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The role of protein dynamics in the evolution of new enzyme function

Nature Chemical Biology volume 12, pages 944–950 (2016)Cite this article

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Abstract

Enzymes must be ordered to allow the stabilization of transition states by their active sites, yet dynamic enough to adopt alternative conformations suited to other steps in their catalytic cycles. The biophysical principles that determine how specific protein dynamics evolve and how remote mutations affect catalytic activity are poorly understood. Here we examine a 'molecular fossil record' that was recently obtained during the laboratory evolution of a phosphotriesterase from Pseudomonas diminuta to an arylesterase. Analysis of the structures and dynamics of nine protein variants along this trajectory, and three rationally designed variants, reveals cycles of structural destabilization and repair, evolutionary pressure to 'freeze out' unproductive motions and sampling of distinct conformations with specific catalytic properties in bi-functional intermediates. This work establishes that changes to the conformational landscapes of proteins are an essential aspect of molecular evolution and that change in function can be achieved through enrichment of preexisting conformational sub-states.

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Figure 1: Locations and effects of substitutions that accumulated across the evolutionary trajectory.
Figure 2: Intermolecular interaction networks in R0 and R22.
Figure 3: Changes in protein disorder and conformation across an evolutionary trajectory.
Figure 4: Conformational sampling of PTE-like and AE-like states by evolutionary intermediates R6 and Rev6.
Figure 5: Epistatic interactions between mutations that accumulate in R22.

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Acknowledgements

We thank D.S. Tawfik for stimulating discussions. C.J.J. thanks the Australian Research Council for a Future Fellowship (FT140101059) and Discovery Project (DP130102144). This research was undertaken on the MX1 and MX2 beamlines at the Australian Synchrotron, Victoria, Australia. F.H. thanks the Biotechnology and Biological Sciences Research Council and European Research Council (starting investigator grants). M.K. thanks the EU Innovative Training Network (ProSA) for a studentship. N.T. is funded as a Canadian Institutes of Health Research new investigator and a Michael Smith Foundation of Health Research (MSFHR) career investigator. N.T. thanks Natural Sciences and Engineering Research Council of Canada Discovery Grant RGPIN 418262-12. A.M.B. is funded as a National Health and Medical Research Senior Research Fellow (1022688). This work was supported by the Victorian Life Sciences Computation Initiative, an initiative of the Victorian Government, Australia.

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Author notes

  1. Eleanor Campbell and Miriam Kaltenbach: These authors contributed equally to this work.

Authors and Affiliations

  1. Research School of Chemistry, Australian National University, Canberra, Australia

    Eleanor Campbell, Galen J Correy, Paul D Carr, Emma K Livingstone, Livnat Afriat-Jurnou & Colin J Jackson

  2. Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada

    Miriam Kaltenbach & Nobuhiko Tokuriki

  3. Department of Biochemistry, University of Cambridge, Cambridge, UK

    Miriam Kaltenbach & Florian Hollfelder

  4. Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia

    Benjamin T Porebski & Ashley M Buckle

  5. Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia

    Benjamin T Porebski & Ashley M Buckle

  6. Institut de Biologie Structurale, University Grenoble Alpes, Commissariat à l'Energie Atomique and Centre National de la Recherche Scientifique, Grenoble, France

    Martin Weik

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Contributions

E.C., M.K., G.J.C., P.D.C., B.T.P., E.K.L. and L.A.-J. performed experiments and analyzed results; A.M.B. and M.W. analyzed results; F.H. conceived the project, designed experiments and analyzed results; N.T. conceived the project, designed experiments, analyzed results and wrote the manuscript; and C.J.J. conceived the project, designed experiments, performed experiments, analyzed results and wrote the manuscript.

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Correspondence to Nobuhiko Tokuriki or Colin J Jackson.

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Campbell, E., Kaltenbach, M., Correy, G. et al. The role of protein dynamics in the evolution of new enzyme function. Nat Chem Biol 12, 944–950 (2016). https://doi.org/10.1038/nchembio.2175

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