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Volumn 49, Issue 48, 2010, Pages 10339-10348

Hydrogen bonding in the active site of ketosteroid isomerase: Electronic inductive effects and hydrogen bond coupling

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; BOND DISTANCE; COMPUTATIONAL STUDIES; ELECTRONIC ABSORPTION; ELECTRONIC ABSORPTION SPECTRA; HYDROGEN BONDING NETWORK; HYDROGEN BONDINGS; INDUCTIVE EFFECTS; ISOMERASES; NMR CHEMICAL SHIFTS; NMR DATA; NONPOLAR ENVIRONMENT; NUCLEAR MAGNETIC RESONANCE CHEMICAL SHIFTS; PROTON DONORS; PROTONATED; QUANTUM MECHANICAL/MOLECULAR MECHANICAL CALCULATIONS; TYROSINE RESIDUES;

EID: 78650899625     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi101428e     Document Type: Article
Times cited : (34)

References (49)
  • 1
    • 4644373998 scopus 로고    scopus 로고
    • Enzymatic mechanisms for catalysis of enolization:Ketosteroid isomerase
    • Pollack, R.M. (2004) Enzymatic mechanisms for catalysis of enolization:Ketosteroid isomerase. Bioorg. Chem. 32, 341-353.
    • (2004) Bioorg. Chem. , vol.32 , pp. 341-353
    • Pollack, R.M.1
  • 2
    • 0026336560 scopus 로고
    • Energetics of 3-oxo-Δ5-steroid isomerase: Source of the catalyticpower of the enzyme
    • Hawkinson, D. C., Eames, T. C. M., and Pollack, R. M. (1991) Energetics of 3-oxo-Δ5-steroid isomerase: Source of the catalyticpower of the enzyme. Biochemistry 30, 10849-10858.
    • (1991) Biochemistry , vol.30 , pp. 10849-10858
    • Hawkinson, D.C.1    Eames, T.C.M.2    Pollack, R.M.3
  • 3
    • 0032512414 scopus 로고    scopus 로고
    • Substituent effects on thebinding of phenols to theD38Nmutant of 3-oxo-Δ5-steroid isomerase:A probe for the nature of hydrogen bonding to the intermediate
    • Petrounia, I. P., and Pollack, R. M. (1998) Substituent effects on thebinding of phenols to theD38Nmutant of 3-oxo-Δ5-steroid isomerase:A probe for the nature of hydrogen bonding to the intermediate.Biochemistry 37, 700-705.
    • (1998) Biochemistry , vol.37 , pp. 700-705
    • Petrounia, I.P.1    Pollack, R.M.2
  • 4
    • 33646262869 scopus 로고    scopus 로고
    • Testing electrostatic complementarityin enzymatic catalysis: Hydrogen bonding in the ketosteroid isomeraseoxyanion hole
    • Kraut, D. A., Sigala, P. A., Pybus, B., Liu, C. W., Ringe, D., Petsko, G. A., and Herschlag, D. (2006) Testing electrostatic complementarityin enzymatic catalysis: Hydrogen bonding in the ketosteroid isomeraseoxyanion hole. PLoS Biol. 4, 501-519.
    • (2006) PLoS Biol. , vol.4 , pp. 501-519
    • Kraut, D.A.1    Sigala, P.A.2    Pybus, B.3    Liu, C.W.4    Ringe, D.5    Petsko, G.A.6    Herschlag, D.7
  • 5
    • 0034635151 scopus 로고    scopus 로고
    • Binding of 2-naphthols to D38E mutants of 3-oxo-Δ5-steroid isomerase: Variationof ligand ionization state with the nature of the electrophiliccomponent
    • Petrounia, I. P., Blotny, G., and Pollack, R. M. (2000) Binding of 2-naphthols to D38E mutants of 3-oxo-Δ5-steroid isomerase: Variationof ligand ionization state with the nature of the electrophiliccomponent. Biochemistry 39, 110-116.
    • (2000) Biochemistry , vol.39 , pp. 110-116
    • Petrounia, I.P.1    Blotny, G.2    Pollack, R.M.3
  • 6
    • 77949824987 scopus 로고    scopus 로고
    • Proton affinity of the oxyanionhole in the active site of ketosteroid isomerase
    • Childs, W., and Boxer, S. G. (2010) Proton affinity of the oxyanionhole in the active site of ketosteroid isomerase. Biochemistry 49, 2725-2731.
    • (2010) Biochemistry , vol.49 , pp. 2725-2731
    • Childs, W.1    Boxer, S.G.2
  • 7
    • 84944811554 scopus 로고
    • The correlation between hydrogenbondlengths and proton chemical shifts in crystals
    • Jeffrey, J., and Yeon, Y. (1986) The correlation between hydrogenbondlengths and proton chemical shifts in crystals. Acta Crystallogr.B42, 410-413.
    • (1986) Acta Crystallogr.B , vol.42 , pp. 410-413
    • Jeffrey, J.1    Yeon, Y.2
  • 8
    • 0030819258 scopus 로고    scopus 로고
    • Hydrogen bonding at the active site of Δ5-3-ketosteroidisomerase
    • Zhao, Q., Abeygunawardana, C., Gittis, A. G., and Mildvan, A. S.(1997) Hydrogen bonding at the active site of Δ5-3-ketosteroidisomerase. Biochemistry 36, 14616-14626.
    • (1997) Biochemistry , vol.36 , pp. 14616-14626
    • Zhao, Q.1    Abeygunawardana, C.2    Gittis, A.G.3    Mildvan, A.S.4
  • 9
    • 0033562690 scopus 로고    scopus 로고
    • High-precision measurementof hydrogen bond lengths in proteins by nuclear magnetic resonancemethods
    • Harris, T. K., and Mildvan, A. S. (1999) High-precision measurementof hydrogen bond lengths in proteins by nuclear magnetic resonancemethods. Proteins: Struct., Funct., Genet. 35, 275-282.
    • (1999) Proteins: Struct., Funct., Genet. , vol.35 , pp. 275-282
    • Harris, T.K.1    Mildvan, A.S.2
  • 10
    • 0025912705 scopus 로고
    • Microscopic rate constants for theacetate ion catalyzed isomerization of 5-androstene-3, 17-dione to4-androstene-3, 17-dione: A model for steroid isomerase
    • Zeng, B., and Pollack, R. M. (1991) Microscopic rate constants for theacetate ion catalyzed isomerization of 5-androstene-3, 17-dione to4-androstene-3, 17-dione: A model for steroid isomerase. J. Am.Chem. Soc. 113, 3838-3842.
    • (1991) J. Am.Chem. Soc. , vol.113 , pp. 3838-3842
    • Zeng, B.1    Pollack, R.M.2
  • 11
    • 0040777049 scopus 로고    scopus 로고
    • Contribution of thehydrogen-bond network involving a tyrosine triad in the active site tothe structure and function of a highly proficient ketosteroid isomerasefrom Pseudomonas putida biotype B
    • Kim, D.-H., Jang, D. S., Nam, G. H., Choi, G., Kim, J.-S., Ha, N.-C., Kim, M.-S., Oh, B.-H., and Choi, K. Y. (2000) Contribution of thehydrogen-bond network involving a tyrosine triad in the active site tothe structure and function of a highly proficient ketosteroid isomerasefrom Pseudomonas putida biotype B. Biochemistry 39, 4581-4589.
    • (2000) Biochemistry , vol.39 , pp. 4581-4589
    • Kim, D.-H.1    Jang, D.S.2    Nam, G.H.3    Choi, G.4    Kim, J.-S.5    Ha, N.-C.6    Kim, M.-S.7    Oh, B.-H.8    Choi, K.Y.9
  • 12
    • 0035849571 scopus 로고    scopus 로고
    • Pseudoreversion of the catalytic activity of Y14F by theadditional substitution(s) of tyrosine with phenylalanine in the hydrogenbond network of Δ5-3-ketosteroid isomerase from Pseudomonasputida biotype B
    • Choi, G., Ha, N.-C., Kim, M.-S., Hong, B.-H., Oh, B.-H., and Choi, K. Y. (2001) Pseudoreversion of the catalytic activity of Y14F by theadditional substitution(s) of tyrosine with phenylalanine in the hydrogenbond network of Δ5-3-ketosteroid isomerase from Pseudomonasputida biotype B. Biochemistry 40, 6828-6835.
    • (2001) Biochemistry , vol.40 , pp. 6828-6835
    • Choi, G.1    Ha, N.-C.2    Kim, M.-S.3    Hong, B.-H.4    Oh, B.-H.5    Choi, K.Y.6
  • 13
    • 4744361169 scopus 로고    scopus 로고
    • Structural doublemutantcycle analysis of a hydrogen bond network in ketosteroidisomerase from Pseudomonas putida biotype B
    • Jang, D. S., Cha, H. J., Cha, S.-S., Hong, B. H., Ha, N.-C., Lee, J. Y., Oh, B.-H., Lee, H.-S., and Choi, K. Y. (2004) Structural doublemutantcycle analysis of a hydrogen bond network in ketosteroidisomerase from Pseudomonas putida biotype B. BioChem. J. 382, 967-973.
    • (2004) BioChem. J. , vol.382 , pp. 967-973
    • Jang, D.S.1    Cha, H.J.2    Cha, S.-S.3    Hong, B.H.4    Ha, N.-C.5    Lee, J.Y.6    Oh, B.-H.7    Lee, H.-S.8    Choi, K.Y.9
  • 16
    • 12944268384 scopus 로고    scopus 로고
    • Catalytic role of enzymes:Short strong H-bond-induced partial proton shuttles and chargeredistributions
    • Kim, K. S., Oh, K. S., and Lee, J. Y. (2000) Catalytic role of enzymes:Short strong H-bond-induced partial proton shuttles and chargeredistributions. Proc. Natl. Acad. Sci. U.S.A. 97, 6373-6378.
    • (2000) Proc. Natl. Acad. Sci. U.S.A. , vol.97 , pp. 6373-6378
    • Kim, K.S.1    Oh, K.S.2    Lee, J.Y.3
  • 17
    • 84962428182 scopus 로고    scopus 로고
    • Theoretical investigation of therole of hydrogen bonding during ketosteroid isomerase catalysis
    • Pan, Y., and McAllister, M. A. (2000) Theoretical investigation of therole of hydrogen bonding during ketosteroid isomerase catalysis.THEOCHEM 504, 29-33.
    • (2000) THEOCHEM , vol.504 , pp. 29-33
    • Pan, Y.1    McAllister, M.A.2
  • 18
    • 0037471672 scopus 로고    scopus 로고
    • Molecular dynamics and quantum chemical studies on the catalytic mechanism of Δ5-3-ketosteroidisomerase: The catalytic diad versus the cooperative hydrogenbond mechanism
    • Park, H., and Merz, K. M., Jr. (2003) Molecular dynamics and quantum chemical studies on the catalytic mechanism of Δ5-3-ketosteroidisomerase: The catalytic diad versus the cooperative hydrogenbond mechanism. J. Am. Chem. Soc. 125, 901-911.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 901-911
    • Park, H.1    Merz, Jr.K.M.2
  • 19
    • 0037207102 scopus 로고    scopus 로고
    • The catalytic power of ketosteroidisomerase investigated by computer simulation
    • Feierberg, I., and Aqvist, J. (2002) The catalytic power of ketosteroidisomerase investigated by computer simulation. Biochemistry 41, 15728-15735.
    • (2002) Biochemistry , vol.41 , pp. 15728-15735
    • Feierberg, I.1    Aqvist, J.2
  • 20
    • 0036025574 scopus 로고    scopus 로고
    • Computational modeling ofenzymatic keto-enol isomerization reactions
    • Feierberg, I., and Aqvist, J. (2002) Computational modeling ofenzymatic keto-enol isomerization reactions. Theor. Chem. Acc.108, 71-84.
    • (2002) Theor. Chem. Acc. , vol.108 , pp. 71-84
    • Feierberg, I.1    Aqvist, J.2
  • 21
    • 0037532737 scopus 로고    scopus 로고
    • Computationalstudy of ketosteroid isomerase: Insights from molecular dynamicssimulation of enzyme bound substrate and intermediate
    • Mazumder, D., Kahn, K., and Bruice, T. C. (2003) Computationalstudy of ketosteroid isomerase: Insights from molecular dynamicssimulation of enzyme bound substrate and intermediate. J. Am. Chem. Soc. 125, 7553-7561.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 7553-7561
    • Mazumder, D.1    Kahn, K.2    Bruice, T.C.3
  • 22
    • 33847006589 scopus 로고    scopus 로고
    • Electrostatic contributions to binding of transition state analoguescan be very different from the corresponding contributions to catalysis:Phenolates binding to the oxyanion hole of ketosteroid isomerase
    • Warshel, A., Sharma, P. K., Chu, Z. T., and Aqvist, J. (2007) Electrostatic contributions to binding of transition state analoguescan be very different from the corresponding contributions to catalysis:Phenolates binding to the oxyanion hole of ketosteroid isomerase.Biochemistry 46, 1466-1476.
    • (2007) Biochemistry , vol.46 , pp. 1466-1476
    • Warshel, A.1    Sharma, P.K.2    Chu, Z.T.3    Aqvist, J.4
  • 23
    • 77749239790 scopus 로고    scopus 로고
    • Ketosteroid isomerase provides further support for the idea thatenzymes work by electrostatic preorganization
    • Kamerlin, S. C. L., Sharma, P. K., Chu, Z. T., and Warshel, A. (2010) Ketosteroid isomerase provides further support for the idea thatenzymes work by electrostatic preorganization. Proc. Natl. Acad.Sci. U.S.A. 107, 4075-4080.
    • (2010) Proc. Natl. Acad.Sci. U.S.A. , vol.107 , pp. 4075-4080
    • Kamerlin, S.C.L.1    Sharma, P.K.2    Chu, Z.T.3    Warshel, A.4
  • 24
    • 70449399334 scopus 로고    scopus 로고
    • Hybrid quantum/classical molecular dynamics simulations ofthe proton transfer reactions catalyzed by ketosteroid isomerase:Analysis of hydrogen bonding, conformational motions, and electrostatics
    • Chakravorty, D. K., Soudackov, A. V., and Hammes-Schiffer, S.(2009) Hybrid quantum/classical molecular dynamics simulations ofthe proton transfer reactions catalyzed by ketosteroid isomerase:Analysis of hydrogen bonding, conformational motions, and electrostatics.Biochemistry 48, 10608-10619.
    • (2009) Biochemistry , vol.48 , pp. 10608-10619
    • Chakravorty, D.K.1    Soudackov, A.V.2    Hammes-Schiffer, S.3
  • 25
    • 77952791645 scopus 로고    scopus 로고
    • Impact of mutationon proton transfer reactions in ketosteroid isomerase: Insights frommolecular dynamics simulations
    • Chakravorty, D.K., and Hammes-Schiffer, S. (2010) Impact of mutationon proton transfer reactions in ketosteroid isomerase: Insights frommolecular dynamics simulations. J. Am. Chem. Soc. 132, 7549-7555.
    • (2010) J. Am. Chem. Soc. , vol.132 , pp. 7549-7555
    • Chakravorty, D.K.1    Hammes-Schiffer, S.2
  • 26
    • 0035838974 scopus 로고    scopus 로고
    • Extending the accuracy limits ofprediction for side-chain conformations
    • Xiang, Z., and Honig, B. (2001) Extending the accuracy limits ofprediction for side-chain conformations. J. Mol. Biol. 311, 421-430.
    • (2001) J. Mol. Biol. , vol.311 , pp. 421-430
    • Xiang, Z.1    Honig, B.2
  • 29
    • 78650876241 scopus 로고    scopus 로고
    • Maestro, version 9.0 (2009) Schrodinger, LLC, New York
    • Maestro, version 9.0 (2009) Schrodinger, LLC, New York.
  • 31
    • 0000020246 scopus 로고    scopus 로고
    • A five-site model forliquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions
    • Mahoney, M. W., and Jorgensen, W. L. (2000) A five-site model forliquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. J. Chem. Phys. 112, 8910-8922.
    • (2000) J. Chem. Phys. , vol.112 , pp. 8910-8922
    • Mahoney, M.W.1    Jorgensen, W.L.2
  • 32
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformationalenergetics and properties of organic liquids
    • Jorgensen, W. L., Maxwell, D. S., and Tirado-Rives, J. (1996) Development and testing of the OPLS all-atom force field on conformationalenergetics and properties of organic liquids. J. Am. Chem. Soc. 118, 11225-11236.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 34
    • 33846823909 scopus 로고
    • Particle mesh Ewald:An N.Log(N) method for Ewald sums in large systems
    • Darden, T., York, D., and Pedersen, L. (1993) Particle mesh Ewald:An N.Log(N) method for Ewald sums in large systems. J. Chem. Phys.98, 10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 35
    • 33646940952 scopus 로고
    • Numericalintegration of the cartesian equations of motion of a system withconstraints: Molecular dynamics of n-alkanes
    • Ryckaert, J. P., Ciccotti, G., and Berendsen, H. J. C. (1977) Numericalintegration of the cartesian equations of motion of a system withconstraints: Molecular dynamics of n-alkanes . J. Comput. Phys. 23, 327.
    • (1977) J. Comput. Phys. , vol.23 , pp. 327
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 36
    • 78650923874 scopus 로고    scopus 로고
    • Desmond Molecular Dynamics System, version 2.2 (2008) D. E. ShawResearch, New York
    • Desmond Molecular Dynamics System, version 2.2 (2008) D. E. ShawResearch, New York.
  • 38
    • 78650902983 scopus 로고    scopus 로고
    • QSite, version 5.5 (2009) Schrodinger, LLC, New York
    • QSite, version 5.5 (2009) Schrodinger, LLC, New York.
  • 39
    • 33746614482 scopus 로고
    • Gaussian basis sets for use in correlatedmolecular calculations: 1. The atoms boron through neon and hydrogen
    • Dunning, T. H., Jr. (1989) Gaussian basis sets for use in correlatedmolecular calculations: 1., The atoms boron through neon and hydrogen. J. Chem. Phys. 90, 1007-1023.
    • (1989) J. Chem. Phys. , vol.90 , pp. 1007-1023
    • Dunning, Jr.T.H.1
  • 40
    • 1242268874 scopus 로고    scopus 로고
    • A comparison of models for calculating nuclear magneticresonance shielding tensors
    • Cheeseman, J. R., Trucks, G. W., Keith, T. A., and Frisch, M. J.(1996) A comparison of models for calculating nuclear magneticresonance shielding tensors. J. Chem. Phys. 104, 5497-5509.
    • (1996) J. Chem. Phys. , vol.104 , pp. 5497-5509
    • Cheeseman, J.R.1    Trucks, G.W.2    Keith, T.A.3    Frisch, M.J.4
  • 41
    • 0000584523 scopus 로고    scopus 로고
    • Ab initio methodsfor the calculation of NMR shielding and indirect spin-spin couplingconstants
    • Helgaker, T., Jaszunski, M., and Ruud, K. (1999) Ab initio methodsfor the calculation of NMR shielding and indirect spin-spin couplingconstants. Chem. Rev. 99, 293-352.
    • (1999) Chem. Rev. , vol.99 , pp. 293-352
    • Helgaker, T.1    Jaszunski, M.2    Ruud, K.3
  • 42
  • 43
    • 0011716738 scopus 로고
    • Protonchemical shift tensors in hydrogen-bonded dimers of RCOOH and ROH
    • Rohlfing, C. M., Allen, L. C., and Ditchfield, R. (1983) Protonchemical shift tensors in hydrogen-bonded dimers of RCOOH and ROH. J. Chem. Phys. 79, 4958-4966.
    • (1983) J. Chem. Phys. , vol.79 , pp. 4958-4966
    • Rohlfing, C.M.1    Allen, L.C.2    Ditchfield, R.3
  • 44
    • 26844506572 scopus 로고
    • The Fourier gridHamiltonian method for bound state eigenvalues and eigenfunctions
    • Marston, C. C., and Balint-Kurti, G. G. (1989) The Fourier gridHamiltonian method for bound state eigenvalues and eigenfunctions. J. Chem. Phys. 91, 3571-3576.
    • (1989) J. Chem. Phys. , vol.91 , pp. 3571-3576
    • Marston, C.C.1    Balint-Kurti, G.G.2
  • 45
    • 0034300544 scopus 로고    scopus 로고
    • Fourier grid Hamiltonianmulticonfigurational self-consistent-field: A method to calculatemultidimensional hydrogen vibrational wavefunctions
    • Webb, S. P., and Hammes-Schiffer, S. (2000) Fourier grid Hamiltonianmulticonfigurational self-consistent-field: A method to calculatemultidimensional hydrogen vibrational wavefunctions. J. Chem. Phys. 113, 5214-5227.
    • (2000) J. Chem. Phys. , vol.113 , pp. 5214-5227
    • Webb, S.P.1    Hammes-Schiffer, S.2
  • 46
    • 0034731147 scopus 로고    scopus 로고
    • Detection of large pKa perturbations of an inhibitor and a catalyticgroup at an enzyme active site, a mechanistic basis for catalytic powerof many enzymes
    • Ha, N.-C., Kim, M.-S., Lee, W., Choi, K. Y., and Oh, B.-H. (2000) Detection of large pKa perturbations of an inhibitor and a catalyticgroup at an enzyme active site, a mechanistic basis for catalytic powerof many enzymes. J. Biol. Chem. 275, 41100-41106.
    • (2000) J. Biol. Chem. , vol.275 , pp. 41100-41106
    • Ha, N.-C.1    Kim, M.-S.2    Lee, W.3    Choi, K.Y.4    Oh, B.-H.5
  • 47
    • 0000842595 scopus 로고
    • Binomial solvent suppression
    • Turner, D. L. (1983) Binomial solvent suppression. J. Magn. Reson.54, 146-148.
    • (1983) J. Magn. Reson. , vol.54 , pp. 146-148
    • Turner, D.L.1
  • 48
    • 0000659222 scopus 로고
    • Defining the domain ofdensity functionals: Charge transfer complexes
    • Ruiz, E., Salahub, D. R., and Vela, A. (1995) Defining the domain ofdensity functionals: Charge transfer complexes. J. Am. Chem. Soc.117, 1141-1142.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 1141-1142
    • Ruiz, E.1    Salahub, D.R.2    Vela, A.3
  • 49
    • 77249127120 scopus 로고    scopus 로고
    • Benchmark databases fornonbonded interactions and their use to test density functional theory
    • Zhao, Y., and Truhlar, D. G. (2005) Benchmark databases fornonbonded interactions and their use to test density functional theory. J. Chem. Theory Comput. 1, 415-432.
    • (2005) J. Chem. Theory Comput. , vol.1 , pp. 415-432
    • Zhao, Y.1    Truhlar, D.G.2


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