J. Chem. Phys.
, vol.110
, pp. 46
-
-
Zhang, Y.1
Lee, T.2
Yang, W.3
-
56
-
-
22944472113
-
Improved pseudobonds for combined ab initio quantum mechanical/molecular mechanical methods
-
Zhang, Y. Improved pseudobonds for combined ab initio quantum mechanical/molecular mechanical methods J. Chem. Phys. 2005, 122, 24114
-
(2005)
J. Chem. Phys.
, vol.122
, pp. 24114
-
-
Zhang, Y.1
-
57
-
-
84906394507
-
-
Shao, Y.; Fusti-Molnar, L.; Jung, Y.; Kussmann, J.; Ochsenfeld, C.; Brown, S. T.; Gilbert, A. T. B.; Slipchenko, L. V.; Levchenko, S. V.; O'Neill, D. P.; DiStasio, R. A., Jr.; Lochan, R. C.; Wang, T.; Beran, G. J. O.; Besley, N. A.; Herbert, J. M.; Lin, C. Y.; Voorhis, T. V.; Chien, S. H.; Sodt, A.; Steele, R. P.; Rassolov, V. A.; Maslen, P. E.; Korambath, P. P.; Adamson, R. D.; Austin, B.; Baker, J.; Byrd, E. F. C.; Dachsel, H.; Doerksen, R. J.; Dreuw, A.; Dunietz, B. D.; Dutoi, A. D.; Furlani, T. R.; Gwaltney, S. R.; Heyden, A.; Hirata, S.; Hsu, C.-P.; Kedziora, G.; Khalliulin, R. Z.; Klunzinger, P.; Lee, A. M.; Lee, M. S.; Liang, W.; Lotan, I.; Nair, N.; Peters, B.; Proynov, E. I.; Pieniazek, P. A.; Rhee, Y. M.; Ritchie, J.; Rosta, E.; Sherrill, C. D.; Simmonett, A. C.; Subotnik, J. E.; Woodcock, H. W., III; Zhang, W.; Bell, A. T.; Chakraborty, A. K.; Chipman, D. M.; Keil, F. J.; Warshel, A.; Hehre, W. J.; Schaefer, H. F., III; Kong, J.; Krylov, A. I.; Gill, P. M. W.; Head-Gordon, M. QChem; 2006.
-
(2006)
QChem
-
-
Shao, Y.1
Fusti-Molnar, L.2
Jung, Y.3
Kussmann, J.4
Ochsenfeld, C.5
Brown, S.T.6
Gilbert, A.T.B.7
Slipchenko, L.V.8
Levchenko, S.V.9
O'Neill, D.P.10
Distasio Jr., R.A.11
Lochan, R.C.12
Wang, T.13
Beran, G.J.O.14
Besley, N.A.15
Herbert, J.M.16
Lin, C.Y.17
Voorhis, T.V.18
Chien, S.H.19
Sodt, A.20
Steele, R.P.21
Rassolov, V.A.22
Maslen, P.E.23
Korambath, P.P.24
Adamson, R.D.25
Austin, B.26
Baker, J.27
Byrd, E.F.C.28
Dachsel, H.29
Doerksen, R.J.30
Dreuw, A.31
Dunietz, B.D.32
Dutoi, A.D.33
Furlani, T.R.34
Gwaltney, S.R.35
Heyden, A.36
Hirata, S.37
Hsu, C.-P.38
Kedziora, G.39
Khalliulin, R.Z.40
Klunzinger, P.41
Lee, A.M.42
Lee, M.S.43
Liang, W.44
Lotan, I.45
Nair, N.46
Peters, B.47
Proynov, E.I.48
Pieniazek, P.A.49
Rhee, Y.M.50
Ritchie, J.51
Rosta, E.52
Sherrill, C.D.53
Simmonett, A.C.54
Subotnik, J.E.55
Iii, W.W.H.56
Zhang, W.57
Bell, A.T.58
Chakraborty, A.K.59
Chipman, D.M.60
Keil, F.J.61
Warshel, A.62
Hehre, W.J.63
Iii, F.S.H.64
Kong, J.65
Krylov, A.I.66
Gill, P.M.W.67
Head-Gordon, M.68
more..
-
59
-
-
0000145441
-
Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface
-
Zhang, Y.; Liu, H.; Yang, W. Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface J. Chem. Phys. 2000, 112, 3483-3492
-
(2000)
J. Chem. Phys.
, vol.112
, pp. 3483-3492
-
-
Zhang, Y.1
Liu, H.2
Yang, W.3
-
60
-
-
0342929614
-
Non-physical sampling distributions in Monte Carlo free energy estimation: Umbrella sampling
-
Torrie, G. M.; Valleau, J. P. Non-physical sampling distributions in Monte Carlo free energy estimation: Umbrella sampling J. Comput. Phys. 1977, 23, 187-199
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 187-199
-
-
Torrie, G.M.1
Valleau, J.P.2
-
61
-
-
0000394426
-
Some multistep methods for use in molecular dynamics calculations
-
Beeman, D. J. Some multistep methods for use in molecular dynamics calculations J. Comput. Phys. 1976, 20, 130-139
-
(1976)
J. Comput. Phys.
, vol.20
, pp. 130-139
-
-
Beeman, D.J.1
-
62
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. Molecular dynamics with coupling to an external bath J. Chem. Phys. 1984, 81, 3684-3690
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
63
-
-
84986519238
-
The weighted histogram analysis method for free energy calculations on biomolecules. 1. The method
-
Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. The weighted histogram analysis method for free energy calculations on biomolecules. 1. The method J. Comput. Chem. 1992, 13, 1011-1021
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.H.3
Kollman, P.A.4
Rosenberg, J.M.5
-
64
-
-
34248219463
-
Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: The case of histone lysine methyltransferase SET7/9
-
DOI 10.1021/jp067147i
-
Wang, S.; Hu, P.; Zhang, Y. Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: The case of histone lysine methyltransferase SET7/9 J. Phys. Chem. B 2007, 111, 3758-3764 (Pubitemid 46724005)
-
(2007)
Journal of Physical Chemistry B
, vol.111
, Issue.14
, pp. 3758-3764
-
-
Wang, S.1
Hu, P.2
Zhang, Y.3
-
65
-
-
41149125431
-
How do SET-domain protein lysine methyltransferases achieve the methylation state specificity? Revisited by Ab initio QM/MM molecular dynamics simulations
-
DOI 10.1021/ja075896n
-
Hu, P.; Wang, S.; Zhang, Y. How do SET-domain protein lysine methyltransferases achieve the methylation state specificity? Revisited by ab initio QM/MM molecular dynamics simulations J. Am. Chem. Soc. 2008, 130, 3806-3813 (Pubitemid 351429846)
-
(2008)
Journal of the American Chemical Society
, vol.130
, Issue.12
, pp. 3806-3813
-
-
Hu, P.1
Wang, S.2
Zhang, Y.3
-
66
-
-
57549110245
-
Highly dissociative and concerted mechanism for the nicotinamide cleavage reaction in Sir2Tm enzyme suggested by ab initio QM/MM molecular dynamics simulations
-
Hu, P.; Wang, S.; Zhang, Y. Highly dissociative and concerted mechanism for the nicotinamide cleavage reaction in Sir2Tm enzyme suggested by ab initio QM/MM molecular dynamics simulations J. Am. Chem. Soc. 2008, 130, 16721-16728
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 16721-16728
-
-
Hu, P.1
Wang, S.2
Zhang, Y.3
-
67
-
-
46949094784
-
On the origin of the stabilization of the zwitterionic resting state of cysteine proteases: A theoretical study
-
DOI 10.1021/ja711043x
-
Mladenovic, M.; Fink, R. F.; Thiel, W.; Schirmeister, T.; Engels, B. On the origin of the stabilization of the Zwitterionic resting state of cysteine proteases: A theoretical study J. Am. Chem. Soc. 2008, 130, 8696-8705 (Pubitemid 351962503)
-
(2008)
Journal of the American Chemical Society
, vol.130
, Issue.27
, pp. 8696-8705
-
-
Mladenovic, M.1
Fink, R.F.2
Thiel, W.3
Schirmeister, T.4
Engels, B.5
|