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Volumn 47, Issue 16, 2008, Pages 4721-4732

The electrostatic driving force for nucleophilic catalysis in L-arginine deiminase: A combined experimental and theoretical study

Author keywords

[No Author keywords available]

Indexed keywords

AMMONIA; CATALYSIS; ELECTROSTATICS; IONIZATION; PERTURBATION TECHNIQUES; REACTION KINETICS;

EID: 42349110120     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi7023496     Document Type: Article
Times cited : (22)

References (67)
  • 1
    • 0014027490 scopus 로고
    • The generation of energy by the arginine dihydrolase pathway in Mycoplasma hominis 07
    • Schimke, R. T., Berlin, C. M., Sweeney, E. W., and Carroll, W. R. (1966) The generation of energy by the arginine dihydrolase pathway in Mycoplasma hominis 07. J. Biol. Chem. 241, 2228-2236.
    • (1966) J. Biol. Chem , vol.241 , pp. 2228-2236
    • Schimke, R.T.1    Berlin, C.M.2    Sweeney, E.W.3    Carroll, W.R.4
  • 2
    • 0018077228 scopus 로고
    • Arginine deiminase from Mycoplasma arthritidis. Structure-activity relationships among substrates and competitive inhibitors
    • Smith, D. W., Ganaway, R. L., and Fahrney, D. E. (1978) Arginine deiminase from Mycoplasma arthritidis. Structure-activity relationships among substrates and competitive inhibitors. J. Biol. Chem. 253, 6016-6020.
    • (1978) J. Biol. Chem , vol.253 , pp. 6016-6020
    • Smith, D.W.1    Ganaway, R.L.2    Fahrney, D.E.3
  • 3
    • 0022531132 scopus 로고
    • Biosynthesis and metabolism of arginine in bacteria
    • Cunin, R., Glansdorff, N., Pierard, A., and Stalon, V. (1986) Biosynthesis and metabolism of arginine in bacteria. Microbiol. Rev. 50, 314-352.
    • (1986) Microbiol. Rev , vol.50 , pp. 314-352
    • Cunin, R.1    Glansdorff, N.2    Pierard, A.3    Stalon, V.4
  • 5
    • 0036840306 scopus 로고    scopus 로고
    • Isolation and molecular analysis of the gene cluster for the arginine deiminase system from Streptococcus gordonii DL1
    • Dong, Y., Chen, Y. Y., Snyder, J. A., and Burne, R. A. (2002) Isolation and molecular analysis of the gene cluster for the arginine deiminase system from Streptococcus gordonii DL1. Appl. Environ. Microbiol. 68, 5549-5553.
    • (2002) Appl. Environ. Microbiol , vol.68 , pp. 5549-5553
    • Dong, Y.1    Chen, Y.Y.2    Snyder, J.A.3    Burne, R.A.4
  • 6
    • 30744434891 scopus 로고    scopus 로고
    • Structure, regulation, and putative function of the arginine deiminase system of Streptococcus suis
    • Gruening, P., Fulde, M., Valentin-Weigand, P., and Goethe, R. (2006) Structure, regulation, and putative function of the arginine deiminase system of Streptococcus suis. J. Bacteriol. 188, 361-369.
    • (2006) J. Bacteriol , vol.188 , pp. 361-369
    • Gruening, P.1    Fulde, M.2    Valentin-Weigand, P.3    Goethe, R.4
  • 8
    • 33751116307 scopus 로고    scopus 로고
    • Reporter metabolite analysis of transcriptional profiles of a Staphylococcus aureus strain with normal phenotype and its isogenic hemB mutant displaying the small-colony-variant phenotype
    • Seggewiss, J., Becker, K., Kotte, O., Eisenacher, M., Yazdi, M. R., Fischer, A., McNamara, P., Al Laham, N., Proctor, R., Peters, G., Heinemann, M., and von Eiff, C. (2006) Reporter metabolite analysis of transcriptional profiles of a Staphylococcus aureus strain with normal phenotype and its isogenic hemB mutant displaying the small-colony-variant phenotype. J. Bacteriol. 188, 7765-7777.
    • (2006) J. Bacteriol , vol.188 , pp. 7765-7777
    • Seggewiss, J.1    Becker, K.2    Kotte, O.3    Eisenacher, M.4    Yazdi, M.R.5    Fischer, A.6    McNamara, P.7    Al Laham, N.8    Proctor, R.9    Peters, G.10    Heinemann, M.11    von Eiff, C.12
  • 10
    • 0032549032 scopus 로고    scopus 로고
    • 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., and Edwards, M. R. (1998) Cloning and expression of a prokaryotic enzyme, arginine deiminase, from a primitive eukaryote Giardia intestinalis. J. Biol. Chem. 273, 4470-4477.
    • (1998) J. Biol. Chem , vol.273 , pp. 4470-4477
    • Knodler, L.A.1    Sekyere, E.O.2    Stewart, T.S.3    Schofield, P.J.4    Edwards, M.R.5
  • 11
    • 0034933985 scopus 로고    scopus 로고
    • Biology of Giardia lamblia
    • Adam, R. D. (2001) Biology of Giardia lamblia. Clin. Microbiol. Rev. 14, 447-475.
    • (2001) Clin. Microbiol. Rev , vol.14 , pp. 447-475
    • Adam, R.D.1
  • 12
    • 34848894621 scopus 로고    scopus 로고
    • Morrison, H. G., McArthur, A. G., Gillin, F. D., Aley, S. B., Adam, R. D., Olsen, G. J., Best, A. A., Cande, W. Z., Chen, F., Cipriano, M. J., Davids, B. J., Dawson, S. C., Elmendorf, H. G., Hehl, A. B., Holder, M. E., Huse, S. M., Kim, U. U., Lasek-Nesselquist, E., Manning, G., Nigam, A., Nixon, J. E., Palm, D., Passamaneck, N. E., Prabhu, A., Reich, C. I., Reiner, D. S., Samuelson, J., Svard, S. G., and Sogin, M. L. (2007) Genomic minimalism in the early diverging intestinal parasite Giardia lamblia. Science 317, 1921-1926.
    • Morrison, H. G., McArthur, A. G., Gillin, F. D., Aley, S. B., Adam, R. D., Olsen, G. J., Best, A. A., Cande, W. Z., Chen, F., Cipriano, M. J., Davids, B. J., Dawson, S. C., Elmendorf, H. G., Hehl, A. B., Holder, M. E., Huse, S. M., Kim, U. U., Lasek-Nesselquist, E., Manning, G., Nigam, A., Nixon, J. E., Palm, D., Passamaneck, N. E., Prabhu, A., Reich, C. I., Reiner, D. S., Samuelson, J., Svard, S. G., and Sogin, M. L. (2007) Genomic minimalism in the early diverging intestinal parasite Giardia lamblia. Science 317, 1921-1926.
  • 13
    • 0037187008 scopus 로고    scopus 로고
    • Characterization of mycoplasma arginine deiminase expressed in E. coli and its inhibitory regulation of nitric oxide synthesis
    • Noh, E. J., Kang, S. W., Shin, Y. J., Kim, D. C., Park, I. S., Kim, M. Y., Chun, B. G., and Min, B. H. (2002) Characterization of mycoplasma arginine deiminase expressed in E. coli and its inhibitory regulation of nitric oxide synthesis. Mol. Cells 13, 137-143.
    • (2002) Mol. Cells , vol.13 , pp. 137-143
    • Noh, E.J.1    Kang, S.W.2    Shin, Y.J.3    Kim, D.C.4    Park, I.S.5    Kim, M.Y.6    Chun, B.G.7    Min, B.H.8
  • 14
    • 0037563766 scopus 로고    scopus 로고
    • Identification of immunoreactive proteins during acute human giardiasis
    • Palm, J. E., Weiland, M. E., Griffiths, W. J., Ljungstrom, I., and Svard, S. G. (2003) Identification of immunoreactive proteins during acute human giardiasis. J. Infect. Dis. 187, 1849-1859.
    • (2003) J. Infect. Dis , vol.187 , pp. 1849-1859
    • Palm, J.E.1    Weiland, M.E.2    Griffiths, W.J.3    Ljungstrom, I.4    Svard, S.G.5
  • 15
    • 0035424604 scopus 로고    scopus 로고
    • A novel superfamily of enzymes that catalyze the modification of guanidino groups
    • Shirai, H., Blundell, T. L., and Mizuguchi, K. (2001) A novel superfamily of enzymes that catalyze the modification of guanidino groups. Trends Biochem. Sci. 26, 465-468.
    • (2001) Trends Biochem. Sci , vol.26 , pp. 465-468
    • Shirai, H.1    Blundell, T.L.2    Mizuguchi, K.3
  • 16
    • 0033214074 scopus 로고    scopus 로고
    • Identification of two human dimethylarginine dimethylaminohydrolases with distinct tissue distributions and homology with microbial arginine deiminases
    • Leiper, J. M., Santa Maria, J., Chubb, A., MacAllister, R. J., Charles, I. G., Whitley, G. S., and Vallance, P. (1999) Identification of two human dimethylarginine dimethylaminohydrolases with distinct tissue distributions and homology with microbial arginine deiminases. Biochem. J. 343, 209-214.
    • (1999) Biochem. J , vol.343 , pp. 209-214
    • Leiper, J.M.1    Santa Maria, J.2    Chubb, A.3    MacAllister, R.J.4    Charles, I.G.5    Whitley, G.S.6    Vallance, P.7
  • 17
    • 0032864893 scopus 로고    scopus 로고
    • Identification of microbial dimethylarginine dimethylaminohydrolase enzymes
    • Santa Maria, J., Vallance, P., Charles, I. G., and Leiper, J. M. (1999) Identification of microbial dimethylarginine dimethylaminohydrolase enzymes. Mol. Microbiol. 33, 1278-1289.
    • (1999) Mol. Microbiol , vol.33 , pp. 1278-1289
    • Santa Maria, J.1    Vallance, P.2    Charles, I.G.3    Leiper, J.M.4
  • 18
    • 23244447251 scopus 로고    scopus 로고
    • Kinetic characterization of protein arginine deiminase 4: A transcriptional corepressor implicated in the onset and progression of rheumatoid arthritis
    • Kearney, P. L., Bhatia, M., Jones, N. G., Yuan, L., Glascock, M. C., Catchings, K. L., Yamada, M., and Thompson, P. R. (2005) Kinetic characterization of protein arginine deiminase 4: A transcriptional corepressor implicated in the onset and progression of rheumatoid arthritis. Biochemistry 44, 10570-10582.
    • (2005) Biochemistry , vol.44 , 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
  • 19
    • 0037351889 scopus 로고    scopus 로고
    • Identification of the putrescine biosynthetic genes in Pseudomonas aeruginosa and characterization of agmatine deiminase and N-carbamoylputrescine amidohydrolase of the arginine decarboxylase pathway
    • Nakada, Y., and Itoh, Y. (2003) Identification of the putrescine biosynthetic genes in Pseudomonas aeruginosa and characterization of agmatine deiminase and N-carbamoylputrescine amidohydrolase of the arginine decarboxylase pathway. Microbiology 149, 707-714.
    • (2003) Microbiology , vol.149 , pp. 707-714
    • Nakada, Y.1    Itoh, Y.2
  • 20
    • 18144380237 scopus 로고    scopus 로고
    • Crystal structure of N-succinylarginine dihydrolase AstB, bound to substrate and product, an enzyme from the arginine catabolic pathway of Escherichia coli
    • Tocilj, A., Schrag, J. D., Li, Y., Schneider, B. L., Reitzer, L., Matte, A., and Cygler, M. (2005) Crystal structure of N-succinylarginine dihydrolase AstB, bound to substrate and product, an enzyme from the arginine catabolic pathway of Escherichia coli. J. Biol. Chem. 280, 15800-15808.
    • (2005) J. Biol. Chem , vol.280 , pp. 15800-15808
    • Tocilj, A.1    Schrag, J.D.2    Li, Y.3    Schneider, B.L.4    Reitzer, L.5    Matte, A.6    Cygler, M.7
  • 21
    • 0036883907 scopus 로고    scopus 로고
    • Blocking NO synthesis: How, where and why?
    • Vallance, P., and Leiper, J. (2002) Blocking NO synthesis: How, where and why? Nat. Rev. Drug Discovery 1, 939-950.
    • (2002) Nat. Rev. Drug Discovery , vol.1 , pp. 939-950
    • Vallance, P.1    Leiper, J.2
  • 22
    • 33751001725 scopus 로고    scopus 로고
    • Histone citrullination by protein arginine deiminase: Is arginine methylation a green light or a roadblock? ACS
    • Thompson, P. R., and Fast, W. (2006) Histone citrullination by protein arginine deiminase: Is arginine methylation a green light or a roadblock? ACS Chem. Biol. 1, 433-441.
    • (2006) Chem. Biol , vol.1 , pp. 433-441
    • Thompson, P.R.1    Fast, W.2
  • 24
    • 0031974911 scopus 로고    scopus 로고
    • Citrulline is an essential constituent of antigenic determinants recognized by rheumatoid arthritis-specific autoantibodies
    • Schellekens, G. A., de Jong, B. A., van den Hoogen, F. H., van de Putte, L. B., and van Venrooij, W. J. (1998) Citrulline is an essential constituent of antigenic determinants recognized by rheumatoid arthritis-specific autoantibodies. J. Clin. Invest. 101, 273-281.
    • (1998) J. Clin. Invest , vol.101 , pp. 273-281
    • Schellekens, G.A.1    de Jong, B.A.2    van den Hoogen, F.H.3    van de Putte, L.B.4    van Venrooij, W.J.5
  • 26
    • 1842450302 scopus 로고    scopus 로고
    • 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., and Arnold, E. (2004) Crystal structures of arginine deiminase with covalent reaction intermediates: Implications for catalytic mechanism. Structure 12, 657-667.
    • (2004) Structure , vol.12 , pp. 657-667
    • Das, K.1    Butler, G.H.2    Kwiatkowski, V.3    Clark Jr., A.D.4    Yadav, P.5    Arnold, E.6
  • 27
    • 0032559012 scopus 로고    scopus 로고
    • Crystal structure of L-arginine:inosamine-phosphate amidinotransferase StrB1 from Streptomyces griseus: An enzyme involved in streptomycin biosynthesis
    • Fritsche, E., Bergner, A., Humm, A., Piepersberg, W., and Huber, R. (1998) Crystal structure of L-arginine:inosamine-phosphate amidinotransferase StrB1 from Streptomyces griseus: An enzyme involved in streptomycin biosynthesis. Biochemistry 37, 17664-17672.
    • (1998) Biochemistry , vol.37 , pp. 17664-17672
    • Fritsche, E.1    Bergner, A.2    Humm, A.3    Piepersberg, W.4    Huber, R.5
  • 28
    • 0033613922 scopus 로고    scopus 로고
    • The ligand-induced structural changes of human L-arginine:glycine amidinotransferase. A mutational and crystallographic study
    • Fritsche, E., Humm, A., and Huber, R. (1999) The ligand-induced structural changes of human L-arginine:glycine amidinotransferase. A mutational and crystallographic study. J. Biol. Chem. 274, 3026-3032.
    • (1999) J. Biol. Chem , vol.274 , pp. 3026-3032
    • Fritsche, E.1    Humm, A.2    Huber, R.3
  • 29
    • 1842639583 scopus 로고    scopus 로고
    • Structural insight into arginine degradation by arginine deiminase, an antibacterial and parasite drug target
    • Galkin, A., Kulakova, L., Sarikaya, E., Lim, K., Howard, A., and Herzberg, O. (2004) Structural insight into arginine degradation by arginine deiminase, an antibacterial and parasite drug target. J. Biol. Chem. 279, 14001-14008.
    • (2004) J. Biol. Chem , vol.279 , pp. 14001-14008
    • Galkin, A.1    Kulakova, L.2    Sarikaya, E.3    Lim, K.4    Howard, A.5    Herzberg, O.6
  • 30
    • 26644450503 scopus 로고    scopus 로고
    • Crystal structures representing the Michaelis complex and the thiouronium reaction intermediate of Pseudomonas aeruginosa arginine deiminase
    • Galkin, A., Lu, X., Dunaway-Mariano, D., and Herzberg, O. (2005) Crystal structures representing the Michaelis complex and the thiouronium reaction intermediate of Pseudomonas aeruginosa arginine deiminase. J. Biol. Chem. 280, 34080-34087.
    • (2005) J. Biol. Chem , vol.280 , pp. 34080-34087
    • Galkin, A.1    Lu, X.2    Dunaway-Mariano, D.3    Herzberg, O.4
  • 31
    • 0030989923 scopus 로고    scopus 로고
    • Structure and reaction mechanism of L-arginine:glycine amidinotransferase
    • Humm, A., Fritsche, E., and Steinbacher, S. (1997) Structure and reaction mechanism of L-arginine:glycine amidinotransferase. Biol. Chem. 378, 193-197.
    • (1997) Biol. Chem , vol.378 , pp. 193-197
    • Humm, A.1    Fritsche, E.2    Steinbacher, S.3
  • 32
    • 33846912925 scopus 로고    scopus 로고
    • The gene cluster for agmatine catabolism of Enterococcus faecalis: Study of recombinant putrescine transcarbamylase and agmatine deiminase and a snapshot of agmatine deiminase catalyzing its reaction
    • Llacer, J. L., Polo, L. M., Tavarez, S., Alarcon, B., Hilario, R., and Rubio, V. (2007) The gene cluster for agmatine catabolism of Enterococcus faecalis: Study of recombinant putrescine transcarbamylase and agmatine deiminase and a snapshot of agmatine deiminase catalyzing its reaction. J. Bacteriol. 189, 1254-1265.
    • (2007) J. Bacteriol , vol.189 , pp. 1254-1265
    • Llacer, J.L.1    Polo, L.M.2    Tavarez, S.3    Alarcon, B.4    Hilario, R.5    Rubio, V.6
  • 33
    • 33749359452 scopus 로고    scopus 로고
    • Inhibitors and inactivators of protein arginine deiminase 4: Functional and structural characterization
    • Luo, Y., Arita, K., Bhatia, M., Knuckley, B., Lee, Y. H., Stallcup, M. R., Sato, M., and Thompson, P. R. (2006) Inhibitors and inactivators of protein arginine deiminase 4: Functional and structural characterization. Biochemistry 45, 11727-11736.
    • (2006) Biochemistry , vol.45 , pp. 11727-11736
    • Luo, Y.1    Arita, K.2    Bhatia, M.3    Knuckley, B.4    Lee, Y.H.5    Stallcup, M.R.6    Sato, M.7    Thompson, P.R.8
  • 34
    • 0034885255 scopus 로고    scopus 로고
    • Structural insights into the hydrolysis of cellular nitric oxide synthase inhibitors by dimethylarginine dimethylaminohydrolase
    • Murray-Rust, J., Leiper, J., McAlister, M., Phelan, J., Tilley, S., Santa Maria, J., Vallance, P., and McDonald, N. (2001) Structural insights into the hydrolysis of cellular nitric oxide synthase inhibitors by dimethylarginine dimethylaminohydrolase. Nat. Struct. Biol. 8, 679-683.
    • (2001) Nat. Struct. Biol , vol.8 , pp. 679-683
    • Murray-Rust, J.1    Leiper, J.2    McAlister, M.3    Phelan, J.4    Tilley, S.5    Santa Maria, J.6    Vallance, P.7    McDonald, N.8
  • 35
    • 2342449187 scopus 로고    scopus 로고
    • Arginine deiminase uses an active-site cysteine in nucleophilic catalysis of L-arginine hydrolysis
    • Lu, X., Galkin, A., Herzberg, O., and Dunaway-Mariano, D. (2004) Arginine deiminase uses an active-site cysteine in nucleophilic catalysis of L-arginine hydrolysis. J. Am. Chem. Soc. 126, 5374-5375.
    • (2004) J. Am. Chem. Soc , vol.126 , pp. 5374-5375
    • Lu, X.1    Galkin, A.2    Herzberg, O.3    Dunaway-Mariano, D.4
  • 36
    • 18244386728 scopus 로고    scopus 로고
    • Characterization of a transient covalent adduct formed during dimethylarginine dimethylaminohydrolase catalysis
    • Stone, E. M., Person, M. D., Costello, N. J., and Fast, W. (2005) Characterization of a transient covalent adduct formed during dimethylarginine dimethylaminohydrolase catalysis. Biochemistry 44, 7069-7078.
    • (2005) Biochemistry , vol.44 , pp. 7069-7078
    • Stone, E.M.1    Person, M.D.2    Costello, N.J.3    Fast, W.4
  • 37
    • 31544455800 scopus 로고    scopus 로고
    • Kinetic analysis of Pseudomonas aeruginosa arginine deiminase mutants and alternate substrates provides insight into structural determinants of function
    • Lu, X., Li, L., Wu, R., Feng, X., Li, Z., Yang, H., Wang, C., Guo, H., Galkin, A., Herzberg, O., Mariano, P. S., Martin, B. M., and Dunaway-Mariano, D. (2006) Kinetic analysis of Pseudomonas aeruginosa arginine deiminase mutants and alternate substrates provides insight into structural determinants of function. Biochemistry 45, 1162-1172.
    • (2006) Biochemistry , vol.45 , 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
  • 38
    • 36849001753 scopus 로고    scopus 로고
    • Inhibition of human dimethylarginine dimethylamionhydrolase-1 by S-nitroso-L-homocysteine and hydrogen peroxide: Analysis, quantification, and implications for hyperhomocysteinemia
    • Hong, L., and Fast, W. (2007) Inhibition of human dimethylarginine dimethylamionhydrolase-1 by S-nitroso-L-homocysteine and hydrogen peroxide: Analysis, quantification, and implications for hyperhomocysteinemia. J. Biol. Chem. 282, 34684-34692.
    • (2007) J. Biol. Chem , vol.282 , pp. 34684-34692
    • Hong, L.1    Fast, W.2
  • 39
    • 28444435875 scopus 로고    scopus 로고
    • Lu, X., Li, L., Feng, X., Wu, Y., Dunaway-Mariano, D., Engen, J. R., and Mariano, P. S. (2005) L-Canavanine is a time-controlled mechanism-based inhibitor of Pseudomonas aeruginosa arginine deiminase. J. Am. Chem. Soc. 127, 16412-16413.
    • Lu, X., Li, L., Feng, X., Wu, Y., Dunaway-Mariano, D., Engen, J. R., and Mariano, P. S. (2005) L-Canavanine is a time-controlled mechanism-based inhibitor of Pseudomonas aeruginosa arginine deiminase. J. Am. Chem. Soc. 127, 16412-16413.
  • 40
    • 31944448153 scopus 로고    scopus 로고
    • A fluoroacetamidine-based inactivator of protein arginine deiminase 4: Design, synthesis, and in vitro and in vivo evaluation
    • Luo, Y., Knuckley, B., Lee, Y. H., Stallcup, M. R., and Thompson, P. R. (2006) A fluoroacetamidine-based inactivator of protein arginine deiminase 4: Design, synthesis, and in vitro and in vivo evaluation. J. Am. Chem. Soc. 128, 1092-1093.
    • (2006) J. Am. Chem. Soc , vol.128 , pp. 1092-1093
    • Luo, Y.1    Knuckley, B.2    Lee, Y.H.3    Stallcup, M.R.4    Thompson, P.R.5
  • 41
    • 27144463085 scopus 로고    scopus 로고
    • Inactivation of two diverse enzymes in the amidinotransferase superfamily by 2-chloroacetamidine: Dimethylargininase and peptidylarginine deiminase
    • Stone, E. M., Schaller, T. H., Bianchi, H., Person, M. D., and Fast, W. (2005) Inactivation of two diverse enzymes in the amidinotransferase superfamily by 2-chloroacetamidine: Dimethylargininase and peptidylarginine deiminase. Biochemistry 44, 13744-13752.
    • (2005) Biochemistry , vol.44 , pp. 13744-13752
    • Stone, E.M.1    Schaller, T.H.2    Bianchi, H.3    Person, M.D.4    Fast, W.5
  • 42
    • 33846250027 scopus 로고    scopus 로고
    • Insight into the catalytic mechanism of arginine deiminase: Functional studies on the crucial sites
    • Wei, Y., Zhou, H., Sun, Y., He, Y., and Luo, Y. (2007) Insight into the catalytic mechanism of arginine deiminase: Functional studies on the crucial sites. Proteins 66, 740-750.
    • (2007) Proteins , vol.66 , pp. 740-750
    • Wei, Y.1    Zhou, H.2    Sun, Y.3    He, Y.4    Luo, Y.5
  • 43
    • 34147183761 scopus 로고    scopus 로고
    • Molecular dynamics and density functional studies of substrate binding and catalysis of arginine deiminase
    • Wang, C., Xu, D., Zhang, L., Xie, D., and Guo, H. (2007) Molecular dynamics and density functional studies of substrate binding and catalysis of arginine deiminase. J. Phys. Chem. B 111, 3267-3273.
    • (2007) J. Phys. Chem. B , vol.111 , pp. 3267-3273
    • Wang, C.1    Xu, D.2    Zhang, L.3    Xie, D.4    Guo, H.5
  • 45
    • 0014622121 scopus 로고
    • Modified methods for the determination of carbamyl aspartate
    • Prescott, L. M., and Jones, M. E. (1969) Modified methods for the determination of carbamyl aspartate. Anal. Biochem. 32, 408-419.
    • (1969) Anal. Biochem , vol.32 , pp. 408-419
    • Prescott, L.M.1    Jones, M.E.2
  • 46
    • 0017725220 scopus 로고
    • Arginine deiminase from Mycoplasma arthritidis. Evidence for multiple forms
    • Weickmann, J. L., and Fahrney, D. E. (1977) Arginine deiminase from Mycoplasma arthritidis. Evidence for multiple forms. J. Biol. Chem. 252, 2615-2620.
    • (1977) J. Biol. Chem , vol.252 , pp. 2615-2620
    • Weickmann, J.L.1    Fahrney, D.E.2
  • 48
    • 0022068152 scopus 로고
    • Active site dynamics in protein molecules: A stochastic boundary molecular-dynamics approach
    • Brooks, C. L., Brunger, A., and Karplus, M. (1985) Active site dynamics in protein molecules: A stochastic boundary molecular-dynamics approach. Biopolymers 24, 843-865.
    • (1985) Biopolymers , vol.24 , pp. 843-865
    • Brooks, C.L.1    Brunger, A.2    Karplus, M.3
  • 49
    • 0017100947 scopus 로고
    • Theoretical studies of enzymatic reactions: Dielectric, electrostation and steric stabilization of carbonium ion in the reaction of lysozyme
    • Warshal, A., and Levitt, M. (1976) Theoretical studies of enzymatic reactions: Dielectric, electrostation and steric stabilization of carbonium ion in the reaction of lysozyme. J. Mol. Biol. 103, 227-249.
    • (1976) J. Mol. Biol , vol.103 , pp. 227-249
    • Warshal, A.1    Levitt, M.2
  • 50
    • 84962367344 scopus 로고    scopus 로고
    • Methods and applications of combined quantum mechanical and molecular mechanical potentials
    • Lipkowitz, K. B, and Boyd, D. B, Eds, pp, VCH, New York
    • Gao, J. (1996) Methods and applications of combined quantum mechanical and molecular mechanical potentials, in Reviews in Computational Chemistry (Lipkowitz, K. B., and Boyd, D. B., Eds.) pp 119-185, VCH, New York.
    • (1996) Reviews in Computational Chemistry , pp. 119-185
    • Gao, J.1
  • 51
    • 0037718593 scopus 로고    scopus 로고
    • Parameterization of semiempirical methods to treat nucleophilic attacks to biological phosphates: AM1/d parameters for phosphorus
    • Lopez, X., and York, D. M. (2003) Parameterization of semiempirical methods to treat nucleophilic attacks to biological phosphates: AM1/d parameters for phosphorus. Theor. Chem. Acc. 109, 149-159.
    • (2003) Theor. Chem. Acc , vol.109 , pp. 149-159
    • Lopez, X.1    York, D.M.2
  • 52
    • 0000189651 scopus 로고
    • Density-functional thermochemistry. III. The role of exact exchange
    • Becke, A. D. (1993) Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 98, 5648-5652.
    • (1993) J. Chem. Phys , vol.98 , pp. 5648-5652
    • Becke, A.D.1
  • 53
    • 0345491105 scopus 로고
    • Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
    • Lee, C., Yang, W., and Parr, R. G. (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B 37, 785-789.
    • (1988) Phys. Rev. B , vol.37 , pp. 785-789
    • Lee, C.1    Yang, W.2    Parr, R.G.3
  • 54
    • 0041784950 scopus 로고    scopus 로고
    • MacKerell, A. D., Jr., Bashford, D., Bellott, D., Dunbrack, R. L., Jr., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., III, Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., and Karplus, M. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102, 3586-3616.
    • MacKerell, A. D., Jr., Bashford, D., Bellott, D., Dunbrack, R. L., Jr., Evanseck, J. D., Field, M. J., Fischer, S., Gao, J., Guo, H., Ha, S., Joseph-McCarthy, D., Kuchnir, L., Kuczera, K., Lau, F. T. K., Mattos, C., Michnick, S., Ngo, T., Nguyen, D. T., Prodhom, B., Reiher, W. E., III, Roux, B., Schlenkrich, M., Smith, J. C., Stote, R., Straub, J., Watanabe, M., Wiorkiewicz-Kuczera, J., Yin, D., and Karplus, M. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102, 3586-3616.
  • 55
    • 84986513644 scopus 로고
    • A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
    • Field, M. J., Bash, P. A., and Karplus, M. (1990) A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J. Comput. Chem. 11, 700-733.
    • (1990) J. Comput. Chem , vol.11 , pp. 700-733
    • Field, M.J.1    Bash, P.A.2    Karplus, M.3
  • 56
    • 0000049872 scopus 로고    scopus 로고
    • Enzyme mechanisms with hybrid quantum and molecular mechanical potentials. I. Theoretical considerations
    • Eurenius, K. P., Chatfield, D. C., Brooks, B. R., and Hodoscek, M. (1996) Enzyme mechanisms with hybrid quantum and molecular mechanical potentials. I. Theoretical considerations. Int. J. Quantum Chem. 60, 1189-1200.
    • (1996) Int. J. Quantum Chem , vol.60 , pp. 1189-1200
    • Eurenius, K.P.1    Chatfield, D.C.2    Brooks, B.R.3    Hodoscek, M.4
  • 57
    • 0015962432 scopus 로고
    • Spectrophotometric determination of mercaptide ion, an activated form of SH-group in thiol enzymens
    • Polgar, L. (1974) Spectrophotometric determination of mercaptide ion, an activated form of SH-group in thiol enzymens. FEBS Lett. 38, 187-190.
    • (1974) FEBS Lett , vol.38 , pp. 187-190
    • Polgar, L.1
  • 58
    • 0024588467 scopus 로고
    • Spectroscopic and kinetic evidence for the thiolate anion of glutathione at the active site of glutathione S-transferase
    • Graminski, G. F., Kubo, Y., and Armstrong, R. N. (1989) Spectroscopic and kinetic evidence for the thiolate anion of glutathione at the active site of glutathione S-transferase. Biochemistry 28, 3562-3568.
    • (1989) Biochemistry , vol.28 , pp. 3562-3568
    • Graminski, G.F.1    Kubo, Y.2    Armstrong, R.N.3
  • 59
    • 0027325607 scopus 로고
    • Peculiar spectroscopic and kinetic properties of Cys-47 in human placental glutathione transferase: Evidence for an atypical thiolate ion pair near the active site
    • Lo Bello, M., Parker, M. W., Desideri, A., Polticelli, F., Falconi, M., Del Boccio, G., Pennelli, A., Federici, G., and Ricci, G. (1993) Peculiar spectroscopic and kinetic properties of Cys-47 in human placental glutathione transferase: Evidence for an atypical thiolate ion pair near the active site. J. Biol. Chem. 268, 19033-19038.
    • (1993) J. Biol. Chem , vol.268 , pp. 19033-19038
    • Lo Bello, M.1    Parker, M.W.2    Desideri, A.3    Polticelli, F.4    Falconi, M.5    Del Boccio, G.6    Pennelli, A.7    Federici, G.8    Ricci, G.9
  • 60
    • 0028360184 scopus 로고
    • Reactivity and ionization of the active site cysteine residues of DsbA, a protein required for disulfide bond formation in vivo
    • Nelson, J. W., and Creighton, T. E. (1994) Reactivity and ionization of the active site cysteine residues of DsbA, a protein required for disulfide bond formation in vivo. Biochemistry 33, 5974-5983.
    • (1994) Biochemistry , vol.33 , pp. 5974-5983
    • Nelson, J.W.1    Creighton, T.E.2
  • 61
    • 0035807060 scopus 로고    scopus 로고
    • Thiolate-imidazolium ion pair is not an obligatory catalytic entity of cysteine peptidases: The active site of picornain 3C
    • Sarkany, Z., Szeltner, Z., and Polgar, L. (2001) Thiolate-imidazolium ion pair is not an obligatory catalytic entity of cysteine peptidases: The active site of picornain 3C. Biochemistry 40, 10601-10606.
    • (2001) Biochemistry , vol.40 , pp. 10601-10606
    • Sarkany, Z.1    Szeltner, Z.2    Polgar, L.3
  • 62
    • 33646371495 scopus 로고    scopus 로고
    • Substrate-assisted cysteine deprotonation in the mechanism of dimethylargininase (DDAH) from Pseudomonas aeruginosa
    • Stone, E. M., Costello, A. L., Tierney, D. L., and Fast, W. (2006) Substrate-assisted cysteine deprotonation in the mechanism of dimethylargininase (DDAH) from Pseudomonas aeruginosa. Biochemistry 45, 5618-5630.
    • (2006) Biochemistry , vol.45 , pp. 5618-5630
    • Stone, E.M.1    Costello, A.L.2    Tierney, D.L.3    Fast, W.4
  • 64
    • 0031024788 scopus 로고    scopus 로고
    • Effects of buried charged groups on cysteine thiol ionization and reactivity in Escherichia coli thioredoxin: Structural and functional characterization of mutants of Asp 26 and Lys 57
    • Dyson, H. J., Jeng, M. F., Tennant, L. L., Slaby, I., Lindell, M., Cui, D. S., Kuprin, S., and Holmgren, A. (1997) Effects of buried charged groups on cysteine thiol ionization and reactivity in Escherichia coli thioredoxin: Structural and functional characterization of mutants of Asp 26 and Lys 57. Biochemistry 36, 2622-2636.
    • (1997) Biochemistry , vol.36 , pp. 2622-2636
    • Dyson, H.J.1    Jeng, M.F.2    Tennant, L.L.3    Slaby, I.4    Lindell, M.5    Cui, D.S.6    Kuprin, S.7    Holmgren, A.8
  • 66
    • 0034680253 scopus 로고    scopus 로고
    • Determination of the pKa value of C115 in MurA (UDP-N-acetylglucosamine enolpyruvyltransferase) from Enterobacter cloacae
    • Krekel, F., Samland, A. K., Macheroux, P., Amrhein, N., and Evans, J. N. (2000) Determination of the pKa value of C115 in MurA (UDP-N-acetylglucosamine enolpyruvyltransferase) from Enterobacter cloacae. Biochemistry 39, 12671-12677.
    • (2000) Biochemistry , vol.39 , pp. 12671-12677
    • Krekel, F.1    Samland, A.K.2    Macheroux, P.3    Amrhein, N.4    Evans, J.N.5
  • 67
    • 34249877154 scopus 로고    scopus 로고
    • Protein arginine deiminase 4: Evidence for a reverse protonation mechanism
    • Knuckley, B., Bhatia, M., and Thompson, P. R. (2007) Protein arginine deiminase 4: Evidence for a reverse protonation mechanism. Biochemistry 46, 6578-6587.
    • (2007) Biochemistry , vol.46 , pp. 6578-6587
    • Knuckley, B.1    Bhatia, M.2    Thompson, P.R.3


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