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Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling

Nature Chemistry volume 9, pages 1005–1011 (2017)Cite this article

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Abstract

Protein–protein association is fundamental to many life processes. However, a microscopic model describing the structures and kinetics during association and dissociation is lacking on account of the long lifetimes of associated states, which have prevented efficient sampling by direct molecular dynamics (MD) simulations. Here we demonstrate protein–protein association and dissociation in atomistic resolution for the ribonuclease barnase and its inhibitor barstar by combining adaptive high-throughput MD simulations and hidden Markov modelling. The model reveals experimentally consistent intermediate structures, energetics and kinetics on timescales from microseconds to hours. A variety of flexibly attached intermediates and misbound states funnel down to a transition state and a native basin consisting of the loosely bound near-native state and the tightly bound crystallographic state. These results offer a deeper level of insight into macromolecular recognition and our approach opens the door for understanding and manipulating a wide range of macromolecular association processes.

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Figure 1: Simulation of protein–protein association and dissociation.
Figure 2: Kinetic model of barnase–barstar association.
Figure 3: Late steps in binding from late intermediates to the loosely bound state.
Figure 4: Native substate conformational dynamics.
Figure 5: Comparison of kinetics between wild type and E73A mutant.

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Acknowledgements

We are grateful to the following researchers for inspiring discussions and extensive feedback on the manuscript: J. Clark, C. Clementi, O. Daumke, W. A. Eaton, M. Gruebele, K. Lindorff-Larsen, S. Olsson, F. Paul, B. Roux, U. Schwarz, S. Sukenik, R. Wade and T. Weikl. Funding is acknowledged from the European Commission (ERC StG pcCells and PRACE project 2014102337 to F.N.), Deutsche Forschungsgemeinschaft (NO 825/3-1, SFB 958/A4, SFB 740/D7 to F.N.), Einstein Foundation Berlin (project SoOPic to N.P.), MINECO (BIO2014-53095-P) and FEDER (to G.D.F.), Acellera Ltd. (to S.D.). We thank the volunteers of GPUGRID for donating computing time for simulations.

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Authors and Affiliations

  1. Department of Mathematics and Computer Science, Freie Universität Berlin, Arnimallee 6, Berlin, 14195, Germany

    Nuria Plattner & Frank Noé

  2. Computational Biophysics Laboratory (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), C/ Doctor Aiguader 88, Barcelona, 08003, Spain

    Stefan Doerr & Gianni De Fabritiis

  3. Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluis Companys 23, Barcelona, 08010, Spain

    Gianni De Fabritiis

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  1. Nuria Plattner
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N.P., S.D., G.D.F and F.N. designed research and developed/implemented software. N.P. and S.D. conducted simulations. N.P., S.D. and F.N. analysed simulations. F.N. developed methods. N.P. and F.N. wrote the paper.

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Correspondence to Nuria Plattner or Frank Noé.

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Plattner, N., Doerr, S., De Fabritiis, G. et al. Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling. Nature Chem 9, 1005–1011 (2017). https://doi.org/10.1038/nchem.2785

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