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Volumn 126, Issue 1-3, 2007, Pages 80-85

Low-frequency normal modes in horse liver alcohol dehydrogenase and motions of residues involved in the enzymatic reaction

Author keywords

Horse liver alcohol dehydrogenase; Normal mode analysis

Indexed keywords

ALCOHOL DEHYDROGENASE; VALINE;

EID: 33846575268     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2006.05.009     Document Type: Article
Times cited : (13)

References (41)
  • 3
    • 0020479867 scopus 로고
    • Binding of substrate in a ternary complex of horse liver alcohol dehydrogenase
    • Eklund H., Plapp B.V., Samama J.-P., and Brändén C.I. Binding of substrate in a ternary complex of horse liver alcohol dehydrogenase. J. Biol. Chem. 23 (1982) 14349-14358
    • (1982) J. Biol. Chem. , vol.23 , pp. 14349-14358
    • Eklund, H.1    Plapp, B.V.2    Samama, J.-P.3    Brändén, C.I.4
  • 5
    • 0027196492 scopus 로고
    • Unmasking of hydrogen tunneling in the horse liver alcohol dehydrogenase reaction by site-directed mutagenesis
    • Bahnson B.J., Park D.-H., Kim K., Plapp B.V., and Klinman J.P. Unmasking of hydrogen tunneling in the horse liver alcohol dehydrogenase reaction by site-directed mutagenesis. Biochemistry 32 (1993) 5503-5507
    • (1993) Biochemistry , vol.32 , pp. 5503-5507
    • Bahnson, B.J.1    Park, D.-H.2    Kim, K.3    Plapp, B.V.4    Klinman, J.P.5
  • 7
    • 0000500410 scopus 로고
    • Evaluation of the factors influencing reactivity and stereospecificity in NAD(P)H dependent enzymes
    • Almarsson Ö., and Bruice T.C. Evaluation of the factors influencing reactivity and stereospecificity in NAD(P)H dependent enzymes. J. Am. Chem. Soc. 115 (1993) 2125-2138
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 2125-2138
    • Almarsson, Ö.1    Bruice, T.C.2
  • 9
    • 0020442184 scopus 로고
    • Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 Å resolution
    • Filman D.J., Bolin J.T., Matthews D.A., and Kraut J. Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 Å resolution. J. Biol. Chem. 257 (1982) 13663
    • (1982) J. Biol. Chem. , vol.257 , pp. 13663
    • Filman, D.J.1    Bolin, J.T.2    Matthews, D.A.3    Kraut, J.4
  • 10
    • 0024413884 scopus 로고
    • Refined crystal structure of cytoplasmic malate dehydrogenase at 2.5-Å resolution
    • Birktoft J.J., Rhodes G., and Banascak L.J. Refined crystal structure of cytoplasmic malate dehydrogenase at 2.5-Å resolution. Biochemistry 28 (1989) 6065
    • (1989) Biochemistry , vol.28 , pp. 6065
    • Birktoft, J.J.1    Rhodes, G.2    Banascak, L.J.3
  • 11
    • 0016772655 scopus 로고
    • Studies of asymmetry in the three-dimensional structure of lobster d-glyceraldehyde-3-phosphate dehydrogenase
    • Moras D., Olson K.W., Sabesan M.N., Buehner M., Ford G.C., and Rossmann M.G. Studies of asymmetry in the three-dimensional structure of lobster d-glyceraldehyde-3-phosphate dehydrogenase. J. Biol. Chem. 250 (1975) 9137
    • (1975) J. Biol. Chem. , vol.250 , pp. 9137
    • Moras, D.1    Olson, K.W.2    Sabesan, M.N.3    Buehner, M.4    Ford, G.C.5    Rossmann, M.G.6
  • 12
    • 0000286714 scopus 로고
    • Mechanism of one-electron oxidation of NAD(P)H and function of NADPH bound to catalase
    • Almarsson Ö., Sinha A., Gopinath E., and Bruice T.C. Mechanism of one-electron oxidation of NAD(P)H and function of NADPH bound to catalase. J. Am. Chem. Soc. 115 (1993) 7093-7102
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 7093-7102
    • Almarsson, Ö.1    Sinha, A.2    Gopinath, E.3    Bruice, T.C.4
  • 13
    • 0032817216 scopus 로고    scopus 로고
    • 2OH on the distance between reactants when catalyzed by horse liver alcohol dehydrogenase and 203 single point mutants
    • 2OH on the distance between reactants when catalyzed by horse liver alcohol dehydrogenase and 203 single point mutants. Bioorganic Chem. 27 N4 (1999) 289-296
    • (1999) Bioorganic Chem. , vol.27 , Issue.N4 , pp. 289-296
    • Luo, J.1    Kahn, K.2    Bruice, T.C.3
  • 14
    • 0035827163 scopus 로고    scopus 로고
    • Inclusion of quantum-mechanical vibrational energy in reactive potentials of mean force
    • Garcia-Viloca M., Alhambra C., Truhlar D.G., and Gao J. Inclusion of quantum-mechanical vibrational energy in reactive potentials of mean force. J. Chem. Phys. 114 (2001) 9953-9958
    • (2001) J. Chem. Phys. , vol.114 , pp. 9953-9958
    • Garcia-Viloca, M.1    Alhambra, C.2    Truhlar, D.G.3    Gao, J.4
  • 16
    • 0026652564 scopus 로고
    • Progressive sequence alignment and molecular evolution of the Zn-containing alcohol dehydrogenase family
    • Sun H.-W., and Plapp B.V. Progressive sequence alignment and molecular evolution of the Zn-containing alcohol dehydrogenase family. J. Mol. Evol. 34 (1992) 522-535
    • (1992) J. Mol. Evol. , vol.34 , pp. 522-535
    • Sun, H.-W.1    Plapp, B.V.2
  • 18
    • 0037452898 scopus 로고    scopus 로고
    • Amino acid residues in the nicotinamide binding site contribute to catalysis by horse liver alcohol dehydrogenase
    • Rubach J.K., and Plapp B.V. Amino acid residues in the nicotinamide binding site contribute to catalysis by horse liver alcohol dehydrogenase. Biochemistry 42 (2003) 2907-2915
    • (2003) Biochemistry , vol.42 , pp. 2907-2915
    • Rubach, J.K.1    Plapp, B.V.2
  • 19
    • 4444371260 scopus 로고    scopus 로고
    • Anticorrelated motions as a driving force in enzyme catalysis: the dehygrogenase reaction
    • Luo J., and Bruice T.C. Anticorrelated motions as a driving force in enzyme catalysis: the dehygrogenase reaction. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 13152-13156
    • (2004) Proc. Natl. Acad. Sci. U. S. A. , vol.101 , pp. 13152-13156
    • Luo, J.1    Bruice, T.C.2
  • 22
    • 0020771265 scopus 로고
    • Dynamics of a small globular proteins in terms of low-frequency vibrational modes
    • Go N., Noguti T., and Nishikawa T. Dynamics of a small globular proteins in terms of low-frequency vibrational modes. Proc. Natl. Acad. Sci. U. S. A. 80 (1983) 3696-3700
    • (1983) Proc. Natl. Acad. Sci. U. S. A. , vol.80 , pp. 3696-3700
    • Go, N.1    Noguti, T.2    Nishikawa, T.3
  • 23
    • 0000991642 scopus 로고
    • Harmonic dynamics of proteins: normal mode and fluctuations in bovine pancreatic trypsin inhibitor
    • Brooks B., and Karplus M. Harmonic dynamics of proteins: normal mode and fluctuations in bovine pancreatic trypsin inhibitor. Proc. Natl. Acad. Sci. U. S. A. 80 (1983) 6571-6575
    • (1983) Proc. Natl. Acad. Sci. U. S. A. , vol.80 , pp. 6571-6575
    • Brooks, B.1    Karplus, M.2
  • 24
    • 0022419152 scopus 로고
    • Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme
    • Levitt M., Sander C., and Stern P.S. Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme. J. Mol. Biol. 181 (1985) 423-447
    • (1985) J. Mol. Biol. , vol.181 , pp. 423-447
    • Levitt, M.1    Sander, C.2    Stern, P.S.3
  • 25
    • 0025066772 scopus 로고
    • Normal mode analysis of human lysozyme: study of the relative motion of the two domains and characterization of the harmonic motion
    • Gibrat J.F., and Go N. Normal mode analysis of human lysozyme: study of the relative motion of the two domains and characterization of the harmonic motion. Proteins 8 (1990) 258-279
    • (1990) Proteins , vol.8 , pp. 258-279
    • Gibrat, J.F.1    Go, N.2
  • 26
    • 0029560322 scopus 로고
    • Hinge-bending motion in citrate synthase arising from normal mode calculations
    • Marques O., and Sanejouand Y.H. Hinge-bending motion in citrate synthase arising from normal mode calculations. Proteins 23 (1995) 557-560
    • (1995) Proteins , vol.23 , pp. 557-560
    • Marques, O.1    Sanejouand, Y.H.2
  • 27
    • 0029835942 scopus 로고    scopus 로고
    • A comparative study of dynamic structures between phage 434 cro and repressor proteins by normal mode analysis
    • Wako H., Tachikawa M., and Ogawa A. A comparative study of dynamic structures between phage 434 cro and repressor proteins by normal mode analysis. Proteins 26 (1996) 72-80
    • (1996) Proteins , vol.26 , pp. 72-80
    • Wako, H.1    Tachikawa, M.2    Ogawa, A.3
  • 28
    • 0030004936 scopus 로고    scopus 로고
    • Analysis of the low frequency normal modes of the T-state of aspartate transcarbamylase
    • Thomas A., Field M.J., and Perahia D. Analysis of the low frequency normal modes of the T-state of aspartate transcarbamylase. J. Mol. Biol. 257 (1996) 1070-1087
    • (1996) J. Mol. Biol. , vol.257 , pp. 1070-1087
    • Thomas, A.1    Field, M.J.2    Perahia, D.3
  • 29
    • 0032533790 scopus 로고    scopus 로고
    • Analysis of domain motions by approximate normal mode calculations
    • Hinsen K. Analysis of domain motions by approximate normal mode calculations. Proteins 33 (1998) 417-429
    • (1998) Proteins , vol.33 , pp. 417-429
    • Hinsen, K.1
  • 30
    • 0033117937 scopus 로고    scopus 로고
    • Investigating protein dynamics in collective coordinate space
    • Kitao A., and Go N. Investigating protein dynamics in collective coordinate space. Curr. Opin. Struck. Biol. 9 (1999) 164-169
    • (1999) Curr. Opin. Struck. Biol. , vol.9 , pp. 164-169
    • Kitao, A.1    Go, N.2
  • 31
    • 0033548074 scopus 로고    scopus 로고
    • Enzyme specificity under dynamic control: a normal mode analysis of α-Lytic protease
    • Miller D.W., and Agard D.A. Enzyme specificity under dynamic control: a normal mode analysis of α-Lytic protease. J. Mol. Biol. 286 (1999) 267-278
    • (1999) J. Mol. Biol. , vol.286 , pp. 267-278
    • Miller, D.W.1    Agard, D.A.2
  • 32
    • 0033856299 scopus 로고    scopus 로고
    • Significance of a two-domain structure in subunits of phycobiliproteins revealed by the normal mode analysis
    • Kikuchi H., Wako H., Yura K., Go M., and Mimuro M. Significance of a two-domain structure in subunits of phycobiliproteins revealed by the normal mode analysis. Biophys. J. 79 (2000) 1587-1600
    • (2000) Biophys. J. , vol.79 , pp. 1587-1600
    • Kikuchi, H.1    Wako, H.2    Yura, K.3    Go, M.4    Mimuro, M.5
  • 33
    • 0034127361 scopus 로고    scopus 로고
    • Collective protein dynamics in relation to function
    • Berendsen H.J.C., and Hayward S. Collective protein dynamics in relation to function. Curr. Opin. Struck. Biol. 10 (2000) 165-169
    • (2000) Curr. Opin. Struck. Biol. , vol.10 , pp. 165-169
    • Berendsen, H.J.C.1    Hayward, S.2
  • 34
    • 0037436340 scopus 로고    scopus 로고
    • Mega-Dalton biomolecular motion captured from electron microscopy reconstructions
    • Chacon P., Tama F., and Wriggers W. Mega-Dalton biomolecular motion captured from electron microscopy reconstructions. J. Mol. Biol. 326 (2003) 485-492
    • (2003) J. Mol. Biol. , vol.326 , pp. 485-492
    • Chacon, P.1    Tama, F.2    Wriggers, W.3
  • 35
    • 0042424707 scopus 로고    scopus 로고
    • Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
    • Tama F., Valle M., Frank J., and Brooks III C.L. Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 9319-9323
    • (2003) Proc. Natl. Acad. Sci. U. S. A. , vol.100 , pp. 9319-9323
    • Tama, F.1    Valle, M.2    Frank, J.3    Brooks III, C.L.4
  • 36
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • Tama F., and Sanejouand Y.-H. Conformational change of proteins arising from normal mode calculations. Protein Eng. 14 (2001) 1-6
    • (2001) Protein Eng. , vol.14 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.-H.2
  • 37
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Tirion M.M. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 77 (1996) 1905-1908
    • (1996) Phys. Rev. Lett. , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 39
    • 0043235788 scopus 로고    scopus 로고
    • Protein promoting vibrations in enzyme catalysis-A conserved evolutionary motif
    • Mincer J.S., and Schwartz S.D. Protein promoting vibrations in enzyme catalysis-A conserved evolutionary motif. J. Proteome Res. 2 (2003) 437-439
    • (2003) J. Proteome Res. , vol.2 , pp. 437-439
    • Mincer, J.S.1    Schwartz, S.D.2
  • 40
    • 0037012441 scopus 로고    scopus 로고
    • Identification of a protein-promoting vibration in the reaction catalyzed by horse liver alcohol dehydrogenase
    • Caratzoulas S., Mincer J.S., and Schwartz S.D. Identification of a protein-promoting vibration in the reaction catalyzed by horse liver alcohol dehydrogenase. J. Am. Chem. Soc. 124 (2002) 3270-3276
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 3270-3276
    • Caratzoulas, S.1    Mincer, J.S.2    Schwartz, S.D.3
  • 41
    • 0037426823 scopus 로고    scopus 로고
    • A computational method to identify residues important in creating a protein promoting vibration in enzymes
    • Mincer J.S., and Schwartz S.D. A computational method to identify residues important in creating a protein promoting vibration in enzymes. J. Phys. Chem., B 107 (2003) 366-371
    • (2003) J. Phys. Chem., B , vol.107 , pp. 366-371
    • Mincer, J.S.1    Schwartz, S.D.2


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