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Volumn 7, Issue 11, 2012, Pages

A Measure of the Broad Substrate Specificity of Enzymes Based on 'Duplicate' Catalytic Residues

Author keywords

[No Author keywords available]

Indexed keywords

ACETYL HYDROLASE; ALKALINE PHOSPHATASE; ASPARAGINE; ENZYME; GLUTAMIC ACID; GLYCINE; METHYLTRANSFERASE; PALMITOYL PROTEIN THIOESTERASE; PALMITOYL PROTEIN THIOESTERASE 1; RNA METHYLTRANSFERASE; THROMBOCYTE ACTIVATING FACTOR; UNCLASSIFIED DRUG;

EID: 84869211870     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0049313     Document Type: Article
Times cited : (14)

References (74)
  • 2
    • 0001858251 scopus 로고
    • Application of a Theory of Enzyme Specificity to Protein Synthesis
    • Koshland DE, (1958) Application of a Theory of Enzyme Specificity to Protein Synthesis. Proc Natl Acad Sci USA 44: 98-104.
    • (1958) Proc Natl Acad Sci USA , vol.44 , pp. 98-104
    • Koshland, D.E.1
  • 3
    • 0024973407 scopus 로고
    • Structural plasticity broadens the specificity of an engineered protease
    • Bone R, Silen JL, Agard DA, (1989) Structural plasticity broadens the specificity of an engineered protease. Nature 339: 191-195.
    • (1989) Nature , vol.339 , pp. 191-195
    • Bone, R.1    Silen, J.L.2    Agard, D.A.3
  • 4
    • 0037013143 scopus 로고    scopus 로고
    • The conformational plasticity of protein kinases
    • Huse M, Kuriyan J, (2002) The conformational plasticity of protein kinases. Cell 109: 275-282.
    • (2002) Cell , vol.109 , pp. 275-282
    • Huse, M.1    Kuriyan, J.2
  • 5
    • 33645238421 scopus 로고    scopus 로고
    • Structural basis for conformational plasticity of the Parkinson's disease-associated ubiquitin hydrolase UCH-L1
    • Das C, Hoang QQ, Kreinbring CA, Luchansky SJ, Meray RK, et al. (2006) Structural basis for conformational plasticity of the Parkinson's disease-associated ubiquitin hydrolase UCH-L1. Proc Natl Acad Sci USA 103: 4675-4680.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 4675-4680
    • Das, C.1    Hoang, Q.Q.2    Kreinbring, C.A.3    Luchansky, S.J.4    Meray, R.K.5
  • 6
    • 0041818050 scopus 로고    scopus 로고
    • Crystal structure of extended-spectrum β-lactamase Toho-1: insights into the molecular mechanism for catalytic reaction and substrate specificity expansion
    • Ibuka AS, Ishii Y, Galleni M, Ishiguro M, Yamaguchi K, et al. (2003) Crystal structure of extended-spectrum β-lactamase Toho-1: insights into the molecular mechanism for catalytic reaction and substrate specificity expansion. Biochemistry 42: 10634-10643.
    • (2003) Biochemistry , vol.42 , pp. 10634-10643
    • Ibuka, A.S.1    Ishii, Y.2    Galleni, M.3    Ishiguro, M.4    Yamaguchi, K.5
  • 7
    • 33745620493 scopus 로고    scopus 로고
    • Crystal structure of the Mycobac-terium fortuitum class A β-lactamase: structural basis for broad substrate specificity
    • Sauvage E, Fonze E, Quinting B, Galleni M, Frere JM, et al. (2006) Crystal structure of the Mycobac-terium fortuitum class A β-lactamase: structural basis for broad substrate specificity. Antimicrob Agents Chemother 50: 2516-2521.
    • (2006) Antimicrob Agents Chemother , vol.50 , pp. 2516-2521
    • Sauvage, E.1    Fonze, E.2    Quinting, B.3    Galleni, M.4    Frere, J.M.5
  • 8
    • 63449139456 scopus 로고    scopus 로고
    • Structure of P-glycoprotein reveals a molecular basis for poly-specific drug binding
    • Aller SG, Yu J, Ward A, Weng Y, Chittaboina S, et al. (2009) Structure of P-glycoprotein reveals a molecular basis for poly-specific drug binding. Science 323: 1718-1722.
    • (2009) Science , vol.323 , pp. 1718-1722
    • Aller, S.G.1    Yu, J.2    Ward, A.3    Weng, Y.4    Chittaboina, S.5
  • 9
    • 0028933234 scopus 로고
    • Molecular evolution of a class C β-lactamase extending its substrate specificity
    • Nukaga M, Haruta S, Tanimoto K, Kogure K, Taniguchi K, et al. (1995) Molecular evolution of a class C β-lactamase extending its substrate specificity. J Biol Chem 270: 5729-5735.
    • (1995) J Biol Chem , vol.270 , pp. 5729-5735
    • Nukaga, M.1    Haruta, S.2    Tanimoto, K.3    Kogure, K.4    Taniguchi, K.5
  • 10
    • 0036304570 scopus 로고    scopus 로고
    • Directed evolution of restriction endonuclease BstYI to achieve increased substrate specificity
    • Samuelson JC, Xu SY, (2002) Directed evolution of restriction endonuclease BstYI to achieve increased substrate specificity. J Mol Biol 319: 673-683.
    • (2002) J Mol Biol , vol.319 , pp. 673-683
    • Samuelson, J.C.1    Xu, S.Y.2
  • 11
    • 80055109953 scopus 로고    scopus 로고
    • The molecular basis for the broad substrate specificity of human sulfotransferase 1A1
    • Berger I, Guttman C, Amar D, Zarivach R, Aharoni A, (2011) The molecular basis for the broad substrate specificity of human sulfotransferase 1A1. PLoS ONE 6: e26794.
    • (2011) PLoS ONE , vol.6
    • Berger, I.1    Guttman, C.2    Amar, D.3    Zarivach, R.4    Aharoni, A.5
  • 12
    • 33845737883 scopus 로고    scopus 로고
    • Monoterpenes as novel substrates for oxidation and halo-hydroxylation with chloroperoxidase from Caldariomyces fumago
    • Kaup BA, Piantini U, Wust M, Schrader J, (2007) Monoterpenes as novel substrates for oxidation and halo-hydroxylation with chloroperoxidase from Caldariomyces fumago. Appl Microbiol Biotechnol 73: 1087-1096.
    • (2007) Appl Microbiol Biotechnol , vol.73 , pp. 1087-1096
    • Kaup, B.A.1    Piantini, U.2    Wust, M.3    Schrader, J.4
  • 13
    • 8544219754 scopus 로고    scopus 로고
    • Site-saturation mutagenesis of Tyr-105 reveals its im-portance in substrate stabilization and discrimination in TEM-1 beta-lactamase
    • Doucet N, De Wals PY, Pelletier JN, (2004) Site-saturation mutagenesis of Tyr-105 reveals its im-portance in substrate stabilization and discrimination in TEM-1 beta-lactamase. J Biol Chem 279: 46295-46303.
    • (2004) J Biol Chem , vol.279 , pp. 46295-46303
    • Doucet, N.1    de Wals, P.Y.2    Pelletier, J.N.3
  • 14
    • 37849001771 scopus 로고    scopus 로고
    • A quantitative index of substrate promiscuity
    • Nath A, Atkins WM, (2008) A quantitative index of substrate promiscuity. Biochemistry 47: 157-166.
    • (2008) Biochemistry , vol.47 , pp. 157-166
    • Nath, A.1    Atkins, W.M.2
  • 15
    • 0017272554 scopus 로고
    • Enzyme recruitment in evolution of new function
    • Jensen RA, (1976) Enzyme recruitment in evolution of new function. Annu Rev Microbiol 30: 409-425.
    • (1976) Annu Rev Microbiol , vol.30 , pp. 409-425
    • Jensen, R.A.1
  • 16
    • 0017771466 scopus 로고
    • Evolution and tinkering
    • Jacob F, (1977) Evolution and tinkering. Science 196: 1161-1166.
    • (1977) Science , vol.196 , pp. 1161-1166
    • Jacob, F.1
  • 17
    • 0037396292 scopus 로고    scopus 로고
    • Enzymes with extra talents: moonlighting functions and catalytic promiscuity
    • Copley SD, (2003) Enzymes with extra talents: moonlighting functions and catalytic promiscuity. Curr Opin Chem Biol 7: 265-272.
    • (2003) Curr Opin Chem Biol , vol.7 , pp. 265-272
    • Copley, S.D.1
  • 18
    • 77953623874 scopus 로고    scopus 로고
    • Enzyme promiscuity: a mechanistic and evolutionary perspective
    • Khersonsky O, Tawfik DS, (2010) Enzyme promiscuity: a mechanistic and evolutionary perspective. Annu Rev Biochem 79: 471-505.
    • (2010) Annu Rev Biochem , vol.79 , pp. 471-505
    • Khersonsky, O.1    Tawfik, D.S.2
  • 19
    • 82955246714 scopus 로고    scopus 로고
    • Active site detection by spatial conformity and electrostatic analysis - unravelling a proteolytic function in shrimp alkaline phosphatase
    • Chakraborty S, Minda R, Salaye L, Bhattacharjee SK, Rao BJ, (2011) Active site detection by spatial conformity and electrostatic analysis- unravelling a proteolytic function in shrimp alkaline phosphatase. PLoS ONE 6: e28470.
    • (2011) PLoS ONE , vol.6
    • Chakraborty, S.1    Minda, R.2    Salaye, L.3    Bhattacharjee, S.K.4    Rao, B.J.5
  • 20
    • 84857124305 scopus 로고    scopus 로고
    • A measure of the promiscuity of proteins and characteristics of residues in the vicinity of the catalytic site that regulate promiscuity
    • Chakraborty S, Rao BJ, (2012) A measure of the promiscuity of proteins and characteristics of residues in the vicinity of the catalytic site that regulate promiscuity. PLoS ONE 7: e32011.
    • (2012) PLoS ONE , vol.7
    • Chakraborty, S.1    Rao, B.J.2
  • 21
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • Honig B, Nicholls A, (1995) Classical electrostatics in biology and chemistry. Science 268: 1144-1149.
    • (1995) Science , vol.268 , pp. 1144-1149
    • Honig, B.1    Nicholls, A.2
  • 23
    • 62949096122 scopus 로고    scopus 로고
    • Moonlighting proteins-an update
    • Jeffery CJ, (2009) Moonlighting proteins-an update. Mol Biosyst 5: 345-350.
    • (2009) Mol Biosyst , vol.5 , pp. 345-350
    • Jeffery, C.J.1
  • 24
    • 0345864027 scopus 로고    scopus 로고
    • The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data
    • Porter CT, Bartlett GJ, Thornton JM, (2004) The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res 32: D129-133.
    • (2004) Nucleic Acids Res , vol.32
    • Porter, C.T.1    Bartlett, G.J.2    Thornton, J.M.3
  • 25
    • 28144441826 scopus 로고    scopus 로고
    • The bacterial ribosome as a target for antibiotics
    • Poehlsgaard J, Douthwaite S, (2005) The bacterial ribosome as a target for antibiotics. Nat Rev Microbiol 3: 870-881.
    • (2005) Nat Rev Microbiol , vol.3 , pp. 870-881
    • Poehlsgaard, J.1    Douthwaite, S.2
  • 26
    • 0028963496 scopus 로고
    • Erythromycin resistance by ribosome modification
    • Weisblum B, (1995) Erythromycin resistance by ribosome modification. Antimicrob Agents Chemother 39: 577-585.
    • (1995) Antimicrob Agents Chemother , vol.39 , pp. 577-585
    • Weisblum, B.1
  • 27
    • 0036917889 scopus 로고    scopus 로고
    • SAM (dependent) I AM: the S-adenosylmethionine-dependent methyltransferase fold
    • Martin JL, McMillan FM, (2002) SAM (dependent) I AM: the S-adenosylmethionine-dependent methyltransferase fold. Curr Opin Struct Biol 12: 783-793.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 783-793
    • Martin, J.L.1    McMillan, F.M.2
  • 28
    • 0033522646 scopus 로고    scopus 로고
    • The 2.2 Å structure of the rRNA methyltransferase ErmC' and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism
    • Schluckebier G, Zhong P, Stewart KD, Kavanaugh TJ, Abad-Zapatero C, (1999) The 2.2 Å structure of the rRNA methyltransferase ErmC' and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism. J Mol Biol 289: 277-291.
    • (1999) J Mol Biol , vol.289 , pp. 277-291
    • Schluckebier, G.1    Zhong, P.2    Stewart, K.D.3    Kavanaugh, T.J.4    Abad-Zapatero, C.5
  • 29
    • 0032544482 scopus 로고    scopus 로고
    • ErmE methyltransferase recognition elements in RNA substrates
    • Vester B, Nielsen AK, Hansen LH, Douthwaite S, (1998) ErmE methyltransferase recognition elements in RNA substrates. J Mol Biol 282: 255-264.
    • (1998) J Mol Biol , vol.282 , pp. 255-264
    • Vester, B.1    Nielsen, A.K.2    Hansen, L.H.3    Douthwaite, S.4
  • 30
    • 50049114778 scopus 로고    scopus 로고
    • Discovery of protein-palmitoylating enzymes
    • Tsutsumi R, Fukata Y, Fukata M, (2008) Discovery of protein-palmitoylating enzymes. Pflügers Arch 456: 1199-1206.
    • (2008) Pflügers Arch , vol.456 , pp. 1199-1206
    • Tsutsumi, R.1    Fukata, Y.2    Fukata, M.3
  • 31
    • 82255161850 scopus 로고    scopus 로고
    • The role of palmitoylation in signalling, cellular trafficking and plasma membrane localization of protease-activated receptor-2
    • Adams MN, Christensen ME, He Y, Waterhouse NJ, Hooper JD, (2011) The role of palmitoylation in signalling, cellular trafficking and plasma membrane localization of protease-activated receptor-2. PLoS ONE 6: e28018.
    • (2011) PLoS ONE , vol.6
    • Adams, M.N.1    Christensen, M.E.2    He, Y.3    Waterhouse, N.J.4    Hooper, J.D.5
  • 32
    • 0038321812 scopus 로고    scopus 로고
    • New insights into the mechanisms of protein palmitoylation
    • Linder ME, Deschenes RJ, (2003) New insights into the mechanisms of protein palmitoylation. Bio-chemistry 42: 4311-4320.
    • (2003) Bio-Chemistry , vol.42 , pp. 4311-4320
    • Linder, M.E.1    Deschenes, R.J.2
  • 33
    • 0034712969 scopus 로고    scopus 로고
    • The crystal structure of palmitoyl protein thioesterase 1 and the molecular basis of infantile neuronal ceroid lipofuscinosis
    • Bellizzi JJ, Widom J, Kemp C, Lu JY, Das AK, et al. (2000) The crystal structure of palmitoyl protein thioesterase 1 and the molecular basis of infantile neuronal ceroid lipofuscinosis. Proc Natl Acad Sci USA 97: 4573-4578.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 4573-4578
    • Bellizzi, J.J.1    Widom, J.2    Kemp, C.3    Lu, J.Y.4    Das, A.K.5
  • 34
    • 0141621057 scopus 로고    scopus 로고
    • The crystal structure of palmitoyl protein thioesterase-2 (PPT2) reveals the basis for divergent substrate specificities of the two lysosomal thioesterases, PPT1 and PPT2
    • Calero G, Gupta P, Nonato MC, Tandel S, Biehl ER, et al. (2003) The crystal structure of palmitoyl protein thioesterase-2 (PPT2) reveals the basis for divergent substrate specificities of the two lysosomal thioesterases, PPT1 and PPT2. J Biol Chem 278: 37957-37964.
    • (2003) J Biol Chem , vol.278 , pp. 37957-37964
    • Calero, G.1    Gupta, P.2    Nonato, M.C.3    Tandel, S.4    Biehl, E.R.5
  • 35
    • 0027169561 scopus 로고
    • Platelet-activating factor: receptors and signal transduction
    • Chao W, Olson MS, (1993) Platelet-activating factor: receptors and signal transduction. Biochem J 292 (Pt 3): 617-629.
    • (1993) Biochem J , vol.292 , Issue.Pt 3 , pp. 617-629
    • Chao, W.1    Olson, M.S.2
  • 37
    • 79551554497 scopus 로고    scopus 로고
    • Platelet activating factor blocks interkinetic nuclear migration in retinal progenitors through an arrest of the cell cycle at the S/G2 transition
    • Fragel-Madeira L, Meletti T, Mariante RM, Monteiro RQ, Einicker-Lamas M, et al. (2011) Platelet activating factor blocks interkinetic nuclear migration in retinal progenitors through an arrest of the cell cycle at the S/G2 transition. PLoS ONE 6: e16058.
    • (2011) PLoS ONE , vol.6
    • Fragel-Madeira, L.1    Meletti, T.2    Mariante, R.M.3    Monteiro, R.Q.4    Einicker-Lamas, M.5
  • 39
    • 0032859479 scopus 로고    scopus 로고
    • Probing the substrate specificity of the intracellular brain platelet-activating factor acetylhydrolase
    • Ho YS, Sheffield PJ, Masuyama J, Arai H, Li J, et al. (1999) Probing the substrate specificity of the intracellular brain platelet-activating factor acetylhydrolase. Protein Eng 12: 693-700.
    • (1999) Protein Eng , vol.12 , pp. 693-700
    • Ho, Y.S.1    Sheffield, P.J.2    Masuyama, J.3    Arai, H.4    Li, J.5
  • 40
    • 0000282461 scopus 로고
    • Zinc: biological functions and coordination motifs
    • Vallee BL, Auld DS, (1993) Zinc: biological functions and coordination motifs. Acc. Chem. Res 26: 543-551.
    • (1993) Acc. Chem. Res , vol.26 , pp. 543-551
    • Vallee, B.L.1    Auld, D.S.2
  • 41
    • 58149251795 scopus 로고    scopus 로고
    • The 1.4 Å crystal structure of the large and cold-active Vibrio sp. alkaline phosphatase
    • Helland R, Larsen RL, Asgeirsson B, (2009) The 1.4 Å crystal structure of the large and cold-active Vibrio sp. alkaline phosphatase. Biochim Biophys Acta 1794: 297-308.
    • (2009) Biochim Biophys Acta , vol.1794 , pp. 297-308
    • Helland, R.1    Larsen, R.L.2    Asgeirsson, B.3
  • 42
    • 0037378779 scopus 로고    scopus 로고
    • Catalysis by ribonuclease A is limited by the rate of substrate association
    • Park C, Raines RT, (2003) Catalysis by ribonuclease A is limited by the rate of substrate association. Biochemistry 42: 3509-3518.
    • (2003) Biochemistry , vol.42 , pp. 3509-3518
    • Park, C.1    Raines, R.T.2
  • 43
    • 77649239492 scopus 로고    scopus 로고
    • An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily
    • van Loo B, Jonas S, Babtie AC, Benjdia A, Berteau O, et al. (2010) An efficient, multiply promiscuous hydrolase in the alkaline phosphatase superfamily. Proc Natl Acad Sci USA 107: 2740-2745.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 2740-2745
    • van Loo, B.1    Jonas, S.2    Babtie, A.C.3    Benjdia, A.4    Berteau, O.5
  • 44
    • 0001858251 scopus 로고
    • Application of a Theory of Enzyme Specificity to Protein Synthesis
    • Koshland DE, (1958) Application of a Theory of Enzyme Specificity to Protein Synthesis. Proc Natl Acad Sci USA 44: 98-104.
    • (1958) Proc Natl Acad Sci USA , vol.44 , pp. 98-104
    • Koshland, D.E.1
  • 45
    • 3042784274 scopus 로고    scopus 로고
    • Generating mutant libraries using error-prone PCR
    • Cirino PC, Mayer KM, Umeno D, (2003) Generating mutant libraries using error-prone PCR. Methods Mol Biol 231: 3-9.
    • (2003) Methods Mol Biol , vol.231 , pp. 3-9
    • Cirino, P.C.1    Mayer, K.M.2    Umeno, D.3
  • 46
    • 0028050350 scopus 로고
    • Rapid evolution of a protein in vitro by DNA shuffling
    • Stemmer WP, (1994) Rapid evolution of a protein in vitro by DNA shuffling. Nature 370: 389-391.
    • (1994) Nature , vol.370 , pp. 389-391
    • Stemmer, W.P.1
  • 47
    • 0031909113 scopus 로고    scopus 로고
    • Molecular evolution by staggered extension process (StEP) in vitro recombination
    • Zhao H, Giver L, Shao Z, Affholter JA, Arnold FH, (1998) Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat Biotechnol 16: 258-261.
    • (1998) Nat Biotechnol , vol.16 , pp. 258-261
    • Zhao, H.1    Giver, L.2    Shao, Z.3    Affholter, J.A.4    Arnold, F.H.5
  • 48
    • 0035014185 scopus 로고    scopus 로고
    • Directed evolution of proteins by exon shuffling
    • Kolkman JA, Stemmer WP, (2001) Directed evolution of proteins by exon shuffling. Nat Biotechnol 19: 423-428.
    • (2001) Nat Biotechnol , vol.19 , pp. 423-428
    • Kolkman, J.A.1    Stemmer, W.P.2
  • 49
    • 34248567845 scopus 로고    scopus 로고
    • Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes
    • Reetz MT, Carballeira JD, (2007) Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nat Protoc 2: 891-903.
    • (2007) Nat Protoc , vol.2 , pp. 891-903
    • Reetz, M.T.1    Carballeira, J.D.2
  • 51
    • 33747234745 scopus 로고    scopus 로고
    • Expanding the substrate scope of enzymes: combining mutations obtained by CASTing
    • Reetz MT, Carballeira JD, Peyralans J, Hobenreich H, Maichele A, et al. (2006) Expanding the substrate scope of enzymes: combining mutations obtained by CASTing. Chemistry 12: 6031-6038.
    • (2006) Chemistry , vol.12 , pp. 6031-6038
    • Reetz, M.T.1    Carballeira, J.D.2    Peyralans, J.3    Hobenreich, H.4    Maichele, A.5
  • 52
    • 33751525692 scopus 로고    scopus 로고
    • New algorithms and an in silico benchmark for computational enzyme design
    • Zanghellini A, Jiang L, Wollacott AM, Cheng G, Meiler J, et al. (2006) New algorithms and an in silico benchmark for computational enzyme design. Protein Sci 15: 2785-2794.
    • (2006) Protein Sci , vol.15 , pp. 2785-2794
    • Zanghellini, A.1    Jiang, L.2    Wollacott, A.M.3    Cheng, G.4    Meiler, J.5
  • 53
    • 0030793767 scopus 로고    scopus 로고
    • De novo protein design: fully automated sequence selection
    • Dahiyat BI, Mayo SL, (1997) De novo protein design: fully automated sequence selection. Science 278: 82-87.
    • (1997) Science , vol.278 , pp. 82-87
    • Dahiyat, B.I.1    Mayo, S.L.2
  • 54
    • 70349330137 scopus 로고    scopus 로고
    • Automated scaffold selection for enzyme design
    • Malisi C, Kohlbacher O, Hocker B, (2009) Automated scaffold selection for enzyme design. Proteins 77: 74-83.
    • (2009) Proteins , vol.77 , pp. 74-83
    • Malisi, C.1    Kohlbacher, O.2    Hocker, B.3
  • 55
    • 46449106372 scopus 로고    scopus 로고
    • The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles
    • Georgiev I, Lilien RH, Donald BR, (2008) The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles. J Comput Chem 29: 1527-1542.
    • (2008) J Comput Chem , vol.29 , pp. 1527-1542
    • Georgiev, I.1    Lilien, R.H.2    Donald, B.R.3
  • 57
    • 84863836923 scopus 로고    scopus 로고
    • An automated flow for directed evolution based on detection of promiscuous scaffolds using spatial and electrostatic properties of catalytic residues
    • Chakraborty S, (2012) An automated flow for directed evolution based on detection of promiscuous scaffolds using spatial and electrostatic properties of catalytic residues. PLoS ONE 7: e40408.
    • (2012) PLoS ONE , vol.7
    • Chakraborty, S.1
  • 58
    • 0035807809 scopus 로고    scopus 로고
    • Enzyme-like proteins by computational design
    • Bolon DN, Mayo SL, (2001) Enzyme-like proteins by computational design. Proc Natl Acad Sci USA 98: 14274-14279.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 14274-14279
    • Bolon, D.N.1    Mayo, S.L.2
  • 61
    • 77954811495 scopus 로고    scopus 로고
    • Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction
    • Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, et al. (2010) Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 329: 309-313.
    • (2010) Science , vol.329 , pp. 309-313
    • Siegel, J.B.1    Zanghellini, A.2    Lovick, H.M.3    Kiss, G.4    Lambert, A.R.5
  • 63
    • 25844507152 scopus 로고    scopus 로고
    • Structural and dynamical basis of broad substrate specificity, catalytic mechanism, and inhibition of cytochrome P450 3A4
    • Park H, Lee S, Suh J, (2005) Structural and dynamical basis of broad substrate specificity, catalytic mechanism, and inhibition of cytochrome P450 3A4. J Am Chem Soc 127: 13634-13642.
    • (2005) J Am Chem Soc , vol.127 , pp. 13634-13642
    • Park, H.1    Lee, S.2    Suh, J.3
  • 64
    • 70350414205 scopus 로고    scopus 로고
    • Broad substrate specificity and catalytic mechanism of Pseudomonas stutzeri L-rhamnose isomerase: insights from QM/MM molecular dynamics simulations
    • Wu R, Xie H, Mo Y, Cao Z, (2009) Broad substrate specificity and catalytic mechanism of Pseudomonas stutzeri L-rhamnose isomerase: insights from QM/MM molecular dynamics simulations. J Phys Chem A 113: 11595-11603.
    • (2009) J Phys Chem A , vol.113 , pp. 11595-11603
    • Wu, R.1    Xie, H.2    Mo, Y.3    Cao, Z.4
  • 65
    • 0026049801 scopus 로고
    • Serine beta-lactamases and penicillin-binding proteins
    • Ghuysen JM, (1991) Serine beta-lactamases and penicillin-binding proteins. Annu Rev Microbiol 45: 37-67.
    • (1991) Annu Rev Microbiol , vol.45 , pp. 37-67
    • Ghuysen, J.M.1
  • 66
    • 0033082703 scopus 로고    scopus 로고
    • The beta-lactamase cycle: a tale of selective pressure and bacterial ingenuity
    • Matagne A, Dubus A, Galleni M, Frere JM, (1999) The beta-lactamase cycle: a tale of selective pressure and bacterial ingenuity. Nat Prod Rep 16: 1-19.
    • (1999) Nat Prod Rep , vol.16 , pp. 1-19
    • Matagne, A.1    Dubus, A.2    Galleni, M.3    Frere, J.M.4
  • 67
    • 0036829003 scopus 로고    scopus 로고
    • Structural basis for the beta lactam resistance of PBP2a from methicillin-resistant Staphylococcus aureus
    • Lim D, Strynadka NC, (2002) Structural basis for the beta lactam resistance of PBP2a from methicillin-resistant Staphylococcus aureus. Nat Struct Biol 9: 870-876.
    • (2002) Nat Struct Biol , vol.9 , pp. 870-876
    • Lim, D.1    Strynadka, N.C.2
  • 68
    • 75149136742 scopus 로고    scopus 로고
    • Coordination sphere of the third metal site is essential to the activity and metal selectivity of alkaline phosphatases
    • Koutsioulis D, Lyskowski A, Maki S, Guthrie E, Feller G, et al. (2010) Coordination sphere of the third metal site is essential to the activity and metal selectivity of alkaline phosphatases. Protein Sci 75-84.
    • (2010) Protein Sci , pp. 75-84
    • Koutsioulis, D.1    Lyskowski, A.2    Maki, S.3    Guthrie, E.4    Feller, G.5
  • 69
    • 3242886771 scopus 로고    scopus 로고
    • PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations
    • Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA, (2004) PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 32: W665-667.
    • (2004) Nucleic Acids Res , vol.32
    • Dolinsky, T.J.1    Nielsen, J.E.2    McCammon, J.A.3    Baker, N.A.4
  • 71
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: the European Molecular Biology Open Software Suite
    • Rice P, Longden I, Bleasby A, (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16: 276-277.
    • (2000) Trends Genet , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 73
    • 0033613813 scopus 로고    scopus 로고
    • Recognition of spatial motifs in protein structures
    • Kleywegt GJ, (1999) Recognition of spatial motifs in protein structures. J Mol Biol 285: 1887-1897.
    • (1999) J Mol Biol , vol.285 , pp. 1887-1897
    • Kleywegt, G.J.1
  • 74
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
    • Altschul SF, Madden TL, Schaer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
    • (1997) Nucleic Acids Res , vol.25 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaer, A.A.3    Zhang, J.4    Zhang, Z.5


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