메뉴 건너뛰기




Volumn 9, Issue 6, 2014, Pages

Computational design of a pH stable enzyme: Understanding molecular mechanism of penicillin acylase's adaptation to alkaline conditions

Author keywords

[No Author keywords available]

Indexed keywords

ASPARAGINE; ASPARTIC ACID; GLUTAMIC ACID; PENICILLIN AMIDASE; PROTEIN BINDING; RECOMBINANT PROTEIN;

EID: 84903518473     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0100643     Document Type: Article
Times cited : (57)

References (108)
  • 1
    • 0028174310 scopus 로고
    • How does a protein fold?
    • DOI 10.1038/369248a0
    • Sali A, Shakhnovich E, Karplus M (1994) How does a protein fold? Nature 369: 248-251. (Pubitemid 24154805)
    • (1994) Nature , vol.369 , Issue.6477 , pp. 248-251
    • Sali, A.1    Shakhnovich, E.2    Karplus, M.3
  • 3
    • 84883190318 scopus 로고    scopus 로고
    • Under-folded proteins: Conformational ensembles and their roles in protein folding, function and pathogenesis
    • Uversky VN (2013) Under-folded proteins: Conformational ensembles and their roles in protein folding, function and pathogenesis. Biopolymers 99: 870-887
    • (2013) Biopolymers , vol.99 , pp. 870-887
    • Uversky, V.N.1
  • 4
    • 0019332167 scopus 로고
    • How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins
    • Lesk AM, Chothia C (1980) How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. J Mol Biol 136(3): 225-70.
    • (1980) J Mol Biol , vol.136 , Issue.3 , pp. 225-270
    • Lesk, A.M.1    Chothia, C.2
  • 5
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5(4): 823-826.
    • (1986) EMBO J , vol.5 , Issue.4 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 11
    • 0036384211 scopus 로고    scopus 로고
    • Structural bases of stability-function tradeoffs in enzymes
    • Beadle BM, Shoichet BK (2002) Structural bases of stability-function tradeoffs in enzymes. J Mol Biol 321(2): 285-296.
    • (2002) J Mol Biol , vol.321 , Issue.2 , pp. 285-296
    • Beadle, B.M.1    Shoichet, B.K.2
  • 12
    • 84887030986 scopus 로고    scopus 로고
    • Introduction-Principles and Historical Landmarks of Enzyme Catalysis in Organic Synthesis
    • Drauz K, Gröger H, May O, editors. Weinheim: Wiley-VCH
    • Gröger H, Asano Y (2012) Introduction-Principles and Historical Landmarks of Enzyme Catalysis in Organic Synthesis. In: Drauz K, Gröger H, May O, editors. Enzyme Catalysis in Organic Synthesis, Third Edition. Weinheim: Wiley-VCH. pp.1-42
    • (2012) Enzyme Catalysis in Organic Synthesis, Third Edition , pp. 1-42
    • Gröger, H.1    Asano, Y.2
  • 13
    • 0030220763 scopus 로고    scopus 로고
    • Engineering enzymes for stability
    • DOI 10.1016/S0959-440X(96)80122-9
    • Shaw A, Bott R (1996) Engineering enzymes for stability. Curr Opin Struct Biol 6(4): 546-550. (Pubitemid 26315851)
    • (1996) Current Opinion in Structural Biology , vol.6 , Issue.4 , pp. 546-550
    • Shaw, A.1    Bott, R.2
  • 16
    • 50849139867 scopus 로고    scopus 로고
    • Enzyme stability and stabilization - aqueous and non-aqueous environment
    • Iyer PV, Ananthanarayan L (2008) Enzyme stability and stabilization - aqueous and non-aqueous environment. Process Biochem 43(10): 1019-1032.
    • (2008) Process Biochem , vol.43 , Issue.10 , pp. 1019-1032
    • Iyer, P.V.1    Ananthanarayan, L.2
  • 17
    • 79952199938 scopus 로고    scopus 로고
    • Engineering protein stability
    • O'Fagain C (2011) Engineering protein stability. Methods Mol. Biol 681: 103-136.
    • (2011) Methods Mol. Biol , vol.681 , pp. 103-136
    • O'Fagain, C.1
  • 20
  • 21
    • 0035806466 scopus 로고    scopus 로고
    • Highly efficient and enantioselective enzymatic acylation of amines in aqueous medium
    • DOI 10.1016/S0957-4166(01)00263-4, PII S0957416601002634
    • Guranda DT, van Langen LM, van Rantwijk F, Sheldon RA, Švedas VK (2001) Highly efficient and enantioselective enzymatic acylation of amines in aqueous medium. Tetrahedron Asymmetry 12(11): 1645-1650. (Pubitemid 32728151)
    • (2001) Tetrahedron Asymmetry , vol.12 , Issue.11 , pp. 1645-1650
    • Guranda, D.T.1    Van Langen, L.M.2    Van Rantwijk, F.3    Sheldon, R.A.4    Svedas, V.K.5
  • 22
    • 4644225294 scopus 로고    scopus 로고
    • An 'easy-on, easy-off' protecting group for the enzymatic resolution of (±)-1-phenylethylamine in an aqueous medium
    • DOI 10.1016/j.tetasy.2004.06.051, PII S0957416604005786, Integrating Biocatalysis into Organic Syntheses
    • Guranda DT, Khimiuk AI, van Langen LM, van Rantwijk F, Sheldon RA, et al. (2004) An 'easy-on, easy-off' protecting group for the enzymatic resolution of (±)-1-phenylethylamine in an aqueous medium. Tetrahedron Asymmetry 15(18): 2901-2906. (Pubitemid 39278026)
    • (2004) Tetrahedron Asymmetry , vol.15 , Issue.18 , pp. 2901-2906
    • Guranda, D.T.1    Khimiuk, A.I.2    Van Langen, L.M.3    Van Rantwijk, F.4    Sheldon, R.A.5    Svedas, V.K.6
  • 23
    • 80054898670 scopus 로고    scopus 로고
    • Penicillin Acylase-Catalyzed Effective and Stereoselective Acylation of 1-phenylethylamine in Aqueous Medium using Non-Activated Acyl Donor
    • Guranda DT, Ushakov GA, Švedas VK (2010) Penicillin Acylase-Catalyzed Effective and Stereoselective Acylation of 1-phenylethylamine in Aqueous Medium using Non-Activated Acyl Donor. Acta Naturae 2(1): 94-96.
    • (2010) Acta Naturae , vol.2 , Issue.1 , pp. 94-96
    • Guranda, D.T.1    Ushakov, G.A.2    Švedas, V.K.3
  • 24
    • 0042832897 scopus 로고    scopus 로고
    • Resolution of (RS)-phenylglycinonitrile by penicillin acylase-catalyzed acylation in aqueous medium
    • DOI 10.1016/S0957-4166(03)00523-8
    • Chilov GG, Moody HM, Boesten WH, Švedas VK (2003) Resolution of (RS)-phenylglycinonitrile by penicillin acylase-catalyzed acylation in aqueous medium. Tetrahedron Asymmetry 14(17): 2613-2617. (Pubitemid 37093880)
    • (2003) Tetrahedron Asymmetry , vol.14 , Issue.17 , pp. 2613-2617
    • Chilov, G.G.1    Moody, H.M.2    Boesten, W.H.J.3    Svedas, V.K.4
  • 25
    • 41549144816 scopus 로고    scopus 로고
    • A green, fully enzymatic procedure for amine resolution, using a lipase and a penicillin G acylase
    • DOI 10.1039/b714088f
    • Ismail H, Lau RM, van Langen LM, van Rantwijk F, Švedas VK, et al. (2008) A green, fully enzymatic procedure for amine resolution, using a lipase and a penicillin G acylase. Green Chemistry 10(4): 415-418. (Pubitemid 351466546)
    • (2008) Green Chemistry , vol.10 , Issue.4 , pp. 415-418
    • Ismail, H.1    Lau, R.M.2    Van Langen, L.M.3    Van Rantwijk, F.4    Svedas, V.K.5    Sheldon, R.A.6
  • 26
    • 0027179354 scopus 로고
    • Enzymatic preparation of both L- and D-enantiomers of phosphonic and phosphonous analogues of alanine using penicillin acylase
    • DOI 10.1016/S0957-4166(00)82240-5
    • Solodenko VA, Belik MY, Galushko SV, Kukhar VP, Kozlova EV, et al. (1993) Enzymatic preparation of both L-and D-enantiomers of phosphonic and phosphonous analogues of alanine using penicillin acylase. Tetrahedron Asymmetry 4(9): 1965-1968. (Pubitemid 23281244)
    • (1993) Tetrahedron Asymmetry , vol.4 , Issue.9 , pp. 1965-1968
    • Solodenko, V.A.1    Belik, M.Y.2    Galushko, S.V.3    Kukhar, V.P.4    Kozlova, E.V.5    Mironenko, D.A.6    Svedas, V.K.7
  • 27
    • 0001534452 scopus 로고    scopus 로고
    • Biomimetic Transamination of α-Alkyl β-Keto Carboxylic Esters. Chemoenzymatic Approach to the Stereochemically Defined α-Alkyl β-Fluoroalkyl β-Amino Acids
    • Soloshonok VA, Soloshonok IV, Kukhar VP, Švedas VK (1998) Biomimetic Transamination of α-Alkyl β-Keto Carboxylic Esters. Chemoenzymatic Approach to the Stereochemically Defined α-Alkyl β-Fluoroalkyl β-Amino Acids. J Org Chem 63(6): 1878-1884. (Pubitemid 128499819)
    • (1998) Journal of Organic Chemistry , vol.63 , Issue.6 , pp. 1878-1884
    • Soloshonok, V.A.1    Soloshonok, I.V.2    Kukhar, V.P.3    Svedas, V.K.4
  • 28
    • 84857880335 scopus 로고    scopus 로고
    • Improving the Diastereoselectivity of Penicillin G Acylase for Ampicillin Synthesis from Racemic Substrates
    • Deaguero AL, Blum JK, Bommarius AS (2012) Improving the Diastereoselectivity of Penicillin G Acylase for Ampicillin Synthesis from Racemic Substrates. Protein Eng Des Sel 25(3): 135-144.
    • (2012) Protein Eng des Sel , vol.25 , Issue.3 , pp. 135-144
    • Deaguero, A.L.1    Blum, J.K.2    Bommarius, A.S.3
  • 31
    • 0035988032 scopus 로고    scopus 로고
    • Penicillin G acylase - Fatty lipid biocomposite films show excellent catalytic activity and long term stability/reusability
    • DOI 10.1021/bp015504v
    • Phadtare S, Parekh P, Gole A, Patil M, Pundle A, et al. (2002) Penicillin G Acylase-Fatty Lipid Biocomposite Films Show Excellent Catalytic Activity and Long Term Stability/Reusability. Biotechnol Prog 18(3): 483-488. (Pubitemid 34623222)
    • (2002) Biotechnology Progress , vol.18 , Issue.3 , pp. 483-488
    • Phadtare, S.1    Parekh, P.2    Gole, A.3    Patil, M.4    Pundle, A.5    Prabhune, A.6    Sastry, M.7
  • 32
    • 0030185060 scopus 로고    scopus 로고
    • Novel crystalline catalysts
    • Margolin AL (1996) Novel crystalline catalysts. Trends Biotechnol 14(7): 223-230.
    • (1996) Trends Biotechnol , vol.14 , Issue.7 , pp. 223-230
    • Margolin, A.L.1
  • 33
    • 20544476972 scopus 로고    scopus 로고
    • Immobilization of penicillin G acylase: The key to optimum performance
    • DOI 10.1002/adsc.200505042
    • Kallenberg AI, van Rantwijk F, Sheldon RA (2005) Immobilization of penicillin G acylase: the key to optimum performance. Adv Synth Catal 347(7-8): 905-926. (Pubitemid 40846447)
    • (2005) Advanced Synthesis and Catalysis , vol.347 , Issue.7-8 , pp. 905-926
    • Kallenberg, A.I.1    Van Rantwijk, F.2    Sheldon, R.A.3
  • 34
    • 58249132554 scopus 로고    scopus 로고
    • Quantitative characteristic of the catalytic properties and microstructure of cross-linked enzyme aggregates of penicillin acylase
    • Pchelintsev NA, Youshko MI, Švedas VK (2009) Quantitative characteristic of the catalytic properties and microstructure of cross-linked enzyme aggregates of penicillin acylase. J Mol Catal B Enzym 56(4): 202-207.
    • (2009) J Mol Catal B Enzym , vol.56 , Issue.4 , pp. 202-207
    • Pchelintsev, N.A.1    Youshko, M.I.2    Švedas, V.K.3
  • 35
    • 0034274420 scopus 로고    scopus 로고
    • Eupergit C, a carrier for immobilization of enzymes of industrial potential
    • DOI 10.1016/S1381-1177(00)00124-7, PII S1381117700001247
    • Katchalski-Katzir E, Kraemer DM (2000) Eupergit C, a carrier for immobilization of enzymes of industrial potential. J Mol Catal B Enzym 10(1): 157-176. (Pubitemid 30479832)
    • (2000) Journal of Molecular Catalysis - B Enzymatic , vol.10 , Issue.1-3 , pp. 157-176
    • Katchalski-Katzir, E.1    Kraemer, D.M.2
  • 37
    • 34547143840 scopus 로고    scopus 로고
    • In silico analysis of enzyme surface and glycosylation effect as a tool for efficient covalent immobilisation of CalB and PGA on Sepabeads
    • Basso A, Braiuca P, Cantone S, Ebert C, Linda P, et al. (2007) In silico analysis of enzyme surface and glycosylation effect as a tool for efficient covalent immobilisation of CalB and PGA on Sepabeads. Adv Synth Catal 349(6): 877-886.
    • (2007) Adv Synth Catal , vol.349 , Issue.6 , pp. 877-886
    • Basso, A.1    Braiuca, P.2    Cantone, S.3    Ebert, C.4    Linda, P.5
  • 41
    • 33751253539 scopus 로고    scopus 로고
    • Structure-guided consensus approach to create a more thermostable penicillin G acylase
    • Polizzi KM, Chaparro-Riggers JF, Vazquez-Figueroa E, Bommarius AS (2006) Structure-guided consensus approach to create a more thermostable penicillin G acylase. J Biotechnol 1(5): 531-536.
    • (2006) J Biotechnol , vol.1 , Issue.5 , pp. 531-536
    • Polizzi, K.M.1    Chaparro-Riggers, J.F.2    Vazquez-Figueroa, E.3    Bommarius, A.S.4
  • 42
    • 85047694896 scopus 로고    scopus 로고
    • pH stability of penicillin acylase from escherichia coli
    • DOI 10.1007/s10541-005-0010-x, 10
    • Guranda DT, Volovik TS, Švedas VK (2004) pH stability of penicillin acylase from Escherichia coli. Biochem (Mosc) 69(12): 1386-1390. (Pubitemid 40329548)
    • (2004) Biochemistry (Moscow) , vol.69 , Issue.12 , pp. 1386-1390
    • Guranda, D.T.1    Volovik, T.S.2    Svedas, V.K.3
  • 43
    • 0001050205 scopus 로고
    • Improvement in the alkaline stability of subtilisin using an efficient random mutagenesis and screening procedure
    • Cunningham BC, Wells JA (1987) Improvement in the alkaline stability of subtilisin using an efficient random mutagenesis and screening procedure. Protein Eng 1(4): 319-325. (Pubitemid 18024008)
    • (1987) Protein Engineering , vol.1 , Issue.4 , pp. 319-325
    • Cunningham, B.C.1    Wells, J.A.2
  • 44
    • 0141858719 scopus 로고    scopus 로고
    • Directed evolution of a bacterial α-amylase: Toward enhanced pH-performance and higher specific activity
    • DOI 10.1110/ps.0384403
    • Bessler C, Schmitt J, Maurer KH, Schmid RD (2003) Directed evolution of a bacterial α-amylase: Toward enhanced pH-performance and higher specific activity. Protein science 12(10): 2141-2149. (Pubitemid 37163349)
    • (2003) Protein Science , vol.12 , Issue.10 , pp. 2141-2149
    • Bessler, C.1    Schmitt, J.2    Maurer, K.-H.3    Schmid, R.D.4
  • 45
    • 43849110605 scopus 로고    scopus 로고
    • Engineering endoglucanase II from Trichoderma reesei to improve the catalytic efficiency at a higher pH optimum
    • Qin Y, Wei X, Song X, Qu Y (2008) Engineering endoglucanase II from Trichoderma reesei to improve the catalytic efficiency at a higher pH optimum. J Biotechnol 135(2): 190-195.
    • (2008) J Biotechnol , vol.135 , Issue.2 , pp. 190-195
    • Qin, Y.1    Wei, X.2    Song, X.3    Qu, Y.4
  • 46
    • 61449128254 scopus 로고    scopus 로고
    • Error-prone PCR of a fungal xylanase for improvement of its alkaline and thermal stability
    • Stephens DE, Singh S, Permaul K (2009) Error-prone PCR of a fungal xylanase for improvement of its alkaline and thermal stability. FEMS Microbiol Lett 293(1): 42-47.
    • (2009) FEMS Microbiol Lett , vol.293 , Issue.1 , pp. 42-47
    • Stephens, D.E.1    Singh, S.2    Permaul, K.3
  • 47
    • 84865289946 scopus 로고    scopus 로고
    • Improvement of the acid stability of Bacillus licheniformis alpha amylase by error-prone PCR
    • Liu YH, Hu B, Xu YJ, Bo JX, Fan S, et al. (2012) Improvement of the acid stability of Bacillus licheniformis alpha amylase by error-prone PCR. J Appl Microbiol 113(3): 541-549.
    • (2012) J Appl Microbiol , vol.113 , Issue.3 , pp. 541-549
    • Liu, Y.H.1    Hu, B.2    Xu, Y.J.3    Bo, J.X.4    Fan, S.5
  • 48
    • 0025327584 scopus 로고
    • Protein stability and electrostatic interactions between solvent exposed charged side chains
    • DOI 10.1002/prot.340080106
    • Akke M, Forsén S (1990) Protein stability and electrostatic interactions between solvent exposed charged side chains. Proteins 8(1): 23-29 (Pubitemid 20235329)
    • (1990) Proteins: Structure, Function and Genetics , vol.8 , Issue.1 , pp. 23-29
    • Akke, M.1    Forsen, S.2
  • 49
    • 0030840103 scopus 로고    scopus 로고
    • High-resolution crystal structure of M-protease: Phylogeny aided analysis of the high-alkaline adaptation mechanism
    • Shirai T, Suzuki A, Yamane T, Ashida T, Kobayashi T, et al. (1997) High-resolution crystal structure of M-protease: phylogeny aided analysis of the high-alkaline adaptation mechanism. Protein Eng 10(6): 627-634. (Pubitemid 27332069)
    • (1997) Protein Engineering , vol.10 , Issue.6 , pp. 627-634
    • Shirai, T.1    Suzuki, A.2    Yamane, T.3    Ashida, T.4    Kobayashi, T.5    Hitomi, J.6    Ito, S.7
  • 50
    • 0035958721 scopus 로고    scopus 로고
    • Crystal structure of alkaline cellulase K: Insight into the alkaline adaptation of an industrial enzyme
    • DOI 10.1006/jmbi.2001.4835
    • Shirai T, Ishida H, Noda JI, Yamane T, Ozaki K, et al. (2001) Crystal structure of alkaline cellulase K: insight into the alkaline adaptation of an industrial enzyme. J Mol Biol 310(5): 1079-1087. (Pubitemid 32738379)
    • (2001) Journal of Molecular Biology , vol.310 , Issue.5 , pp. 1079-1087
    • Shirai, T.1    Ishida, H.2    Noda, J.-I.3    Yamane, T.4    Ozaki, K.5    Hakamada, Y.6    Ito, S.7
  • 51
    • 0032407988 scopus 로고    scopus 로고
    • Crystallographic and mutational analyses of an extremely acidophilic and acid-stable xylanase: Biased distribution of acidic residues and importance of Asp37 for catalysis at low pH
    • Fushinobu S, Ito K, Konno M, Wakagi T, Matsuzawa H (1998) Crystallographic and mutational analyses of an extremely acidophilic and acid-stable xylanase: biased distribution of acidic residues and importance of Asp37 for catalysis at low pH. Protein Eng 11(12): 1121-1128. (Pubitemid 29012122)
    • (1998) Protein Engineering , vol.11 , Issue.12 , pp. 1121-1128
    • Fushinobu, S.1    Ito, K.2    Konno, M.3    Wakagi, T.4    Matsuzawa, H.5
  • 52
    • 18044366388 scopus 로고    scopus 로고
    • Directed evolution for engineering pH profile of endoglucanase III from Trichoderma reesei
    • DOI 10.1016/j.bioeng.2004.10.003, Directed Enzyme Evolution
    • Wang T, Liu X, Yu Q, Zhang X, Qu Y, et al. (2005) Directed evolution for engineering pH profile of endoglucanase III from Trichoderma reesei. Biomol Eng 22(1): 89-94. (Pubitemid 40602598)
    • (2005) Biomolecular Engineering , vol.22 , Issue.1-3 , pp. 89-94
    • Wang, T.1    Liu, X.2    Yu, Q.3    Zhang, X.4    Qu, Y.5    Gao, P.6    Wang, T.7
  • 53
    • 66049105477 scopus 로고    scopus 로고
    • Rational pH-engineering of the thermostable xylanase based on computational model
    • Liu L, Wang B, Chen H, Wang S, Wang M, et al. (2009) Rational pH-engineering of the thermostable xylanase based on computational model. Process Biochem 44(8): 912-915.
    • (2009) Process Biochem , vol.44 , Issue.8 , pp. 912-915
    • Liu, L.1    Wang, B.2    Chen, H.3    Wang, S.4    Wang, M.5
  • 54
    • 84875092633 scopus 로고    scopus 로고
    • Structure-based engineering of histidine residues in the catalytic domain of α-amylase from Bacillus subtilis for improved protein stability and catalytic efficiency under acidic conditions
    • Yang H, Liu L, Shin HD, Chen RR, Li J, et al. (2013) Structure-based engineering of histidine residues in the catalytic domain of α-amylase from Bacillus subtilis for improved protein stability and catalytic efficiency under acidic conditions. J Biotechnol 164(1): 59-66
    • (2013) J Biotechnol , vol.164 , Issue.1 , pp. 59-66
    • Yang, H.1    Liu, L.2    Shin, H.D.3    Chen, R.R.4    Li, J.5
  • 55
  • 56
    • 0037412172 scopus 로고    scopus 로고
    • Engineering streptococcal protein G for increased alkaline stability
    • Gülich S, Linhult M, Ståhl S, Hober S (2002) Engineering streptococcal protein G for increased alkaline stability. Protein Eng 15(10) 835-842. (Pubitemid 36050064)
    • (2002) Protein Engineering , vol.15 , Issue.10 , pp. 835-842
    • Gulich, S.1    Linhult, M.2    Stahl, S.3    Hober, S.4
  • 57
    • 41549104499 scopus 로고    scopus 로고
    • Design of stability at extreme alkaline pH in streptococcal protein G
    • Palmer B, Angus K, Taylor L, Warwicker J, Derrick JP (2008) Design of stability at extreme alkaline pH in streptococcal protein G. J Biotechnol 134(3): 222-230.
    • (2008) J Biotechnol , vol.134 , Issue.3 , pp. 222-230
    • Palmer, B.1    Angus, K.2    Taylor, L.3    Warwicker, J.4    Derrick, J.P.5
  • 58
    • 76849098696 scopus 로고    scopus 로고
    • Computational design-based molecular engineering of the glycosyl hydrolase family 11 B. Subtilis XynA endoxylanase improves its acid stability
    • Beliën T, Joye IJ, Delcour JA, Courtin CM (2009) Computational design-based molecular engineering of the glycosyl hydrolase family 11 B. subtilis XynA endoxylanase improves its acid stability. Protein Eng Des Sel 22(10): 587-596.
    • (2009) Protein Eng des Sel , vol.22 , Issue.10 , pp. 587-596
    • Beliën, T.1    Joye, I.J.2    Delcour, J.A.3    Courtin, C.M.4
  • 59
    • 84876974824 scopus 로고    scopus 로고
    • Alkalophilic adaptation of XynB endoxylanase from Aspergillus niger via rational design of pKa of catalytic residues
    • Xu H, Zhang F, Shang H, Li X, Wang J, et al. (2013) Alkalophilic adaptation of XynB endoxylanase from Aspergillus niger via rational design of pKa of catalytic residues. J Biosci Bioeng 115(6): 618-622
    • (2013) J Biosci Bioeng , vol.115 , Issue.6 , pp. 618-622
    • Xu, H.1    Zhang, F.2    Shang, H.3    Li, X.4    Wang, J.5
  • 60
    • 74549207309 scopus 로고    scopus 로고
    • Assessing computational methods for predicting protein stability upon mutation: Good on average but not in the details
    • Potapov V, Cohen M, Schreiber G (2009) Assessing computational methods for predicting protein stability upon mutation: good on average but not in the details. Protein Eng Des Sel 22(9): 553-560.
    • (2009) Protein Eng des Sel , vol.22 , Issue.9 , pp. 553-560
    • Potapov, V.1    Cohen, M.2    Schreiber, G.3
  • 61
    • 77952706843 scopus 로고    scopus 로고
    • Performance of protein stability predictors
    • Khan S, Vihinen M (2010) Performance of protein stability predictors. Hum Mutat 31(6): 675-684.
    • (2010) Hum Mutat , vol.31 , Issue.6 , pp. 675-684
    • Khan, S.1    Vihinen, M.2
  • 62
    • 0027231258 scopus 로고
    • On the pH dependence of protein stability
    • Yang AS, Honig B (1993) On the pH dependence of protein stability. J Mol Biol 231(2): 459.
    • (1993) J Mol Biol , vol.231 , Issue.2 , pp. 459
    • Yang, A.S.1    Honig, B.2
  • 63
    • 0024792699 scopus 로고
    • Genetic analysis of protein stability and function
    • Pakula AA, Sauer RT (1989) Genetic analysis of protein stability and function. Annu Rev Genet 23(1): 289-310. (Pubitemid 20033405)
    • (1989) Annual Review of Genetics , vol.23 , pp. 289-310
    • Pakula, A.A.1    Sauer, R.T.2
  • 64
    • 0027255479 scopus 로고
    • Structural and genetic analysis of protein stability
    • Matthews BW (1993) Structural and genetic analysis of protein stability. Annu Rev Biochem 62(1): 139-160.
    • (1993) Annu Rev Biochem , vol.62 , Issue.1 , pp. 139-160
    • Matthews, B.W.1
  • 65
    • 0035850792 scopus 로고    scopus 로고
    • Crystal structures of penicillin acylase enzyme-substrate complexes: Structural insights into the catalytic mechanism
    • DOI 10.1006/jmbi.2001.5043
    • McVey CE, Walsh MA, Dodson GG, Wilson KS, Brannigan JA (2001) Crystal structures of penicillin acylase enzyme-substrate complexes: structural insights into the catalytic mechanism. J Mol Biol 313(1): 139-150. (Pubitemid 33001171)
    • (2001) Journal of Molecular Biology , vol.313 , Issue.1 , pp. 139-150
    • McVey, C.E.1    Walsh, M.A.2    Dodson, G.G.3    Wilson, K.S.4    Brannigan, J.A.5
  • 66
    • 84876578144 scopus 로고    scopus 로고
    • New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures
    • Sillitoe I, Cuff AL, Dessailly BH, Dawson NL, Furnham N, et al. (2013) New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. Nucleic Acids Res 41(D1): D490-D498.
    • (2013) Nucleic Acids Res , vol.41 , Issue.D1
    • Sillitoe, I.1    Cuff, A.L.2    Dessailly, B.H.3    Dawson, N.L.4    Furnham, N.5
  • 67
    • 0034495297 scopus 로고    scopus 로고
    • Structural comparison of Ntn-hydrolases
    • Oinonen C, Rouvinen J (2000) Structural comparison of Ntn-hydrolases. Protein Science 9(12): 2329-2337. (Pubitemid 32105715)
    • (2000) Protein Science , vol.9 , Issue.12 , pp. 2329-2337
    • Oinonen, C.1    Rouvinen, J.2
  • 68
    • 84889688951 scopus 로고    scopus 로고
    • Bioinformatic analysis of protein families for identification of variable amino acid residues responsible for functional diversity
    • Suplatov D, Shalaeva D, Kirilin E, Arzhanik V, Švedas V (2014) Bioinformatic analysis of protein families for identification of variable amino acid residues responsible for functional diversity. J Biomol Struct Dyn 32(1): 75-87.
    • (2014) J Biomol Struct Dyn , vol.32 , Issue.1 , pp. 75-87
    • Suplatov, D.1    Shalaeva, D.2    Kirilin, E.3    Arzhanik, V.4    Švedas, V.5
  • 69
    • 84868572912 scopus 로고    scopus 로고
    • Bioinformatic analysis of alpha/beta-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities
    • Suplatov DA, Besenmatter W, Švedas VK, Svendsen A (2012) Bioinformatic analysis of alpha/beta-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities. Protein Eng Des Sel 25(11): 689-697.
    • (2012) Protein Eng des Sel , vol.25 , Issue.11 , pp. 689-697
    • Suplatov, D.A.1    Besenmatter, W.2    Švedas, V.K.3    Svendsen, A.4
  • 71
    • 0037154980 scopus 로고    scopus 로고
    • Protein folding and unfolding at atomic resolution
    • Fersht AR, Daggett V (2002) Protein folding and unfolding at atomic resolution. Cell 108(4): 573.
    • (2002) Cell , vol.108 , Issue.4 , pp. 573
    • Fersht, A.R.1    Daggett, V.2
  • 72
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • DOI 10.1038/nsb0902-646
    • Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. Nat Struct Mol Biol 9(9): 646-652. (Pubitemid 34977295)
    • (2002) Nature Structural Biology , vol.9 , Issue.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 73
    • 40449100818 scopus 로고    scopus 로고
    • Modeling structure and flexibility of Candida antarctica lipase B in organic solvents
    • Trodler P, Pleiss J (2008) Modeling structure and flexibility of Candida antarctica lipase B in organic solvents. BMC Struct Biol 8(1): 9.
    • (2008) BMC Struct Biol , vol.8 , Issue.1 , pp. 9
    • Trodler, P.1    Pleiss, J.2
  • 74
    • 78349281122 scopus 로고    scopus 로고
    • Solvent-induced lid opening in lipases: A molecular dynamics study
    • Rehm S, Trodler P, Pleiss J (2010) Solvent-induced lid opening in lipases: A molecular dynamics study. Protein Science 19(11): 2122-2130.
    • (2010) Protein Science , vol.19 , Issue.11 , pp. 2122-2130
    • Rehm, S.1    Trodler, P.2    Pleiss, J.3
  • 75
    • 84874640883 scopus 로고    scopus 로고
    • Rational Design of Enzymes
    • Drauz K, Gröger H, May O, editors. Weinheim: Wiley-VCH
    • Pleiss J (2012) Rational Design of Enzymes. In: Drauz K, Gröger H, May O, editors. Enzyme Catalysis in Organic Synthesis, Third Edition. Weinheim: Wiley-VCH. pp.89-117
    • (2012) Enzyme Catalysis in Organic Synthesis, Third Edition , pp. 89-117
    • Pleiss, J.1
  • 76
    • 0020476552 scopus 로고
    • Carboxyl-carboxylate interactions in proteins
    • Sawyer L, James MN (1982) Carboxyl-carboxylate interactions in proteins. Nature 295: 79-80
    • (1982) Nature , vol.295 , pp. 79-80
    • Sawyer, L.1    James, M.N.2
  • 77
    • 0042324606 scopus 로고    scopus 로고
    • Probing pH-dependent functional elements in proteins: Modification of carboxylic acid pairs in Trichoderma reesei cellobiohydrolase ce16A
    • DOI 10.1021/bi034954o
    • Wohlfahrt G, Pellikka T, Boer H, Teeri TT, Koivula A (2003) Probing pH-dependent functional elements in proteins: modification of carboxylic acid pairs in Trichoderma reesei cellobiohydrolase Cel6A. Biochemistry 42(34): 10095-10103. (Pubitemid 37052029)
    • (2003) Biochemistry , vol.42 , Issue.34 , pp. 10095-10103
    • Wohlfahrt, G.1    Pellikka, T.2    Boer, H.3    Teeri, T.T.4    Koivula, A.5
  • 78
    • 23044435317 scopus 로고    scopus 로고
    • Statistical and molecular dynamics studies of buried waters in globular proteins
    • DOI 10.1002/prot.20511
    • Park S, Saven JG (2005) Statistical and molecular dynamics studies of buried waters in globular proteins. Proteins 60(3): 450-463. (Pubitemid 41061638)
    • (2005) Proteins: Structure, Function and Genetics , vol.60 , Issue.3 , pp. 450-463
    • Park, S.1    Saven, J.G.2
  • 80
    • 0030853283 scopus 로고    scopus 로고
    • Kinetic study of penicillin acylase from Alcaligenes faecalis
    • DOI 10.1016/S0014-5793(97)01289-1, PII S0014579397012891
    • Švedas V, Guranda D, van Langen L, van Rantwijk F, Sheldon R (1997) Kinetic study of penicillin acylase from Alcaligenes faecalis. FEBS Lett 417(3): 414-418. (Pubitemid 27511634)
    • (1997) FEBS Letters , vol.417 , Issue.3 , pp. 414-418
    • Svedas, V.1    Guranda, D.2    Van Langen, L.3    Van Rantwijk, F.4    Sheldon, R.5
  • 83
    • 0027441807 scopus 로고
    • Step-wise mutation of barnase to binase. A procedure for engineering increased stability of proteins and an experimental analysis of the evolution of protein stability
    • DOI 10.1006/jmbi.1993.1508
    • Serrano L, Day AG, Fersht AR (1993) Step-wise mutation of barnase to binase: a procedure for engineering increased stability of proteins and an experimental analysis of the evolution of protein stability. J Mol Biol 233(2): 305-312. (Pubitemid 23297599)
    • (1993) Journal of Molecular Biology , vol.233 , Issue.2 , pp. 305-312
    • Serrano, L.1    Day, A.G.2    Fersht, A.R.3
  • 84
    • 0032430395 scopus 로고    scopus 로고
    • Totally enzymatic synthesis of peptides. Penicillin acylase-catalyzed protection and deprotection of amino groups as important building blocks of this strategy
    • DOI 10.1111/j.1749-6632.1998.tb10373.x
    • Švedas VK, Beltser AI (1998) Totally Enzymatic Synthesis of Peptides: Penicillin Acylase-Catalyzed Protection and Deprotection of Amino Groups as Important Building Blocks of This Strategy. Ann N Y Acad Sci 864(1): 524-527. (Pubitemid 29048181)
    • (1998) Annals of the New York Academy of Sciences , vol.864 , pp. 524-527
    • Svedas, V.K.1    Beltser, A.I.2
  • 85
    • 0346199337 scopus 로고    scopus 로고
    • Enantioselective acylation of chiral amines catalysed by serine hydrolases
    • van Rantwijk F, Sheldon RA (2004) Enantioselective acylation of chiral amines catalysed by serine hydrolases. Tetrahedron 60(3): 501-519.
    • (2004) Tetrahedron , vol.60 , Issue.3 , pp. 501-519
    • Van Rantwijk, F.1    Sheldon, R.A.2
  • 86
    • 17044422037 scopus 로고    scopus 로고
    • Biomolecular simulations at constant pH
    • Mongan J, Case DA (2005) Biomolecular simulations at constant pH. Curr Opin Struct Biol 15(2): 157-163.
    • (2005) Curr Opin Struct Biol , vol.15 , Issue.2 , pp. 157-163
    • Mongan, J.1    Case, D.A.2
  • 87
    • 34249930405 scopus 로고    scopus 로고
    • Protein-folding dynamics: Overview of molecular simulation techniques
    • DOI 10.1146/annurev.physchem.58.032806.104614
    • Scheraga HA, Khalili M, Liwo A. (2007) Protein-folding dynamics: overview of molecular simulation techniques. Annu Rev Phys Chem 58: 57-83. (Pubitemid 46877585)
    • (2007) Annual Review of Physical Chemistry , vol.58 , pp. 57-83
    • Scheraga, H.A.1    Khalili, M.2    Liwo, A.3
  • 88
    • 9244223045 scopus 로고    scopus 로고
    • Constant pH molecular dynamics in generalized Born implicit solvent
    • Mongan J, Case DA, McCammon JA (2004) Constant pH molecular dynamics in generalized Born implicit solvent. J Comp Chem 25(16): 2038-2048.
    • (2004) J Comp Chem , vol.25 , Issue.16 , pp. 2038-2048
    • Mongan, J.1    Case, D.A.2    McCammon, J.A.3
  • 89
    • 0036968512 scopus 로고    scopus 로고
    • Increasing temperature accelerates protein unfolding without changing the pathway of unfolding
    • DOI 10.1016/S0022-2836(02)00672-1
    • Day R, Bennion BJ, Ham S, Daggett V (2002) Increasing temperature accelerates protein unfolding without changing the pathway of unfolding. J Mol Biol 322(1): 189-203. (Pubitemid 36132678)
    • (2002) Journal of Molecular Biology , vol.322 , Issue.1 , pp. 189-203
    • Day, R.1    Bennion, B.J.2    Ham, S.3    Daggett, V.4
  • 91
    • 70349932423 scopus 로고    scopus 로고
    • AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
    • Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, et al. (2009) AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem 30(16): 2785-2791.
    • (2009) J Comput Chem , vol.30 , Issue.16 , pp. 2785-2791
    • Morris, G.M.1    Huey, R.2    Lindstrom, W.3    Sanner, M.F.4    Belew, R.K.5
  • 93
    • 70349448250 scopus 로고    scopus 로고
    • Computing and visualizing dynamic time warping alignments in R: The dtw package
    • Giorgino T (2009) Computing and visualizing dynamic time warping alignments in R: the dtw package. J Stat Softw 31(7): 1-24.
    • (2009) J Stat Softw , vol.31 , Issue.7 , pp. 1-24
    • Giorgino, T.1
  • 94
    • 29844433160 scopus 로고    scopus 로고
    • A thesis presented to the University of Waterloo in fulfillment of the thesis requirement for the degree of Doctor of Philosophy in Computer Science
    • Chen L (2005) Similarity Search Over Time Series and Trajectory Data. A thesis presented to the University of Waterloo in fulfillment of the thesis requirement for the degree of Doctor of Philosophy in Computer Science.
    • (2005) Similarity Search over Time Series and Trajectory Data
    • Chen, L.1
  • 96
    • 84872008300 scopus 로고    scopus 로고
    • Molecular modeling of different substrate-binding modes and their role in penicillin acylase catalysis
    • Novikov FN, Stroganov OV, Khaliullin IG, Panin NV, Shapovalova IV, et al. (2013) Molecular modeling of different substrate-binding modes and their role in penicillin acylase catalysis. FEBS J 280(1): 115-126.
    • (2013) FEBS J , vol.280 , Issue.1 , pp. 115-126
    • Novikov, F.N.1    Stroganov, O.V.2    Khaliullin, I.G.3    Panin, N.V.4    Shapovalova, I.V.5
  • 97
    • 34547559704 scopus 로고    scopus 로고
    • PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations
    • Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, et al. (2007) PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res (suppl 2): W522-W525.
    • (2007) Nucleic Acids Res , Issue.SUPPL. 2
    • Dolinsky, T.J.1    Czodrowski, P.2    Li, H.3    Nielsen, J.E.4    Jensen, J.H.5
  • 99
    • 13444307044 scopus 로고    scopus 로고
    • Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
    • DOI 10.1107/S0907444904026460
    • Krissinel E, Henrick K (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 60(12): 2256-2268. (Pubitemid 41742778)
    • (2004) Acta Crystallographica Section D: Biological Crystallography , vol.60 , Issue.12 I , pp. 2256-2268
    • Krissinel, E.1    Henrick, K.2
  • 101
    • 40049091146 scopus 로고    scopus 로고
    • Prediction of protein functional residues from sequence by probability density estimation
    • DOI 10.1093/bioinformatics/btm626
    • Fischer JD, Mayer CE, Söding J (2008) Prediction of protein functional residues from sequence by probability density estimation. Bioinformatics 24(5): 613-20 (Pubitemid 351321204)
    • (2008) Bioinformatics , vol.24 , Issue.5 , pp. 613-620
    • Fischer, J.D.1    Mayer, C.E.2    Soding, J.3
  • 102
    • 38949150854 scopus 로고    scopus 로고
    • Matt: Local flexibility aids protein multiple structure alignment
    • Menke M, Berger B, Cowen L (2008) Matt: local flexibility aids protein multiple structure alignment. PLoS Comput Biol 4(1): e10.
    • (2008) PLoS Comput Biol , vol.4 , Issue.1
    • Menke, M.1    Berger, B.2    Cowen, L.3
  • 103
    • 80054796108 scopus 로고    scopus 로고
    • Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures
    • Taly JF, Magis C, Bussotti G, Chang JM, Di Tommaso P, et al. (2011) Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures. Nat Protoc 6(11): 1669-1682.
    • (2011) Nat Protoc , vol.6 , Issue.11 , pp. 1669-1682
    • Taly, J.F.1    Magis, C.2    Bussotti, G.3    Chang, J.M.4    Di Tommaso, P.5
  • 104
    • 84905680227 scopus 로고    scopus 로고
    • Zebra: Web-server for bioinformatic analysis of diverse protein families
    • in press, DOI:10.1080/07391102.2013.834514
    • Suplatov D, Kirilin E, Takhaveev V, Švedas V (2013). Zebra: web-server for bioinformatic analysis of diverse protein families, J Biomol Struct Dyn, in press, DOI:10.1080/07391102.2013.834514
    • (2013) J Biomol Struct Dyn
    • Suplatov, D.1    Kirilin, E.2    Takhaveev, V.3    Švedas, V.4
  • 107
    • 0000702781 scopus 로고
    • Inactivation of soluble and immobilized penicillin amidase from E. Coli by phenylmethylsulfonylfluoride, kinetic analysis and titration of enzyme active sites
    • Švedas VK, Margolin AL, Sherstiuk SF, Klyosov AA, Berezin IV (1977) Inactivation of soluble and immobilized penicillin amidase from E. coli by phenylmethylsulfonylfluoride, kinetic analysis and titration of enzyme active sites. Bioorg. Khimiya (Russ.) 3: 546-553.
    • (1977) Bioorg. Khimiya (Russ.) , vol.3 , pp. 546-553
    • Švedas, V.K.1    Margolin, A.L.2    Sherstiuk, S.F.3    Klyosov, A.A.4    Berezin, I.V.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.