Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations

Fabian Paul, Christoph Wehmeyer, Esam T. Abualrous, Hao Wu, Michael D. Crabtree, Johannes Schöneberg, Jane Clarke, Christian Freund, Thomas R. Weikl and Frank Noé ()
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Fabian Paul: University of California
Christoph Wehmeyer: University of California
Esam T. Abualrous: University of California
Hao Wu: University of California
Michael D. Crabtree: University of Cambridge
Johannes Schöneberg: University of California
Jane Clarke: University of Cambridge
Christian Freund: Freie Universität Berlin
Thomas R. Weikl: Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems
Frank Noé: University of California

Nature Communications, 2017, vol. 8, issue 1, 1-10

Abstract: Abstract Understanding and control of structures and rates involved in protein ligand binding are essential for drug design. Unfortunately, atomistic molecular dynamics (MD) simulations cannot directly sample the excessively long residence and rearrangement times of tightly binding complexes. Here we exploit the recently developed multi-ensemble Markov model framework to compute full protein-peptide kinetics of the oncoprotein fragment 25–109Mdm2 and the nano-molar inhibitor peptide PMI. Using this system, we report, for the first time, direct estimates of kinetics beyond the seconds timescale using simulations of an all-atom MD model, with high accuracy and precision. These results only require explicit simulations on the sub-milliseconds timescale and are tested against existing mutagenesis data and our own experimental measurements of the dissociation and association rates. The full kinetic model reveals an overall downhill but rugged binding funnel with multiple pathways. The overall strong binding arises from a variety of conformations with different hydrophobic contact surfaces that interconvert on the milliseconds timescale.

Date: 2017
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DOI: 10.1038/s41467-017-01163-6

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