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Volumn 14, Issue 5, 2010, Pages 636-643

Choreographing an enzyme's dance

Author keywords

[No Author keywords available]

Indexed keywords

CYCLOPHILIN A; ENZYME; HYDROGEN; PURINE NUCLEOSIDE PHOSPHORYLASE;

EID: 77957753399     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2010.08.007     Document Type: Review
Times cited : (78)

References (55)
  • 1
    • 37249032102 scopus 로고    scopus 로고
    • Dynamic personalities of proteins
    • Henzler-Wildman K., Kern D. Dynamic personalities of proteins. Nature 2007, 450:964-972.
    • (2007) Nature , vol.450 , pp. 964-972
    • Henzler-Wildman, K.1    Kern, D.2
  • 2
    • 45849108388 scopus 로고    scopus 로고
    • How enzymes work
    • Ringe D., Petsko G.A. How enzymes work. Science 2008, 320:1428-1429.
    • (2008) Science , vol.320 , pp. 1428-1429
    • Ringe, D.1    Petsko, G.A.2
  • 3
    • 0346726109 scopus 로고    scopus 로고
    • How enzymes work: analysis by modern rate theory and computer simulations
    • Garcia-Viloca M., Gao J., Karplus M., Truhlar D.G. How enzymes work: analysis by modern rate theory and computer simulations. Science 2004, 303:186-195.
    • (2004) Science , vol.303 , pp. 186-195
    • Garcia-Viloca, M.1    Gao, J.2    Karplus, M.3    Truhlar, D.G.4
  • 4
    • 77951226274 scopus 로고    scopus 로고
    • At the dawn of the 21st century: is dynamics the missing link for understanding enzyme catalysis?
    • Kamerlin S.C.L., Warshel A. At the dawn of the 21st century: is dynamics the missing link for understanding enzyme catalysis?. Protein Struct Funct Bioinform 2010, 78:1339-1375.
    • (2010) Protein Struct Funct Bioinform , vol.78 , pp. 1339-1375
    • Kamerlin, S.C.L.1    Warshel, A.2
  • 5
    • 70350453758 scopus 로고    scopus 로고
    • Enzyme millisecond conformational dynamics do not catalyze the chemical step
    • Pisliakov A.V., Cao J., Kamerlin S.C.L., Warshel A. Enzyme millisecond conformational dynamics do not catalyze the chemical step. Proc Natl Acad Sci U S A 2009, 106:17359-17364.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 17359-17364
    • Pisliakov, A.V.1    Cao, J.2    Kamerlin, S.C.L.3    Warshel, A.4
  • 7
    • 0026320866 scopus 로고
    • The energy landscapes and motions of proteins
    • Frauenfelder H., Sligar S.G., Wolynes P.G. The energy landscapes and motions of proteins. Science 1991, 254:1598-1603.
    • (1991) Science , vol.254 , pp. 1598-1603
    • Frauenfelder, H.1    Sligar, S.G.2    Wolynes, P.G.3
  • 8
    • 68049085675 scopus 로고    scopus 로고
    • A 21(st) century revisionist's view at a turning point in enzymology
    • Nagel Z.D., Klinman J.P. A 21(st) century revisionist's view at a turning point in enzymology. Nat Chem Biol 2009, 5:543-550.
    • (2009) Nat Chem Biol , vol.5 , pp. 543-550
    • Nagel, Z.D.1    Klinman, J.P.2
  • 9
    • 0028153517 scopus 로고
    • Extremely large isotope effects in the soybean lipoxygenase-linoleic acid reaction
    • Glickman M.H., Wiseman J.S., Klinman J.P. Extremely large isotope effects in the soybean lipoxygenase-linoleic acid reaction. J Am Chem Soc 1994, 116:793-794.
    • (1994) J Am Chem Soc , vol.116 , pp. 793-794
    • Glickman, M.H.1    Wiseman, J.S.2    Klinman, J.P.3
  • 10
    • 0037123216 scopus 로고    scopus 로고
    • Temperature-dependent isotope effects in soybean lipoxygenase-1: correlating hydrogen tunneling with protein dynamics
    • Knapp M.J., Rickert K., Klinman J.P. Temperature-dependent isotope effects in soybean lipoxygenase-1: correlating hydrogen tunneling with protein dynamics. J Am Chem Soc 2002, 124:3865-3874.
    • (2002) J Am Chem Soc , vol.124 , pp. 3865-3874
    • Knapp, M.J.1    Rickert, K.2    Klinman, J.P.3
  • 11
    • 39549094013 scopus 로고    scopus 로고
    • Enzyme structure and dynamics affect hydrogen tunneling: the impact of a remote side chain (1553) in soybean lipoxygenase-1
    • Meyer M.P., Tomchick D.R., Klinman J.P. Enzyme structure and dynamics affect hydrogen tunneling: the impact of a remote side chain (1553) in soybean lipoxygenase-1. Proc Natl Acad Sci U S A 2008, 105:1146-1151.
    • (2008) Proc Natl Acad Sci U S A , vol.105 , pp. 1146-1151
    • Meyer, M.P.1    Tomchick, D.R.2    Klinman, J.P.3
  • 12
    • 28644449439 scopus 로고    scopus 로고
    • Modeling temperature dependent kinetic isotope effects for hydrogen transfer in a series of soybean lipoxygenase mutants: the effect of anharmonicity upon transfer distance
    • Meyer M.P., Klinman J.P. Modeling temperature dependent kinetic isotope effects for hydrogen transfer in a series of soybean lipoxygenase mutants: the effect of anharmonicity upon transfer distance. Chem Phys 2005, 319:283-296.
    • (2005) Chem Phys , vol.319 , pp. 283-296
    • Meyer, M.P.1    Klinman, J.P.2
  • 13
    • 0033519723 scopus 로고    scopus 로고
    • Enzyme dynamics and hydrogen tunnelling in a thermophilic alcohol dehydrogenase
    • Kohen A., Cannio R., Bartolucci S., Klinman J.P. Enzyme dynamics and hydrogen tunnelling in a thermophilic alcohol dehydrogenase. Nature 1999, 399:496-499.
    • (1999) Nature , vol.399 , pp. 496-499
    • Kohen, A.1    Cannio, R.2    Bartolucci, S.3    Klinman, J.P.4
  • 14
    • 3042709505 scopus 로고    scopus 로고
    • Thermal-activated protein mobility and its correlation with catalysis in thermophilic alcohol dehydrogenase
    • Liang Z.X., Lee T., Resing K.A., Ahn N.G., Klinman J.P. Thermal-activated protein mobility and its correlation with catalysis in thermophilic alcohol dehydrogenase. Proc Natl Acad Sci U S A 2004, 101:9556-9561.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 9556-9561
    • Liang, Z.X.1    Lee, T.2    Resing, K.A.3    Ahn, N.G.4    Klinman, J.P.5
  • 15
    • 33750441144 scopus 로고    scopus 로고
    • Coordinated effects of distal mutations on environmentally coupled tunneling in dihydrofolate reductase
    • Wang L., Goodey N.M., Benkovic S.J., Kohen A. Coordinated effects of distal mutations on environmentally coupled tunneling in dihydrofolate reductase. Proc Natl Acad Sci U S A 2006, 103:15753-15758.
    • (2006) Proc Natl Acad Sci U S A , vol.103 , pp. 15753-15758
    • Wang, L.1    Goodey, N.M.2    Benkovic, S.J.3    Kohen, A.4
  • 17
    • 33748781457 scopus 로고    scopus 로고
    • The dynamic energy landscape of dihydrofolate reductase catalysis
    • Boehr D.D., McElheny D., Dyson H.J., Wright P.E. The dynamic energy landscape of dihydrofolate reductase catalysis. Science 2006, 313:1638-1642.
    • (2006) Science , vol.313 , pp. 1638-1642
    • Boehr, D.D.1    McElheny, D.2    Dyson, H.J.3    Wright, P.E.4
  • 19
    • 35348956350 scopus 로고    scopus 로고
    • Enzymatic transition state theory and transition state analogue design
    • Schramm V.L. Enzymatic transition state theory and transition state analogue design. J Biol Chem 2007, 282:28297-28300.
    • (2007) J Biol Chem , vol.282 , pp. 28297-28300
    • Schramm, V.L.1
  • 20
    • 68049093016 scopus 로고    scopus 로고
    • Enzymatic transition states and dynamic motion in barrier crossing
    • Schwartz S.D., Schramm V.L. Enzymatic transition states and dynamic motion in barrier crossing. Nat Chem Biol 2009, 5:552-559.
    • (2009) Nat Chem Biol , vol.5 , pp. 552-559
    • Schwartz, S.D.1    Schramm, V.L.2
  • 22
    • 36849039429 scopus 로고    scopus 로고
    • A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
    • Henzler-Wildman K.A., Lei M., Thai V., Kerns S.J., Karplus M., Kern D. A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 2007, 450:913-916.
    • (2007) Nature , vol.450 , pp. 913-916
    • Henzler-Wildman, K.A.1    Lei, M.2    Thai, V.3    Kerns, S.J.4    Karplus, M.5    Kern, D.6
  • 24
    • 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., Alber T. Hidden alternative structures of proline isomerase essential for catalysis. Nature 2009, 462:669-673.
    • (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
  • 26
    • 0035937443 scopus 로고    scopus 로고
    • Two-state allosteric behavior in a single-domain signaling protein
    • Volkman B.F., Lipson D., Wemmer D.E., Kern D. Two-state allosteric behavior in a single-domain signaling protein. Science 2001, 291:2429-2433.
    • (2001) Science , vol.291 , pp. 2429-2433
    • Volkman, B.F.1    Lipson, D.2    Wemmer, D.E.3    Kern, D.4
  • 28
    • 70449769332 scopus 로고    scopus 로고
    • Observing biological dynamics at atomic resolution using NMR
    • Mittermaier A.K., Kay L.E. Observing biological dynamics at atomic resolution using NMR. Trends Biochem Sci 2009, 34:601-611.
    • (2009) Trends Biochem Sci , vol.34 , pp. 601-611
    • Mittermaier, A.K.1    Kay, L.E.2
  • 29
    • 0033577288 scopus 로고    scopus 로고
    • A relaxation-compensated Carr-Purcell-Meiboom-Gill sequence for characterizing chemical exchange by NMR spectroscopy
    • Loria J.P., Rance M., Palmer A.G. A relaxation-compensated Carr-Purcell-Meiboom-Gill sequence for characterizing chemical exchange by NMR spectroscopy. J Am Chem Soc 1999, 121:2331-2332.
    • (1999) J Am Chem Soc , vol.121 , pp. 2331-2332
    • Loria, J.P.1    Rance, M.2    Palmer, A.G.3
  • 32
    • 77950432266 scopus 로고    scopus 로고
    • Atomically detailed simulation of the recovery stroke in myosin by Milestoning
    • Elber R., West A. Atomically detailed simulation of the recovery stroke in myosin by Milestoning. Proc Natl Acad Sci U S A 2010, 107:5001-5005.
    • (2010) Proc Natl Acad Sci U S A , vol.107 , pp. 5001-5005
    • Elber, R.1    West, A.2
  • 34
    • 58149299971 scopus 로고    scopus 로고
    • Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
    • Laio A., Gervasio F.L. Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science. Rep Prog Phys 2008, 71:22.
    • (2008) Rep Prog Phys , vol.71 , pp. 22
    • Laio, A.1    Gervasio, F.L.2
  • 35
    • 34548494273 scopus 로고    scopus 로고
    • Transition path sampling simulations of biological systems
    • Springer-Verlag, Berlin, 291-317, Atomistic Approaches in Modern Biology: From Quantum Chemistry to Molecular Simulations
    • Dellago C., Bolhuis P.G. Transition path sampling simulations of biological systems. Topics in Current Chemistry 2007, vol 268. Springer-Verlag, Berlin, 291-317.
    • (2007) Topics in Current Chemistry , vol.268
    • Dellago, C.1    Bolhuis, P.G.2
  • 36
    • 77951688892 scopus 로고    scopus 로고
    • Transition-path theory and path-finding algorithms for the study of rare events
    • Vanden-Eijnden E.W.E. Transition-path theory and path-finding algorithms for the study of rare events. Annu Rev Phys Chem 2010, 61:391-420.
    • (2010) Annu Rev Phys Chem , vol.61 , pp. 391-420
    • Vanden-Eijnden, E.W.E.1
  • 37
    • 20544464457 scopus 로고    scopus 로고
    • How well can simulation predict protein folding kinetics and thermodynamics?
    • Snow C.D., Sorin E.J., Rhee Y.M., Pande V.S. How well can simulation predict protein folding kinetics and thermodynamics?. Annu Rev Biophys Biomol Struct 2005, 34:43-69.
    • (2005) Annu Rev Biophys Biomol Struct , vol.34 , pp. 43-69
    • Snow, C.D.1    Sorin, E.J.2    Rhee, Y.M.3    Pande, V.S.4
  • 38
    • 33746255471 scopus 로고    scopus 로고
    • String method in collective variables: minimum free energy paths and isocommittor surfaces
    • Maragliano L., Fischer A., Vanden-Eijnden E., Ciccotti G. String method in collective variables: minimum free energy paths and isocommittor surfaces. J Chem Phys 2006, 125:15.
    • (2006) J Chem Phys , vol.125 , pp. 15
    • Maragliano, L.1    Fischer, A.2    Vanden-Eijnden, E.3    Ciccotti, G.4
  • 40
    • 0028455053 scopus 로고
    • Targeted molecular-dynamics-a new approach for searching pathways of conformational transitions
    • Schlitter J., Engels M., Kruger P. Targeted molecular-dynamics-a new approach for searching pathways of conformational transitions. J Mol Graph 1994, 12:84-89.
    • (1994) J Mol Graph , vol.12 , pp. 84-89
    • Schlitter, J.1    Engels, M.2    Kruger, P.3
  • 41
    • 69449087027 scopus 로고    scopus 로고
    • Segmented transition pathway of the signaling protein nitrogen regulatory protein C
    • Lei M., Velos J., Gardino A., Kivenson A., Karplus M., Kern D. Segmented transition pathway of the signaling protein nitrogen regulatory protein C. J Mol Biol 2009, 392:823-836.
    • (2009) J Mol Biol , vol.392 , pp. 823-836
    • Lei, M.1    Velos, J.2    Gardino, A.3    Kivenson, A.4    Karplus, M.5    Kern, D.6
  • 42
    • 62549151081 scopus 로고    scopus 로고
    • Protein conformational transitions: the closure mechanism of a kinase explored by atomistic simulations
    • Berteotti A., Cavalli A., Branduardi D., Gervasio F.L., Recanatini M., Parrinello M. Protein conformational transitions: the closure mechanism of a kinase explored by atomistic simulations. J Am Chem Soc 2009, 131:244-250.
    • (2009) J Am Chem Soc , vol.131 , pp. 244-250
    • Berteotti, A.1    Cavalli, A.2    Branduardi, D.3    Gervasio, F.L.4    Recanatini, M.5    Parrinello, M.6
  • 43
    • 66049142191 scopus 로고    scopus 로고
    • Revisiting the finite temperature string method for the calculation of reaction tubes and free energies
    • Vanden-Eijnden E., Venturoli M. Revisiting the finite temperature string method for the calculation of reaction tubes and free energies. J Chem Phys 2009, 130:17.
    • (2009) J Chem Phys , vol.130 , pp. 17
    • Vanden-Eijnden, E.1    Venturoli, M.2
  • 44
  • 46
    • 16244419691 scopus 로고    scopus 로고
    • Enzyme dynamics during catalysis measured by NMR spectroscopy
    • Elsevier Academic Press Inc, 507-524, Nuclear Magnetic Resonance of Biological Macromolecules, Part C
    • Kern D., Eisenmesser E.Z., Wolf-Watz M. Enzyme dynamics during catalysis measured by NMR spectroscopy. Methods in Enzymology 2005, vol 394. Elsevier Academic Press Inc, 507-524.
    • (2005) Methods in Enzymology , vol.394
    • Kern, D.1    Eisenmesser, E.Z.2    Wolf-Watz, M.3
  • 49
    • 43049123356 scopus 로고    scopus 로고
    • Advances in laboratory evolution of enzymes
    • Bershtein S., Tawfik D.S. Advances in laboratory evolution of enzymes. Curr Opin Chem Biol 2008, 12:151-158.
    • (2008) Curr Opin Chem Biol , vol.12 , pp. 151-158
    • Bershtein, S.1    Tawfik, D.S.2
  • 50
    • 56149121547 scopus 로고    scopus 로고
    • Directed enzyme evolution via small and effective neutral drift libraries
    • Gupta R.D., Tawfik D.S. Directed enzyme evolution via small and effective neutral drift libraries. Nat Methods 2008, 5:939-942.
    • (2008) Nat Methods , vol.5 , pp. 939-942
    • Gupta, R.D.1    Tawfik, D.S.2
  • 51
    • 68049106179 scopus 로고    scopus 로고
    • Directed evolution drives the next generation of biocatalysts
    • Turner N.J. Directed evolution drives the next generation of biocatalysts. Nat Chem Biol 2009, 5:568-574.
    • (2009) Nat Chem Biol , vol.5 , pp. 568-574
    • Turner, N.J.1
  • 53
    • 77649271939 scopus 로고    scopus 로고
    • Evolutionary optimization of computationally designed enzymes: kemp eliminases of the KE07 series
    • Khersonsky O., Rothlisberger D., Dym O., Albeck S., Jackson C.J., Baker D., Tawfik D.S. Evolutionary optimization of computationally designed enzymes: kemp eliminases of the KE07 series. J Mol Biol 2010, 396:1025-1042.
    • (2010) J Mol Biol , vol.396 , pp. 1025-1042
    • Khersonsky, O.1    Rothlisberger, D.2    Dym, O.3    Albeck, S.4    Jackson, C.J.5    Baker, D.6    Tawfik, D.S.7
  • 54
    • 67650287695 scopus 로고    scopus 로고
    • In the light of directed evolution: pathways of adaptive protein evolution
    • Bloom J.D., Arnold F.H. In the light of directed evolution: pathways of adaptive protein evolution. Proc Natl Acad Sci U S A 2009, 106:9995-10000.
    • (2009) Proc Natl Acad Sci U S A , vol.106 , pp. 9995-10000
    • Bloom, J.D.1    Arnold, F.H.2
  • 55
    • 73949127824 scopus 로고    scopus 로고
    • Free energy and kinetics of conformational transitions from Voronoi tessellated milestoning with restraining potentials
    • Maragliano L., Vanden-Eijnden E., Roux B. Free energy and kinetics of conformational transitions from Voronoi tessellated milestoning with restraining potentials. J Chem Theor Comput 2009, 5:2589-2594.
    • (2009) J Chem Theor Comput , vol.5 , pp. 2589-2594
    • Maragliano, L.1    Vanden-Eijnden, E.2    Roux, B.3


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