ArticleProceedings of the National Academy of Sciences of the United States of America2021
Identifying hydrophobic protein patches to inform protein interaction interfaces.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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34 citing papers in PubMed, 104 citations in OpenAlex.
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- Molecular Scale Hydrophobicity and Adsorption Thermodynamics on Hydrophobic-Charged Surfaces.ACS nano · 2026Article
- IscS Kinetics in Native Mass Spectrometry Buffers Reveal Key Physiochemical Properties that Influence Enzyme Activity.Journal of the American Society for Mass Spectrometry · 2026Article
- Untangling the Complexity of Binding Across Biomolecular Interfaces with Interaction Network Models.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Construction of artificial organellesChemical science · 2025Review
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- Silenced cutters: mechanisms and effects of protease inhibition in plant-pathogen interactions.Journal of experimental botany · 2025Review
- Designing single-polymer-chain nanoparticles to mimic biomolecular hydration frustration.Nature chemistry · 2025Article
- Terahertz calorimetry spotlights the role of water in biological processes.Nature reviews. Chemistry · 2025Review
- How allosteric mutations control ligand binding in Lipocalin protein: odorant binding protein as a test case.Cellular and molecular life sciences : CMLS · 2025Article
- Extending the PARCH Scale: Assessing Hydropathy of Proteins across Multiple Water Models.Journal of chemical information and modeling · 2025Article
- Compact Assessment of Molecular Surface Complementarities Enhances Neural Network-Aided Prediction of Key Binding Residues.Journal of chemical information and modeling · 2025Article
- Prediction of antibody-antigen interaction based on backbone aware with invariant point attention.BMC bioinformatics · 2024Article
- Cutting Edge: LAG3 Dimerization Is Required for TCR/CD3 Interaction and Inhibition of Antitumor Immunity.Journal of immunology (Baltimore, Md. : 1950) · 2024Article
- N-terminal truncated phospholipase A1 accessory protein PlaS from Serratia marcescens alleviates inhibitory on host cell growth and enhances PlaA1 enzymatic activity.Bioresources and bioprocessing · 2024Article
- Computation of Overhauser dynamic nuclear polarization processes reveals fundamental correlation between water dynamics, structure, and solvent restructuring entropy.Physical chemistry chemical physics : PCCP · 2024Article
- An Affordable Topography-Based Protocol for Assigning a Residue's Character on a Hydropathy (PARCH) Scale.Journal of chemical theory and computation · 2024Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Interactions between proteins lie at the heart of numerous biological processes and are essential for the proper functioning of the cell. Although the importance of hydrophobic residues in driving protein interactions is universally accepted, a characterization of protein hydrophobicity, which informs its interactions, has remained elusive. The challenge lies in capturing the collective response of the protein hydration waters to the nanoscale chemical and topographical protein patterns, which determine protein hydrophobicity. To address this challenge, here, we employ specialized molecular simulations wherein water molecules are systematically displaced from the protein hydration shell; by identifying protein regions that relinquish their waters more readily than others, we are then able to uncover the most hydrophobic protein patches. Surprisingly, such patches contain a large fraction of polar/charged atoms and have chemical compositions that are similar to the more hydrophilic protein patches. Importantly, we also find a striking correspondence between the most hydrophobic protein patches and regions that mediate protein interactions. Our work thus establishes a computational framework for characterizing the emergent hydrophobicity of amphiphilic solutes, such as proteins, which display nanoscale heterogeneity, and for uncovering their interaction interfaces.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.