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Divergent evolution of protein conformational dynamics in dihydrofolate reductase

Abstract

Molecular evolution is driven by mutations, which may affect the fitness of an organism and are then subject to natural selection or genetic drift. Analysis of primary protein sequences and tertiary structures has yielded valuable insights into the evolution of protein function, but little is known about the evolution of functional mechanisms, protein dynamics and conformational plasticity essential for activity. We characterized the atomic-level motions across divergent members of the dihydrofolate reductase (DHFR) family. Despite structural similarity, Escherichia coli and human DHFRs use different dynamic mechanisms to perform the same function, and human DHFR cannot complement DHFR-deficient E. coli cells. Identification of the primary-sequence determinants of flexibility in DHFRs from several species allowed us to propose a likely scenario for the evolution of functionally important DHFR dynamics following a pattern of divergent evolution that is tuned by cellular environment.

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Figure 1: Human and E. coli DHFRs are structurally conserved but have different active site loop movements.
Figure 2: Active site packing and hinge motions in hDHFR.
Figure 3: Primary-sequence features related to flexibility and conformational change in E. coli and human DHFR.
Figure 4: Conformational changes between reactant and product complexes.
Figure 5: Overview of patterns in length of Met20 loop and hinges.
Figure 6: Human DHFR cannot complement DHFR-knockout E. coli cells and is more sensitive to product inhibition than is E. coli DHFR.

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Acknowledgements

We gratefully acknowledge M. Yamout for assistance with design and preparation of DHFR expression constructs, G. Johnson for assistance with figure preparation, X. Zhang (Scripps Research Institute) for providing anti-hDHFR antibody, D. Boger (Scripps Research Institute) for kindly providing ddTHF, X. Dai for assistance with crystallography data collection, M. Mettlen for assistance with microscopy and J. James and E. Jonsson for assistance with analysis of kinetic data. This work was supported by the US National Institutes of Health (NIH) grant GM75995 and the Skaggs Institute of Chemical Biology (P.E.W.). G.B. is supported as the Merck Fellow of the Damon Runyon Cancer Research Foundation (DRG-2136-12). D.C.E. is supported as a Damon Runyon Fellow by the Damon Runyon Cancer Research Foundation (DRG-2140-12). D.C.E. was supported by a predoctoral fellowship from the Achievement Rewards for College Scientists Foundation, grant GM080209 from the NIH Molecular Evolution Training Program. The Joint Center for Structural Genomics is supported by NIH National Institute of General Medical Sciences (NIGMS) (U54 GM094586). C.M.Z. was supported by NIH grant GM101457. The GM/CA CAT 23-ID-D has been funded in whole or in part with federal funds from the US National Cancer Institute (Y1-CO-1020) and NIGMS (Y1-GM-1104). Use of the Advanced Photon Source was supported by the US Department of Energy, Basic Energy Sciences, Office of Science, under contract DE-AC02-06CH11357.

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G.B. and P.E.W. designed the research. G.B., M.J. and G.K. collected the data. G.B., D.C.E., C.M.Z., A.G., L.M.T., H.J.D., I.A.W. and P.E.W. analyzed the data. All authors contributed to writing the manuscript.

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Correspondence to Peter E Wright.

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Complete list of fully sequenced genomes analyzed. (XLSX 43 kb)

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Bhabha, G., Ekiert, D., Jennewein, M. et al. Divergent evolution of protein conformational dynamics in dihydrofolate reductase. Nat Struct Mol Biol 20, 1243–1249 (2013). https://doi.org/10.1038/nsmb.2676

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