메뉴 건너뛰기




Volumn 450, Issue 7171, 2007, Pages 913-916

A hierarchy of timescales in protein dynamics is linked to enzyme catalysis

Author keywords

[No Author keywords available]

Indexed keywords

ADENYLATE KINASE; ENZYME; PROTEIN;

EID: 36849039429     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature06407     Document Type: Article
Times cited : (897)

References (47)
  • 1
    • 4744343045 scopus 로고    scopus 로고
    • Linkage between dynamics and catalysis in a thermophilicmesophilic enzyme pair
    • Wolf-Watz, M. et al. Linkage between dynamics and catalysis in a thermophilicmesophilic enzyme pair. Nature Struct. Mol. Biol. 11, 945-949 (2004).
    • (2004) Nature Struct. Mol. Biol , vol.11 , pp. 945-949
    • Wolf-Watz, M.1
  • 2
    • 33748619206 scopus 로고    scopus 로고
    • An NMR perspective on enzyme dynamics
    • Boehr, D. D., Dyson, H. J. & Wright, P. E. An NMR perspective on enzyme dynamics. Chem. Rev. 106, 3055-3079 (2006).
    • (2006) Chem. Rev , vol.106 , pp. 3055-3079
    • Boehr, D.D.1    Dyson, H.J.2    Wright, P.E.3
  • 4
    • 36849048228 scopus 로고    scopus 로고
    • Intrinsic motions along an enzymatic reaction trajectory
    • online publication doi:10.1030/nature06410 18 November
    • Henzler-Wildman, K. et al. Intrinsic motions along an enzymatic reaction trajectory. Nature advanced online publication doi:10.1030/nature06410 (18 November 2007).
    • (2007) Nature advanced
    • Henzler-Wildman, K.1
  • 7
    • 33748601471 scopus 로고    scopus 로고
    • Tunneling and dynamics in enzymatic hydride transfer
    • Nagel, Z. D. & Klinman, J. P. Tunneling and dynamics in enzymatic hydride transfer. Chem. Rev. 106, 3095-3118 (2006).
    • (2006) Chem. Rev , vol.106 , pp. 3095-3118
    • Nagel, Z.D.1    Klinman, J.P.2
  • 8
    • 0033598719 scopus 로고    scopus 로고
    • Structural distribution of stability in a thermophilic enzyme
    • Hollien, J. & Marqusee, S. Structural distribution of stability in a thermophilic enzyme. Proc. Natl Acad. Sci. USA 96, 13674-13678 (1999).
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 13674-13678
    • Hollien, J.1    Marqusee, S.2
  • 9
    • 2542487312 scopus 로고    scopus 로고
    • Multiple time scale backbone dynamics of homologous thermophilic and mesophilic ribonuclease HI enzymes
    • Butterwick, J. A. et al. Multiple time scale backbone dynamics of homologous thermophilic and mesophilic ribonuclease HI enzymes. J. Mol. Biol. 339, 855-871 (2004).
    • (2004) J. Mol. Biol , vol.339 , pp. 855-871
    • Butterwick, J.A.1
  • 10
    • 0038068865 scopus 로고    scopus 로고
    • FAST-Modelfree: A program for rapid automated analysis of solution NMR spin-relaxation data
    • Cole, R. & Loria, J. P. FAST-Modelfree: A program for rapid automated analysis of solution NMR spin-relaxation data. J. Biomol. NMR 26, 203-213 (2003).
    • (2003) J. Biomol. NMR , vol.26 , pp. 203-213
    • Cole, R.1    Loria, J.P.2
  • 11
    • 33646719091 scopus 로고
    • Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity
    • Lipari, G. & Szabo, A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J. Am. Chem. Soc. 104, 4546-4559 (1982).
    • (1982) J. Am. Chem. Soc , vol.104 , pp. 4546-4559
    • Lipari, G.1    Szabo, A.2
  • 12
    • 0028941877 scopus 로고
    • Backbone dynamics of Escherichia coli ribonuclease H - correlations with structure and function in an active enzyme
    • Mandel, A. M., Akke, M. & Palmer, A. G. Backbone dynamics of Escherichia coli ribonuclease H - correlations with structure and function in an active enzyme. J. Mol. Biol. 246, 144-163 (1995).
    • (1995) J. Mol. Biol , vol.246 , pp. 144-163
    • Mandel, A.M.1    Akke, M.2    Palmer, A.G.3
  • 13
    • 0023664015 scopus 로고
    • Circular-dichroism investigation of Escherichia coli adenylate kinase
    • Monnot, M. et al. Circular-dichroism investigation of Escherichia coli adenylate kinase. J. Biol. Chem. 262, 2502-2506 (1987).
    • (1987) J. Biol. Chem , vol.262 , pp. 2502-2506
    • Monnot, M.1
  • 14
    • 0030445011 scopus 로고    scopus 로고
    • Dynamics of ribonuclease H: Temperature dependence of motions on multiple time scales
    • Mandel, A. M., Akke, M. & Palmer, A. G. Dynamics of ribonuclease H: Temperature dependence of motions on multiple time scales. Biochemistry 35, 16009-16023 (1996).
    • (1996) Biochemistry , vol.35 , pp. 16009-16023
    • Mandel, A.M.1    Akke, M.2    Palmer, A.G.3
  • 15
    • 0034981542 scopus 로고    scopus 로고
    • Structural basis of thermostability in hyperthermophilic proteins, or "there's more than one way to skin a cat
    • Petsko, G. A. Structural basis of thermostability in hyperthermophilic proteins, or "there's more than one way to skin a cat". Methods Enzymol. 334, 469-478 (2001).
    • (2001) Methods Enzymol , vol.334 , pp. 469-478
    • Petsko, G.A.1
  • 16
    • 33144487234 scopus 로고    scopus 로고
    • Roles of static and dynamic domains in stability and catalysis of adenylate kinase
    • Bae, E. & Phillips, G. N. Roles of static and dynamic domains in stability and catalysis of adenylate kinase. Proc. Natl Acad. Sci. USA 103, 2132-2137 (2006).
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 2132-2137
    • Bae, E.1    Phillips, G.N.2
  • 17
  • 18
    • 0035427398 scopus 로고    scopus 로고
    • Protein flexibility predictions using graph theory
    • Jacobs, D. J., Rader, A. J., Kuhn, L. A. & Thorpe, M. F. Protein flexibility predictions using graph theory. Proteins 44, 150-165 (2001).
    • (2001) Proteins , vol.44 , pp. 150-165
    • Jacobs, D.J.1    Rader, A.J.2    Kuhn, L.A.3    Thorpe, M.F.4
  • 19
    • 0037022347 scopus 로고    scopus 로고
    • Flexibility and packing in proteins
    • Halle, B. Flexibility and packing in proteins. Proc. Natl Acad. Sci. USA 99, 1274-1279 (2002).
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 1274-1279
    • Halle, B.1
  • 20
    • 24644483073 scopus 로고    scopus 로고
    • Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase
    • Maragakis, P. & Karplus, M. Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase. J. Mol. Biol. 352, 807-822 (2005).
    • (2005) J. Mol. Biol , vol.352 , pp. 807-822
    • Maragakis, P.1    Karplus, M.2
  • 21
    • 29444446536 scopus 로고    scopus 로고
    • Concordance of residual dipolar coupling, backbone order parameters and crystallographic B-factors for a small α/β protein: A unified picture of high probability, fast atomic motions in proteins
    • Clore, G. M. & Schweiters, C. D. Concordance of residual dipolar coupling, backbone order parameters and crystallographic B-factors for a small α/β protein: A unified picture of high probability, fast atomic motions in proteins. J. Mol. Biol. 355, 879-886 (2006).
    • (2006) J. Mol. Biol , vol.355 , pp. 879-886
    • Clore, G.M.1    Schweiters, C.D.2
  • 22
    • 33746565283 scopus 로고    scopus 로고
    • Molecular dynamics of apo-adenylate kinase: A principal component analysis
    • Lou, H. F. & Cukier, R. I. Molecular dynamics of apo-adenylate kinase: A principal component analysis. J. Phys. Chem. B 110, 12796-12808 (2006).
    • (2006) J. Phys. Chem. B , vol.110 , pp. 12796-12808
    • Lou, H.F.1    Cukier, R.I.2
  • 23
    • 2542507857 scopus 로고    scopus 로고
    • Thermodynamic interpretation of NMR relaxation parameters in proteins in the presence of motional correlations
    • Prompers, J. J. & Bruschweiler, R. Thermodynamic interpretation of NMR relaxation parameters in proteins in the presence of motional correlations. J. Phys. Chem. B 104, 11416-11424 (2000).
    • (2000) J. Phys. Chem. B , vol.104 , pp. 11416-11424
    • Prompers, J.J.1    Bruschweiler, R.2
  • 25
    • 0242268469 scopus 로고    scopus 로고
    • Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins
    • Miyashita, O., Onuchic, J. N. & Wolynes, P. G. Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proc. Natl Acad. Sci. USA 100, 12570-12575 (2003).
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 12570-12575
    • Miyashita, O.1    Onuchic, J.N.2    Wolynes, P.G.3
  • 26
    • 0019438921 scopus 로고
    • The internal dynamics of globular-proteins
    • Karplus, M. & Mccammon, J. A. The internal dynamics of globular-proteins. CRC Crit. Rev. Biochem. 9, 293-349 (1981).
    • (1981) CRC Crit. Rev. Biochem , vol.9 , pp. 293-349
    • Karplus, M.1    Mccammon, J.A.2
  • 27
    • 84986512474 scopus 로고
    • CHARMM - a program for macromolecular energy, minimization, and dynamics calculations
    • Brooks, B. R. et al. CHARMM - a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4, 187-217 (1983).
    • (1983) J. Comp. Chem , vol.4 , pp. 187-217
    • Brooks, B.R.1
  • 28
    • 0042121237 scopus 로고    scopus 로고
    • Multiple sequence alignment with the Clustal series of programs
    • Chenna, R. et al. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31, 3497-3500 (2003).
    • (2003) Nucleic Acids Res , vol.31 , pp. 3497-3500
    • Chenna, R.1
  • 29
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • Koradi, R., Billeter, M. & Wuthrich, K. MOLMOL: A program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51-55 29-32 (1996).
    • (1996) J. Mol. Graph , vol.14
    • Koradi, R.1    Billeter, M.2    Wuthrich, K.3
  • 30
    • 0000127140 scopus 로고
    • Method for Estimating the Configurational Entropy of Macromolecules
    • Karplus, M. & Kushick, J. N. Method for Estimating the Configurational Entropy of Macromolecules. Macromolecules 14, 325-332 (1981).
    • (1981) Macromolecules , vol.14 , pp. 325-332
    • Karplus, M.1    Kushick, J.N.2
  • 31
    • 0033029875 scopus 로고    scopus 로고
    • Assessing potential bias in the determination of rotational correlation times of proteins by NMR relaxation
    • Lee, A. L. & Wand, A. J. Assessing potential bias in the determination of rotational correlation times of proteins by NMR relaxation. J. Biomol. NMR 13, 101-112 (1999).
    • (1999) J. Biomol. NMR , vol.13 , pp. 101-112
    • Lee, A.L.1    Wand, A.J.2
  • 32
    • 33645786604 scopus 로고    scopus 로고
    • Importance of the CMAP correction to the CHARMM22 protein force field: Dynamics of hen lysozyme
    • Buck, M., Bouguet-Bonnet, S., Pastor, R. W. & MacKerell, A. D. Importance of the CMAP correction to the CHARMM22 protein force field: Dynamics of hen lysozyme. Biophys. J. 90, L36-L38 (2006).
    • (2006) Biophys. J , vol.90
    • Buck, M.1    Bouguet-Bonnet, S.2    Pastor, R.W.3    MacKerell, A.D.4
  • 33
    • 0037150115 scopus 로고    scopus 로고
    • Domain flexibility in ligand-free and inhibitor-bound Escherichia coli adenylate kinase based on a mode-coupling analysis of N-15 spin relaxation
    • Shapiro, Y. E. et al. Domain flexibility in ligand-free and inhibitor-bound Escherichia coli adenylate kinase based on a mode-coupling analysis of N-15 spin relaxation. Biochemistry 41, 6271-6281 (2002).
    • (2002) Biochemistry , vol.41 , pp. 6271-6281
    • Shapiro, Y.E.1
  • 35
    • 0141502348 scopus 로고    scopus 로고
    • Characterization of the overall and local dynamics of a protein with intermediate rotational anisotropy: Differentiating between conformational exchange and anisotropic diffusion in the B3 domain of protein G
    • Hall, J. B. & Fushman, D. Characterization of the overall and local dynamics of a protein with intermediate rotational anisotropy: Differentiating between conformational exchange and anisotropic diffusion in the B3 domain of protein G. J. Biomol. NMR 27, 261-275 (2003).
    • (2003) J. Biomol. NMR , vol.27 , pp. 261-275
    • Hall, J.B.1    Fushman, D.2
  • 36
    • 0035996729 scopus 로고    scopus 로고
    • 15N NMR relaxation data of globular proteins using hydrodynamic calculations with HYDRONMR
    • 15N NMR relaxation data of globular proteins using hydrodynamic calculations with HYDRONMR. J. Biomol. NMR 23, 139-150 (2002).
    • (2002) J. Biomol. NMR , vol.23 , pp. 139-150
    • Bernado, P.1    de la Torre, J.G.2    Pons, M.3
  • 37
    • 0034328380 scopus 로고    scopus 로고
    • HYDRONMR: Prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations
    • de la Torre, J. G., Huertas, M. L. & Carrasco, B. HYDRONMR: Prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations. J. Magn. Reson. 147, 138-146 (2000).
    • (2000) J. Magn. Reson , vol.147 , pp. 138-146
    • de la Torre, J.G.1    Huertas, M.L.2    Carrasco, B.3
  • 38
    • 0033546403 scopus 로고    scopus 로고
    • Backbone dynamics and energetics of a calmodulin domain mutant exchanging between closed and open conformations
    • Evenas, J., Forsen, S., Malmendal, A. & Akke, M. Backbone dynamics and energetics of a calmodulin domain mutant exchanging between closed and open conformations. J. Mol. Biol. 289, 603-617 (1999).
    • (1999) J. Mol. Biol , vol.289 , pp. 603-617
    • Evenas, J.1    Forsen, S.2    Malmendal, A.3    Akke, M.4
  • 39
    • 0033945087 scopus 로고    scopus 로고
    • The role of backbone conformational heat capacity in protein stability: Temperature dependent dynamics of the B1 domain of Streptococcal protein G
    • Seewald, M. J. et al. The role of backbone conformational heat capacity in protein stability: Temperature dependent dynamics of the B1 domain of Streptococcal protein G. Protein Sci. 9, 1177-1193 (2000).
    • (2000) Protein Sci , vol.9 , pp. 1177-1193
    • Seewald, M.J.1
  • 40
    • 0035940465 scopus 로고    scopus 로고
    • Temperature dependence of dynamics and thermodynamics of the regulatory domain of human cardiac troponin C
    • Spyracopoulos, L. et al. Temperature dependence of dynamics and thermodynamics of the regulatory domain of human cardiac troponin C. Biochemistry 40, 12541-12551 (2001).
    • (2001) Biochemistry , vol.40 , pp. 12541-12551
    • Spyracopoulos, L.1
  • 41
    • 4444248119 scopus 로고    scopus 로고
    • Gated electron transfers and electron pathways in azurin: A NMR dynamic study at multiple fields and temperatures
    • Zhuravleva, A. V. et al. Gated electron transfers and electron pathways in azurin: A NMR dynamic study at multiple fields and temperatures. J. Mol. Biol. 342, 1599-1611 (2004).
    • (2004) J. Mol. Biol , vol.342 , pp. 1599-1611
    • Zhuravleva, A.V.1
  • 43
    • 0038037171 scopus 로고    scopus 로고
    • Temperature dependence of anisotropic protein backbone dynamics
    • Wang, T. Z., Cai, S. & Zuiderweg, E. R. P. Temperature dependence of anisotropic protein backbone dynamics. J. Am. Chem. Soc. 125, 8639-8643 (2003).
    • (2003) J. Am. Chem. Soc , vol.125 , pp. 8639-8643
    • Wang, T.Z.1    Cai, S.2    Zuiderweg, E.R.P.3
  • 44
    • 0037668073 scopus 로고    scopus 로고
    • Beyond the decoupling approximation in the model free approach for the interpretation of NMR relaxation of macromolecules in solution
    • Vugmeyster, L., Raleigh, D. P., Palmer, A. G. & Vugmeister, B. E. Beyond the decoupling approximation in the model free approach for the interpretation of NMR relaxation of macromolecules in solution. J. Am. Chem. Soc. 125, 8400-8404 (2003).
    • (2003) J. Am. Chem. Soc , vol.125 , pp. 8400-8404
    • Vugmeyster, L.1    Raleigh, D.P.2    Palmer, A.G.3    Vugmeister, B.E.4
  • 45
    • 0033525126 scopus 로고    scopus 로고
    • Temperature dependence of intramolecular dynamics of the basic leucine zipper of GCN4: Implications for the entropy of association with DNA
    • Bracken, C., Carr, P. A., Cavanagh, J. & Palmer, A. G. Temperature dependence of intramolecular dynamics of the basic leucine zipper of GCN4: Implications for the entropy of association with DNA. J. Mol. Biol. 285, 2133-2146 (1999).
    • (1999) J. Mol. Biol , vol.285 , pp. 2133-2146
    • Bracken, C.1    Carr, P.A.2    Cavanagh, J.3    Palmer, A.G.4
  • 46
    • 31944446215 scopus 로고    scopus 로고
    • Resolving the motional modes that code for RNA adaptation
    • Zhang, Q., Sun, X. Y., Watt, E. D. & Al-Hashimi, H. M. Resolving the motional modes that code for RNA adaptation. Science 311, 653-656 (2006).
    • (2006) Science , vol.311 , pp. 653-656
    • Zhang, Q.1    Sun, X.Y.2    Watt, E.D.3    Al-Hashimi, H.M.4
  • 47
    • 0036888353 scopus 로고    scopus 로고
    • Hayward, S. & Lee, R. A. Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50. J. Mol. Graph. Model. 21, 181-183 2002
    • Hayward, S. & Lee, R. A. Improvements in the analysis of domain motions in proteins from conformational change: DynDom version 1.50. J. Mol. Graph. Model. 21, 181-183 (2002).


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.