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Volumn 55, Issue 9, 2016, Pages 1408-1417

Conformational Disorganization within the Active Site of a Recently Evolved Organophosphate Hydrolase Limits Its Catalytic Efficiency

Author keywords

[No Author keywords available]

Indexed keywords

DETOXIFICATION; ENZYMES; HYDROLASES; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS;

EID: 84960374864     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/acs.biochem.5b01322     Document Type: Article
Times cited : (17)

References (58)
  • 1
    • 0033486287 scopus 로고    scopus 로고
    • Carboxyl/cholinesterases: A case study of the evolution of a successful multigene family
    • Oakeshott, J. G., Claudianos, C., Russell, R. J., and Robin, G. C. (1999) Carboxyl/cholinesterases: a case study of the evolution of a successful multigene family BioEssays 21, 1031-1042 10.1002/(SICI)1521-1878(199912)22:1<1031::AID-BIES7>3.0.CO;2-J
    • (1999) BioEssays , vol.21 , pp. 1031-1042
    • Oakeshott, J.G.1    Claudianos, C.2    Russell, R.J.3    Robin, G.C.4
  • 2
    • 10044275708 scopus 로고    scopus 로고
    • Organophosphates/nerve agent poisoning: Mechanism of action, diagnosis, prophylaxis, and treatment
    • Bajgar, J. (2004) Organophosphates/nerve agent poisoning: mechanism of action, diagnosis, prophylaxis, and treatment Adv. Clin. Chem. 38, 151-216 10.1016/S0065-2423(04)38006-6
    • (2004) Adv. Clin. Chem. , vol.38 , pp. 151-216
    • Bajgar, J.1
  • 4
    • 0030612598 scopus 로고    scopus 로고
    • A single amino acid substitution converts a carboxylesterase to an organophosphorus hydrolase and confers insecticide resistance on a blowfly
    • Newcomb, R. D., Campbell, P. M., Ollis, D. L., Cheah, E., Russell, R. J., and Oakeshott, J. G. (1997) A single amino acid substitution converts a carboxylesterase to an organophosphorus hydrolase and confers insecticide resistance on a blowfly Proc. Natl. Acad. Sci. U. S. A. 94, 7464-7468 10.1073/pnas.94.14.7464
    • (1997) Proc. Natl. Acad. Sci. U. S. A. , vol.94 , pp. 7464-7468
    • Newcomb, R.D.1    Campbell, P.M.2    Ollis, D.L.3    Cheah, E.4    Russell, R.J.5    Oakeshott, J.G.6
  • 7
    • 0028881691 scopus 로고
    • Resistance and the control of sheep ectoparasites
    • Levot, G. W. (1995) Resistance and the control of sheep ectoparasites Int. J. Parasitol. 25, 1355-1362 10.1016/0020-7519(95)00070-I
    • (1995) Int. J. Parasitol. , vol.25 , pp. 1355-1362
    • Levot, G.W.1
  • 8
    • 16444363866 scopus 로고    scopus 로고
    • Multiple mutations and gene duplications conferring organophosphorus insecticide resistance have been selected at the Rop-1 locus of the sheep blowfly, Lucilia cuprina
    • Newcomb, R. D., Gleeson, D. M., Yong, C. G., Russell, R. J., and Oakeshott, J. G. (2005) Multiple mutations and gene duplications conferring organophosphorus insecticide resistance have been selected at the Rop-1 locus of the sheep blowfly, Lucilia cuprina J. Mol. Evol. 60, 207-220 10.1007/s00239-004-0104-x
    • (2005) J. Mol. Evol. , vol.60 , pp. 207-220
    • Newcomb, R.D.1    Gleeson, D.M.2    Yong, C.G.3    Russell, R.J.4    Oakeshott, J.G.5
  • 9
    • 0038148710 scopus 로고    scopus 로고
    • Conformational diversity and protein evolution - A 60-year-old hypothesis revisited
    • James, L. C. and Tawfik, D. S. (2003) Conformational diversity and protein evolution - a 60-year-old hypothesis revisited Trends Biochem. Sci. 28, 361-368 10.1016/S0968-0004(03)00135-X
    • (2003) Trends Biochem. Sci. , vol.28 , pp. 361-368
    • James, L.C.1    Tawfik, D.S.2
  • 10
    • 71449103005 scopus 로고    scopus 로고
    • Hidden alternative structures of proline isomerase essential for catalysis
    • Fraser, J. S., Clarkson, M. W., Degnan, S. C., Erion, R., Kern, D., and Alber, T. (2009) Hidden alternative structures of proline isomerase essential for catalysis Nature 462, 669-673 10.1038/nature08615
    • (2009) Nature , vol.462 , pp. 669-673
    • Fraser, J.S.1    Clarkson, M.W.2    Degnan, S.C.3    Erion, R.4    Kern, D.5    Alber, T.6
  • 12
    • 77953623874 scopus 로고    scopus 로고
    • Enzyme promiscuity: A mechanistic and evolutionary perspective
    • Khersonsky, O. and Tawfik, D. S. (2010) Enzyme promiscuity: a mechanistic and evolutionary perspective Annu. Rev. Biochem. 79, 471-505 10.1146/annurev-biochem-030409-143718
    • (2010) Annu. Rev. Biochem. , vol.79 , pp. 471-505
    • Khersonsky, O.1    Tawfik, D.S.2
  • 13
    • 64849101493 scopus 로고    scopus 로고
    • Protein dynamism and evolvability
    • Tokuriki, N. and Tawfik, D. S. (2009) Protein dynamism and evolvability Science 324, 203-207 10.1126/science.1169375
    • (2009) Science , vol.324 , pp. 203-207
    • Tokuriki, N.1    Tawfik, D.S.2
  • 14
    • 84939644294 scopus 로고    scopus 로고
    • The Moderately Efficient Enzyme: Futile Encounters and Enzyme Floppiness
    • Bar-Even, A., Milo, R., Noor, E., and Tawfik, D. S. (2015) The Moderately Efficient Enzyme: Futile Encounters and Enzyme Floppiness Biochemistry 54, 4969-4977 10.1021/acs.biochem.5b00621
    • (2015) Biochemistry , vol.54 , pp. 4969-4977
    • Bar-Even, A.1    Milo, R.2    Noor, E.3    Tawfik, D.S.4
  • 15
    • 84949117325 scopus 로고    scopus 로고
    • Negative Epistasis and Evolvability in TEM-1 beta-Lactamase - The Thin Line between an Enzyme's Conformational Freedom and Disorder
    • Dellus-Gur, E., Elias, M., Caselli, E., Prati, F., Salverda, M. L., de Visser, J. A., Fraser, J. S., and Tawfik, D. S. (2015) Negative Epistasis and Evolvability in TEM-1 beta-Lactamase - The Thin Line between an Enzyme's Conformational Freedom and Disorder J. Mol. Biol. 427, 2396-2409 10.1016/j.jmb.2015.05.011
    • (2015) J. Mol. Biol. , vol.427 , pp. 2396-2409
    • Dellus-Gur, E.1    Elias, M.2    Caselli, E.3    Prati, F.4    Salverda, M.L.5    De Visser, J.A.6    Fraser, J.S.7    Tawfik, D.S.8
  • 16
    • 67650287695 scopus 로고    scopus 로고
    • In the light of directed evolution: Pathways of adaptive protein evolution
    • Bloom, J. D. and Arnold, F. H. (2009) In the light of directed evolution: pathways of adaptive protein evolution Proc. Natl. Acad. Sci. U. S. A. 106 (Suppl 1) 9995-10000 10.1073/pnas.0901522106
    • (2009) Proc. Natl. Acad. Sci. U. S. A. , vol.106 , pp. 9995-10000
    • Bloom, J.D.1    Arnold, F.H.2
  • 17
    • 84943792201 scopus 로고    scopus 로고
    • Reverse evolution leads to genotypic incompatibility despite functional and active-site convergence
    • Kaltenbach, M., Jackson, C. J., Campbell, E. C., Hollfelder, F., and Tokuriki, N. (2015) Reverse evolution leads to genotypic incompatibility despite functional and active-site convergence eLife 4, e06492 10.7554/eLife.06492
    • (2015) ELife , vol.4
    • Kaltenbach, M.1    Jackson, C.J.2    Campbell, E.C.3    Hollfelder, F.4    Tokuriki, N.5
  • 19
    • 33748525883 scopus 로고    scopus 로고
    • Enzyme promiscuity: Evolutionary and mechanistic aspects
    • Khersonsky, O., Roodveldt, C., and Tawfik, D. S. (2006) Enzyme promiscuity: evolutionary and mechanistic aspects Curr. Opin. Chem. Biol. 10, 498-508 10.1016/j.cbpa.2006.08.011
    • (2006) Curr. Opin. Chem. Biol. , vol.10 , pp. 498-508
    • Khersonsky, O.1    Roodveldt, C.2    Tawfik, D.S.3
  • 22
    • 84861425552 scopus 로고    scopus 로고
    • Linking crystallographic model and data quality
    • Karplus, P. A. and Diederichs, K. (2012) Linking crystallographic model and data quality Science 336, 1030-1033 10.1126/science.1218231
    • (2012) Science , vol.336 , pp. 1030-1033
    • Karplus, P.A.1    Diederichs, K.2
  • 28
    • 0020345697 scopus 로고
    • Buffers of constant ionic strength for studying pH-dependent processes
    • Ellis, K. J. and Morrison, J. F. (1982) Buffers of constant ionic strength for studying pH-dependent processes Methods Enzymol. 87, 405-426 10.1016/S0076-6879(82)87025-0
    • (1982) Methods Enzymol. , vol.87 , pp. 405-426
    • Ellis, K.J.1    Morrison, J.F.2
  • 29
    • 0014454095 scopus 로고
    • Kinetics of the reversible inhibition of enzyme-catalysed reactions by tight-binding inhibitors
    • Morrison, J. F. (1969) Kinetics of the reversible inhibition of enzyme-catalysed reactions by tight-binding inhibitors Biochim. Biophys. Acta 185, 269-286 10.1016/0005-2744(69)90420-3
    • (1969) Biochim. Biophys. Acta , vol.185 , pp. 269-286
    • Morrison, J.F.1
  • 30
    • 0028788139 scopus 로고
    • Design and expression of organophosphorus acid anhydride hydrolase activity in human butyrylcholinesterase
    • Millard, C. B., Lockridge, O., and Broomfield, C. A. (1995) Design and expression of organophosphorus acid anhydride hydrolase activity in human butyrylcholinesterase Biochemistry 34, 15925-15933 10.1021/bi00049a007
    • (1995) Biochemistry , vol.34 , pp. 15925-15933
    • Millard, C.B.1    Lockridge, O.2    Broomfield, C.A.3
  • 32
    • 84899933010 scopus 로고    scopus 로고
    • Testing and validation of the Automated Topology Builder (ATB) version 2.0: Prediction of hydration free enthalpies
    • Koziara, K. B., Stroet, M., Malde, A. K., and Mark, A. E. (2014) Testing and validation of the Automated Topology Builder (ATB) version 2.0: prediction of hydration free enthalpies J. Comput.-Aided Mol. Des. 28, 221-233 10.1007/s10822-014-9713-7
    • (2014) J. Comput.-Aided Mol. Des. , vol.28 , pp. 221-233
    • Koziara, K.B.1    Stroet, M.2    Malde, A.K.3    Mark, A.E.4
  • 34
    • 73349131117 scopus 로고    scopus 로고
    • Staggered Mesh Ewald: An extension of the Smooth Particle-Mesh Ewald method adding great versatility
    • Cerutti, D. S., Duke, R. E., Darden, T. A., and Lybrand, T. P. (2009) Staggered Mesh Ewald: An extension of the Smooth Particle-Mesh Ewald method adding great versatility J. Chem. Theory Comput. 5, 2322-2388 10.1021/ct9001015
    • (2009) J. Chem. Theory Comput. , vol.5 , pp. 2322-2388
    • Cerutti, D.S.1    Duke, R.E.2    Darden, T.A.3    Lybrand, T.P.4
  • 35
    • 0000388705 scopus 로고    scopus 로고
    • LINCS: A linear constraint solver for molecular simulations
    • Hess, B., Bekker, H., Berendsen, H. J. C., and Fraaije, J. G. E. M. (1997) LINCS: A linear constraint solver for molecular simulations J. Comput. Chem. 18, 1463-1472 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.3.CO;2-L
    • (1997) J. Comput. Chem. , vol.18 , pp. 1463-1472
    • Hess, B.1    Bekker, H.2    Berendsen, H.J.C.3    Fraaije, J.G.E.M.4
  • 37
    • 0001305589 scopus 로고
    • The Viscosity of Spc and Spc/E Water at 277-K and 300-K
    • Smith, P. E. and van Gunsteren, W. F. (1993) The Viscosity of Spc and Spc/E Water at 277-K and 300-K Chem. Phys. Lett. 215, 315-318 10.1016/0009-2614(93)85720-9
    • (1993) Chem. Phys. Lett. , vol.215 , pp. 315-318
    • Smith, P.E.1    Van Gunsteren, W.F.2
  • 39
    • 0023513764 scopus 로고
    • Carboxylesterases in guinea-pig plasma and liver. Tissue specific reactivation by diacetylmonoxime after soman inhibition in vitro
    • Sterri, S. H. and Fonnum, F. (1987) Carboxylesterases in guinea-pig plasma and liver. Tissue specific reactivation by diacetylmonoxime after soman inhibition in vitro Biochem. Pharmacol. 36, 3937-3942 10.1016/0006-2952(87)90461-8
    • (1987) Biochem. Pharmacol. , vol.36 , pp. 3937-3942
    • Sterri, S.H.1    Fonnum, F.2
  • 40
    • 80053315434 scopus 로고    scopus 로고
    • Cloning, purification and characterization of a thermostable carboxylesterase from Anoxybacillus sp. PDF1
    • Ay, F., Karaoglu, H., Inan, K., Canakci, S., and Belduz, A. O. (2011) Cloning, purification and characterization of a thermostable carboxylesterase from Anoxybacillus sp. PDF1 Protein Expression Purif. 80, 74-79 10.1016/j.pep.2011.06.019
    • (2011) Protein Expression Purif. , vol.80 , pp. 74-79
    • Ay, F.1    Karaoglu, H.2    Inan, K.3    Canakci, S.4    Belduz, A.O.5
  • 41
    • 84923385007 scopus 로고    scopus 로고
    • Directed evolution of new and improved enzyme functions using an evolutionary intermediate and multidirectional search
    • Porter, J. L., Boon, P. L., Murray, T. P., Huber, T., Collyer, C. A., and Ollis, D. L. (2015) Directed evolution of new and improved enzyme functions using an evolutionary intermediate and multidirectional search ACS Chem. Biol. 10, 611-621 10.1021/cb500809f
    • (2015) ACS Chem. Biol. , vol.10 , pp. 611-621
    • Porter, J.L.1    Boon, P.L.2    Murray, T.P.3    Huber, T.4    Collyer, C.A.5    Ollis, D.L.6
  • 42
    • 0036783381 scopus 로고    scopus 로고
    • Variability in the pKa of histidine side-chains correlates with burial within proteins
    • Edgcomb, S. P. and Murphy, K. P. (2002) Variability in the pKa of histidine side-chains correlates with burial within proteins Proteins: Struct., Funct., Genet. 49, 1-6 10.1002/prot.10177
    • (2002) Proteins: Struct., Funct., Genet. , vol.49 , pp. 1-6
    • Edgcomb, S.P.1    Murphy, K.P.2
  • 43
    • 0021708080 scopus 로고
    • Stereochemical Aspects of Cholinesterase Catalysis
    • Jarv, J. (1984) Stereochemical Aspects of Cholinesterase Catalysis Bioorg. Chem. 12, 259-278 10.1016/0045-2068(84)90010-5
    • (1984) Bioorg. Chem. , vol.12 , pp. 259-278
    • Jarv, J.1
  • 44
    • 37249032102 scopus 로고    scopus 로고
    • Dynamic personalities of proteins
    • Henzler-Wildman, K. and Kern, D. (2007) Dynamic personalities of proteins Nature 450, 964-972 10.1038/nature06522
    • (2007) Nature , vol.450 , pp. 964-972
    • Henzler-Wildman, K.1    Kern, D.2
  • 45
    • 29844449450 scopus 로고    scopus 로고
    • The effects of substrate orientation on the mechanism of a phosphotriesterase
    • Jackson, C. J., Liu, J. W., Coote, M. L., and Ollis, D. L. (2005) The effects of substrate orientation on the mechanism of a phosphotriesterase Org. Biomol. Chem. 3, 4343-4350 10.1039/b512399b
    • (2005) Org. Biomol. Chem. , vol.3 , pp. 4343-4350
    • Jackson, C.J.1    Liu, J.W.2    Coote, M.L.3    Ollis, D.L.4
  • 46
    • 0001193005 scopus 로고
    • Theoretical assessments of the basicity and nucleophilicity of carboxylate syn and anti lone pairs
    • Li, Y. and Houk, K. N. (1989) Theoretical assessments of the basicity and nucleophilicity of carboxylate syn and anti lone pairs J. Am. Chem. Soc. 111, 4505-4507 10.1021/ja00194a059
    • (1989) J. Am. Chem. Soc. , vol.111 , pp. 4505-4507
    • Li, Y.1    Houk, K.N.2
  • 47
    • 21344437661 scopus 로고    scopus 로고
    • Mutants of human butyrylcholinesterase with organophosphate hydrolase activity; Evidence that His117 is a general base catalyst for hydrolysis of echothiophate
    • Schopfer, L. M., Broomfield, C. A., Boeck, A. T., and Lockridge, O. (2004) Mutants of human butyrylcholinesterase with organophosphate hydrolase activity; evidence that His117 is a general base catalyst for hydrolysis of echothiophate J. Med. Chem. Def. 2, 1-15
    • (2004) J. Med. Chem. Def. , vol.2 , pp. 1-15
    • Schopfer, L.M.1    Broomfield, C.A.2    Boeck, A.T.3    Lockridge, O.4
  • 48
    • 84962433300 scopus 로고    scopus 로고
    • Hydrolysis of organophosphate compounds by mutant butyrylcholinesterase: A story of two histidines
    • Amitay, M. and Shurki, A. (2011) Hydrolysis of organophosphate compounds by mutant butyrylcholinesterase: a story of two histidines Proteins: Struct., Funct., Genet. 79, 352-364 10.1002/prot.22864
    • (2011) Proteins: Struct., Funct., Genet. , vol.79 , pp. 352-364
    • Amitay, M.1    Shurki, A.2
  • 49
    • 79251561846 scopus 로고    scopus 로고
    • X-ray crystallographic snapshots of reaction intermediates in the G117H mutant of human butyrylcholinesterase, a nerve agent target engineered into a catalytic bioscavenger
    • Nachon, F., Carletti, E., Wandhammer, M., Nicolet, Y., Schopfer, L. M., Masson, P., and Lockridge, O. (2011) X-ray crystallographic snapshots of reaction intermediates in the G117H mutant of human butyrylcholinesterase, a nerve agent target engineered into a catalytic bioscavenger Biochem. J. 434, 73-82 10.1042/BJ20101648
    • (2011) Biochem. J. , vol.434 , pp. 73-82
    • Nachon, F.1    Carletti, E.2    Wandhammer, M.3    Nicolet, Y.4    Schopfer, L.M.5    Masson, P.6    Lockridge, O.7
  • 50
    • 84949533946 scopus 로고    scopus 로고
    • Modeling reactivation of the phosphorylated human butyrylcholinesterase by QM(DFTB)/MM calculations
    • Kulakova, A., Lushchekina, S., Grigorenko, B., and Nemukhin, A. (2015) Modeling reactivation of the phosphorylated human butyrylcholinesterase by QM(DFTB)/MM calculations J. Theor. Comput. Chem. 14, 1550051 10.1142/S0219633615500510
    • (2015) J. Theor. Comput. Chem. , vol.14 , pp. 1550051
    • Kulakova, A.1    Lushchekina, S.2    Grigorenko, B.3    Nemukhin, A.4
  • 51
    • 0028918401 scopus 로고
    • A proficient enzyme
    • Radzicka, A. and Wolfenden, R. (1995) A proficient enzyme Science 267, 90-93 10.1126/science.7809611
    • (1995) Science , vol.267 , pp. 90-93
    • Radzicka, A.1    Wolfenden, R.2
  • 53
    • 0041989850 scopus 로고    scopus 로고
    • Challenges in enzyme mechanism and energetics
    • Kraut, D. A., Carroll, K. S., and Herschlag, D. (2003) Challenges in enzyme mechanism and energetics Annu. Rev. Biochem. 72, 517-571 10.1146/annurev.biochem.72.121801.161617
    • (2003) Annu. Rev. Biochem. , vol.72 , pp. 517-571
    • Kraut, D.A.1    Carroll, K.S.2    Herschlag, D.3
  • 54
    • 77957754309 scopus 로고    scopus 로고
    • Enzyme dynamics point to stepwise conformational selection in catalysis
    • Ma, B. and Nussinov, R. (2010) Enzyme dynamics point to stepwise conformational selection in catalysis Curr. Opin. Chem. Biol. 14, 652-659 10.1016/j.cbpa.2010.08.012
    • (2010) Curr. Opin. Chem. Biol. , vol.14 , pp. 652-659
    • Ma, B.1    Nussinov, R.2
  • 55
    • 0015101706 scopus 로고
    • Entropic contributions to rate accelerations in enzymic and intramolecular reactions and the chelate effect
    • Page, M. I. and Jencks, W. P. (1971) Entropic contributions to rate accelerations in enzymic and intramolecular reactions and the chelate effect Proc. Natl. Acad. Sci. U. S. A. 68, 1678-1683 10.1073/pnas.68.8.1678
    • (1971) Proc. Natl. Acad. Sci. U. S. A. , vol.68 , pp. 1678-1683
    • Page, M.I.1    Jencks, W.P.2
  • 56
    • 0041876227 scopus 로고    scopus 로고
    • Computer simulations of enzyme catalysis: Methods, progress, and insights
    • Warshel, A. (2003) Computer simulations of enzyme catalysis: methods, progress, and insights Annu. Rev. Biophys. Biomol. Struct. 32, 425-443 10.1146/annurev.biophys.32.110601.141807
    • (2003) Annu. Rev. Biophys. Biomol. Struct. , vol.32 , pp. 425-443
    • Warshel, A.1
  • 57
    • 37549047246 scopus 로고    scopus 로고
    • In crystallo capture of a Michaelis complex and product-binding modes of a bacterial phosphotriesterase
    • Jackson, C. J., Foo, J. L., Kim, H. K., Carr, P. D., Liu, J. W., Salem, G., and Ollis, D. L. (2008) In crystallo capture of a Michaelis complex and product-binding modes of a bacterial phosphotriesterase J. Mol. Biol. 375, 1189-1196 10.1016/j.jmb.2007.10.061
    • (2008) J. Mol. Biol. , vol.375 , pp. 1189-1196
    • Jackson, C.J.1    Foo, J.L.2    Kim, H.K.3    Carr, P.D.4    Liu, J.W.5    Salem, G.6    Ollis, D.L.7


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