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Free Energy Profile and Kinetics for Coupled Folding and Binding of the Intrinsically Disordered Protein p53 with MDM2.

07:00 EST 13th February 2020 | BioPortfolio

Summary of "Free Energy Profile and Kinetics for Coupled Folding and Binding of the Intrinsically Disordered Protein p53 with MDM2."

Intrinsically disordered proteins (IDPs) exert their functions by binding to partner proteins via a complex process that includes coupled folding and binding. Motivated by that inhibiting the binding of the IDP p53 to its partner MDM2 has become a promising strategy for the design of anticancer drugs, we carried out metadynamics simulations to study the coupled folding and binding process linking the IDP p53 to MDM2 in atomic detail. Using bias-exchange metadynamics (BE-MetaD) and infrequent metadynamics (InMetaD) we estimated the binding free energy, the unbinding rate and the binding rate. By analyzing the stable intermediates, we uncovered the role of nonnative interactions played in the p53-MDM2 binding/unbinding process. We used a three-state model to describe the whole binding/unbinding process and to obtain the corresponding rate constants. Our work shows that the binding of p53 favors an induced fit mechanism which proceeds in a stepwise fashion. Our results can be helpful for the in-depth understanding of the coupled folding and binding process needed for the design of MDM2 inhibitors.

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This article was published in the following journal.

Name: Journal of chemical information and modeling
ISSN: 1549-960X
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