Abstract
The synergy between structure and dynamics is essential to the function of biological macromolecules. Thermally driven dynamics on different timescales have been experimentally observed or simulated, and a direct link between micro- to milli-second domain motions and enzymatic function has been established1,2,3,4. However, very little is understood about the connection of these functionally relevant, collective movements with local atomic fluctuations, which are much faster. Here we show that pico- to nano-second timescale atomic fluctuations in hinge regions of adenylate kinase facilitate the large-scale, slower lid motions that produce a catalytically competent state. The fast, local mobilities differ between a mesophilic and hyperthermophilic adenylate kinase, but are strikingly similar at temperatures at which enzymatic activity and free energy of folding are matched. The connection between different timescales and the corresponding amplitudes of motions in adenylate kinase and their linkage to catalytic function is likely to be a general characteristic of protein energy landscapes.
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References
Wolf-Watz, M. et al. Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair. Nature Struct. Mol. Biol. 11, 945ā949 (2004)
Boehr, D. D., Dyson, H. J. & Wright, P. E. An NMR perspective on enzyme dynamics. Chem. Rev. 106, 3055ā3079 (2006)
Austin, R. H., Beeson, K. W., Eisenstein, L., Frauenfelder, H. & Gunsalus, I. C. Dynamics of ligand binding to myoglobin. Biochemistry 14, 5355ā5373 (1975)
Henzler-Wildman, K. et al. Intrinsic motions along an enzymatic reaction trajectory. Nature advanced online publication. doi: 10.1030/nature06410 (18 November 2007)
Vitkup, D., Ringe, D., Petsko, G. A. & Karplus, M. Solvent mobility and the protein 'glass' transition. Nature Struct. Biol. 7, 34ā38 (2000)
Fenimore, P. W., Frauenfelder, H., McMahon, B. H. & Parak, F. G. Slaving: Solvent fluctuations dominate protein dynamics and functions. Proc. Natl Acad. Sci. USA 99, 16047ā16051 (2002)
Nagel, Z. D. & Klinman, J. P. Tunneling and dynamics in enzymatic hydride transfer. Chem. Rev. 106, 3095ā3118 (2006)
Hollien, J. & Marqusee, S. Structural distribution of stability in a thermophilic enzyme. Proc. Natl Acad. Sci. USA 96, 13674ā13678 (1999)
Butterwick, J. A. et al. Multiple time scale backbone dynamics of homologous thermophilic and mesophilic ribonuclease HI enzymes. J. Mol. Biol. 339, 855ā871 (2004)
Cole, R. & Loria, J. P. FAST-Modelfree: A program for rapid automated analysis of solution NMR spin-relaxation data. J. Biomol. NMR 26, 203ā213 (2003)
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, 4546ā4559 (1982)
Mandel, A. M., Akke, M. & Palmer, A. G. Backbone dynamics of Escherichia coli ribonuclease Hācorrelations with structure and function in an active enzyme. J. Mol. Biol. 246, 144ā163 (1995)
Monnot, M. et al. Circular-dichroism investigation of Escherichia coli adenylate kinase. J. Biol. Chem. 262, 2502ā2506 (1987)
Mandel, A. M., Akke, M. & Palmer, A. G. Dynamics of ribonuclease H: Temperature dependence of motions on multiple time scales. Biochemistry 35, 16009ā16023 (1996)
Petsko, G. A. Structural basis of thermostability in hyperthermophilic proteins, or āthere's more than one way to skin a catā. Methods Enzymol. 334, 469ā478 (2001)
Bae, E. & Phillips, G. N. Roles of static and dynamic domains in stability and catalysis of adenylate kinase. Proc. Natl Acad. Sci. USA 103, 2132ā2137 (2006)
Zhang, F. L. & Bruschweiler, R. Contact model for the prediction of NMR 15N-1H order parameters in globular proteins. J. Am. Chem. Soc. 124, 12654ā12655 (2002)
Jacobs, D. J., Rader, A. J., Kuhn, L. A. & Thorpe, M. F. Protein flexibility predictions using graph theory. Proteins 44, 150ā165 (2001)
Halle, B. Flexibility and packing in proteins. Proc. Natl Acad. Sci. USA 99, 1274ā1279 (2002)
Maragakis, P. & Karplus, M. Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase. J. Mol. Biol. 352, 807ā822 (2005)
Clore, G. M. & Schweiters, C. D. Concordance of residual dipolar coupling, backbone order parameters and crystallographic B-factors for a small Ī±/Ī² protein: A unified picture of high probability, fast atomic motions in proteins. J. Mol. Biol. 355, 879ā886 (2006)
Lou, H. F. & Cukier, R. I. Molecular dynamics of apo-adenylate kinase: A principal component analysis. J. Phys. Chem. B 110, 12796ā12808 (2006)
Prompers, J. J. & Bruschweiler, R. Thermodynamic interpretation of NMR relaxation parameters in proteins in the presence of motional correlations. J. Phys. Chem. B 104, 11416ā11424 (2000)
Temiz, N. A., Meirovitch, E. & Bahar, I. Escherichia coli adenylate kinase dynamics: Comparison of elastic network model modes with mode-coupling 15N-NMR relaxation data. Proteins 57, 468ā480 (2004)
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, 12570ā12575 (2003)
Karplus, M. & Mccammon, J. A. The internal dynamics of globular-proteins. CRC Crit. Rev. Biochem. 9, 293ā349 (1981)
Brooks, B. R. et al. CHARMM - a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4, 187ā217 (1983)
Chenna, R. et al. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31, 3497ā3500 (2003)
Koradi, R., Billeter, M. & Wuthrich, K. MOLMOL: A program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51ā55 29ā32 (1996)
Karplus, M. & Kushick, J. N. Method for Estimating the Configurational Entropy of Macromolecules. Macromolecules 14, 325ā332 (1981)
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, 101ā112 (1999)
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, L36āL38 (2006)
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, 6271ā6281 (2002)
Tugarinov, V., Shapiro, Y. E., Liang, Z. C., Freed, J. H. & Meirovitch, E. A novel view of domain flexibility in E. coli adenylate kinase based on structural mode-coupling 15N NMR relaxation. J. Mol. Biol. 315, 155ā170 (2002)
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, 261ā275 (2003)
Bernado, P., de la Torre, J. G. & Pons, M. Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic calculations with HYDRONMR. J. Biomol. NMR 23, 139ā150 (2002)
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, 138ā146 (2000)
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, 603ā617 (1999)
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, 1177ā1193 (2000)
Spyracopoulos, L. et al. Temperature dependence of dynamics and thermodynamics of the regulatory domain of human cardiac troponin C. Biochemistry 40, 12541ā12551 (2001)
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, 1599ā1611 (2004)
Chang, S. L. & Tjandra, N. Temperature dependence of protein backbone motion from carbonyl 13C and amide 15N NMR relaxation. J. Magn. Reson. 174, 43ā53 (2005)
Wang, T. Z., Cai, S. & Zuiderweg, E. R. P. Temperature dependence of anisotropic protein backbone dynamics. J. Am. Chem. Soc. 125, 8639ā8643 (2003)
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, 8400ā8404 (2003)
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, 2133ā2146 (1999)
Zhang, Q., Sun, X. Y., Watt, E. D. & Al-Hashimi, H. M. Resolving the motional modes that code for RNA adaptation. Science 311, 653ā656 (2006)
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, 181ā183 (2002)
Acknowledgements
We thank L. Kay for providing pulse programs. We are grateful to K. O. Stetter for providing DNA isolated from Aquifex aeolicus and the Advanced Biomedical Computing Center for CPU hours. This work was supported by NIH grants (D.K. and K.A.H.-W.), a DOE grant (D.K.) and a fellowship from the American Heart Association (M.L.). The research at Harvard was supported in part by a grant from NIH to M.K.
Author Contributions K.A.H.-W. and M.L. contributed equally to this work. K.A.H.-W. performed the NMR experiments with supervision from D.K., and M.L. carried out the computational analysis with supervision from M.K. and D.K. All authors discussed the results and interpretation. D.K. and K.A.H.-W. wrote the manuscript.
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Henzler-Wildman, K., Lei, M., Thai, V. et al. A hierarchy of timescales in protein dynamics is linked to enzyme catalysis. Nature 450, 913ā916 (2007). https://doi.org/10.1038/nature06407
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DOI: https://doi.org/10.1038/nature06407
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