Markov State Model of Solvent Features Reveals Water Dynamics in Protein-Peptide Binding

J Phys Chem B. 2023 Dec 21;127(50):10682-10690. doi: 10.1021/acs.jpcb.3c04775. Epub 2023 Dec 11.

Abstract

In this work, we investigate the role of solvent in the binding reaction of the p53 transactivation domain (TAD) peptide to its receptor MDM2. Previously, our group generated 831 μs of explicit-solvent aggregate molecular simulation trajectory data for the MDM2-p53 peptide binding reaction using large-scale distributed computing and subsequently built a Markov State Model (MSM) of the binding reaction (Zhou et al. 2017). Here, we perform a tICA analysis and construct an MSM with similar hyperparameters while using only solvent-based structural features. We find a remarkably similar landscape but accelerated implied timescales for the slowest motions. The solvent shells contributing most to the first tICA eigenvector are those centered on Lys24 and Thr18 of the p53 TAD peptide in the range of 3-6 Å. Important solvent shells were visualized to reveal solvation and desolvation transitions along the peptide-protein binding trajectories. Our results provide a solvent-centric view of the hydrophobic effect in action for a realistic peptide-protein binding scenario.

MeSH terms

  • Molecular Dynamics Simulation
  • Peptides / metabolism
  • Protein Binding
  • Proto-Oncogene Proteins c-mdm2 / metabolism
  • Solvents
  • Tumor Suppressor Protein p53* / chemistry
  • Water* / metabolism

Substances

  • Solvents
  • Water
  • Tumor Suppressor Protein p53
  • Peptides
  • Proto-Oncogene Proteins c-mdm2