Bridging Microscopic and Macroscopic Mechanisms of p53-MDM2 Binding with Kinetic Network Models

Area of Science:

• Biochemistry
• Molecular Biology
• Computational Biology

Background:

• The tumor suppressor protein p53 is regulated by MDM2, which targets it for ubiquitination.
• MDM2 binds to the intrinsically disordered transactivation domain (TAD) of p53, initiating this process.
• The precise microscopic details of this binding, particularly the role of disordered domains, remain unclear.

Purpose of the Study:

• To elucidate the binding mechanisms, pathways, and kinetics of p53-MDM2 interaction using advanced computational methods.
• To predict binding pathways and rates with high accuracy by analyzing simulation data.
• To understand how protein dynamics and conformational changes influence biological function.

Main Methods:

• Large-scale, unbiased all-atom molecular dynamics simulations of p53 TAD binding to MDM2.
• Construction and analysis of Markov state models (MSMs) from simulation trajectories.
• Parameterization of a four-state kinetic model using microscopic rate information from MSMs.

Main Results:

• MSMs accurately predicted p53 TAD binding pathways and on-rates, aligning well with experimental data.
• Two critical bound intermediates, featuring nonnative hydrophobic residue arrangements, were identified as key to the overall binding rate.
• The study found that induced-fit pathways dominate binding flux across various concentrations.
• Modulation of p53's residual helicity was shown to affect binding, consistent with experimental observations.

Conclusions:

• Microscopic modeling of peptide binding, combined with kinetic flux models, provides a powerful approach to understanding protein interactions.
• The identified binding intermediates and pathways offer mechanistic insights into p53 regulation by MDM2.
• These findings can inform strategies for modulating p53-MDM2 interactions for therapeutic purposes.