ArticleProteins2023
Total free energy analysis of fully hydrated proteins.
Article in Proteins, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 10 citations in OpenAlex.
- Data-Efficient Equivariant NNPs Enable DFT-Accurate Simulations and Implicit Solvation Free Energies.The journal of physical chemistry. B · 2025Article
- Quantifying Spatially Resolved Hydration Thermodynamics Using Grid Inhomogeneous Solvation Theory [Article v1.0].Living journal of computational molecular science · 2025Article
- DeepConf: Leveraging ANI-ML Potentials for Exploring Local Minima with Application to Bioactive Conformations.Journal of chemical information and modeling · 2025Article
- The biophysics of water in cell biology: perspectives on a keystone for both marine sciences and cancer research.Frontiers in cell and developmental biology · 2024Article
- QSAR modelling, molecular docking, molecular dynamic and ADMET prediction of pyrrolopyrimidine derivatives as novel Bruton's tyrosine kinase (BTK) inhibitors.Saudi pharmaceutical journal : SPJ : the official publication of the Saudi Pharmaceutical Society · 2024Article
- Energy-entropy multiscale cell correlation method to predict toluene-water logPhysical chemistry chemical physics : PCCP · 2023Article
- Total free energy analysis of fully hydrated proteins.Proteins · 2023Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The total free energy of a hydrated biomolecule and its corresponding decomposition of energy and entropy provides detailed information about regions of thermodynamic stability or instability. The free energies of four hydrated globular proteins with different net charges are calculated from a molecular dynamics simulation, with the energy coming from the system Hamiltonian and entropy using multiscale cell correlation. Water is found to be most stable around anionic residues, intermediate around cationic and polar residues, and least stable near hydrophobic residues, especially when more buried, with stability displaying moderate entropy-enthalpy compensation. Conversely, anionic residues in the proteins are energetically destabilized relative to singly solvated amino acids, while trends for other residues are less clear-cut. Almost all residues lose intraresidue entropy when in the protein, enthalpy changes are negative on average but may be positive or negative, and the resulting overall stability is moderate for some proteins and negligible for others. The free energy of water around single amino acids is found to closely match existing hydrophobicity scales. Regarding the effect of secondary structure, water is slightly more stable around loops, of intermediate stability around
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