ArticleBiophysical journal2015
Quantifying the entropy of binding for water molecules in protein cavities by computing correlations.
Article in Biophysical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 72 citations in OpenAlex.
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- Expected and Unexpected "Guests" at the Active Site of Human Orotidine 5'-Monophosphate Decarboxylase.Biochemistry · 2025Article
- Free Energy Density of a Fluid and Its Role in Solvation and Binding.Journal of chemical theory and computation · 2024Article
- Heterogeneous and Allosteric Role of Surface Hydration for Protein-Ligand Binding.Journal of chemical theory and computation · 2023Article
- W254 in furin functions as a molecular gate promoting anti-viral drug binding: Elucidation of putative drug tunneling and docking by non-equilibrium molecular dynamics.Computational and structural biotechnology journal · 2023Article
- Spatially Resolved Hydration Thermodynamics in Biomolecular Systems.The journal of physical chemistry. B · 2022Review
- The ubiquitous buried water in the beta-trefoil architecture contributes to the folding nucleus and ~20% of the folding enthalpy.Protein science : a publication of the Protein Society · 2021Article
- Spatially resolved free-energy contributions of native fold and molten-globule-like Crambin.Biophysical journal · 2021Article
- A Bit Stickier, a Bit Slower, a Lot Stiffer: Specific vs. Nonspecific Binding of Gal4 to DNA.International journal of molecular sciences · 2021Article
- Solvation Thermodynamics from the Perspective of Endpoints DFT.The journal of physical chemistry. B · 2020Review
- A Binary Arginine Methylation Switch on Histone H3 Arginine 2 Regulates Its Interaction with WDR5.Biochemistry · 2020Article
- Conserved buried water molecules enable the β-trefoil architecture.Protein science : a publication of the Protein Society · 2020Article
- A Role for Monosaccharides in Nucleation Inhibition and Transport of Collagen.Bioelectricity · 2020Article
- Entropic bonding of the type 1 pilus from experiment and simulation.Royal Society open science · 2020Article
- Positive Cooperativity in Substrate Binding by Human Thymidylate Synthase.Biophysical journal · 2019Article
- A Fragmenting Protocol with Explicit Hydration for Calculation of Binding Enthalpies of Target-Ligand Complexes at a Quantum Mechanical Level.International journal of molecular sciences · 2019Article
- A super-Gaussian Poisson-Boltzmann model for electrostatic free energy calculation: smooth dielectric distribution for protein cavities and in both water and vacuum states.Journal of mathematical biology · 2019Article
- Spatially-Decomposed Free Energy of Solvation Based on the Endpoint Density-Functional Method.Journal of chemical theory and computation · 2019Article
- Functional Role of Solvent Entropy and Conformational Entropy of Metal Binding in a Dynamically Driven Allosteric System.Journal of the American Chemical Society · 2018Article
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Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
Protein structural analysis demonstrates that water molecules are commonly found in the internal cavities of proteins. Analysis of experimental data on the entropies of inorganic crystals suggests that the entropic cost of transferring such a water molecule to a protein cavity will not typically be greater than 7.0 cal/mol/K per water molecule, corresponding to a contribution of approximately +2.0 kcal/mol to the free energy. In this study, we employ the statistical mechanical method of inhomogeneous fluid solvation theory to quantify the enthalpic and entropic contributions of individual water molecules in 19 protein cavities across five different proteins. We utilize information theory to develop a rigorous estimate of the total two-particle entropy, yielding a complete framework to calculate hydration free energies. We show that predictions from inhomogeneous fluid solvation theory are in excellent agreement with predictions from free energy perturbation (FEP) and that these predictions are consistent with experimental estimates. However, the results suggest that water molecules in protein cavities containing charged residues may be subject to entropy changes that contribute more than +2.0 kcal/mol to the free energy. In all cases, these unfavorable entropy changes are predicted to be dominated by highly favorable enthalpy changes. These findings are relevant to the study of bridging water molecules at protein-protein interfaces as well as in complexes with cognate ligands and small-molecule inhibitors.
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