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

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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Figure 1: Comparison of thermoAdk and mesoAdk flexibility.
Figure 2: Temperature dependence of thermoAdk order parameters.
Figure 3: Temperature dependence of MD order parameters and comparison with experimental S2.
Figure 4: Linkage of motional timescales and characterization of hinges.

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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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Correspondence to Dorothee Kern.

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The file contains Supplementary Discussion with additional references, Supplementary Tables S1-S4 and Supplementary Figures S1-S13 with Legends. (PDF 3255 kb)

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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, 913–916 (2007). https://doi.org/10.1038/nature06407

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