ArticleThe journal of physical chemistry. B2018
Heterogeneous Solvation in Distinctive Protein-Protein Interfaces Revealed by Molecular Dynamics Simulations.
Article in The journal of physical chemistry. B, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- The Role of Water in Protein-Ligand Binding: Decisive Factor, Annoying Feature, or Indispensable Control Element: In Any Case, a Major Challenge.ChemMedChem · 2026Article
- Thermodynamic Data Remain a Hot Tip for Decoding Binding Affinity and Water Impact on Protein-Ligand Complex Formation to Assist Lead Optimization.Journal of medicinal chemistry · 2026Review
- Markov State Model of Solvent Features Reveals Water Dynamics in Protein-Peptide Binding.The journal of physical chemistry. B · 2023Article
- Coupling Monte Carlo, Variational Implicit Solvation, and Binary Level-Set for Simulations of Biomolecular Binding.Journal of chemical theory and computation · 2021Article
- Affinity of small-molecule solutes to hydrophobic, hydrophilic, and chemically patterned interfaces in aqueous solution.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Exploring the Free-Energy Landscape and Thermodynamics of Protein-Protein Association.Biophysical journal · 2020Article
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2 authors.
Funding
Abstract
Water, despite being a driving force in biochemical processes, has an elusively complex microscopic behavior. While water can increase its local density near amphiphilic protein surfaces, water is also thought to evaporate from hydrophobic surfaces and cavities, an effect known as "dewetting". The existence and extent of dewetting effects remains elusive due to the difficulty in observing clear "drying" transitions in experiments or simulations. Here, we use explicit solvent molecular dynamics (MD) simulations to study the molecular solvation at the binding interfaces of two distinctive molecular complexes: the highly hydrophilic barnase-barstar and the highly hydrophobic MDM2-p53. Our simulations, in conjunction with simple volumetric analyses, reveal a strikingly different water behavior at the binding interfaces of these two molecular complexes. In both complexes, we observe significant changes in the water local density as the two proteins approach, supporting the existence of a clear dewetting transition in the case of MDM2-p53, with an onset distance of 5.6-7.6 Å. Furthermore, the solvation analysis reported herein is a valuable tool to capture and quantify persistent or transient dewetting events in future explicit solvent MD simulations.
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