ArticleActa crystallographica. Section D, Biological crystallography2015
Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures.
Article in Acta crystallographica. Section D, Biological crystallography, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed.
- Predicting water at the protein interface in cryo-EM structures from MD-excess chemical potential.Biophysical journal · 2026Article
- How protein hydration depends on amino acid composition, peptide conformation, and force fields.Biophysical journal · 2026Article
- Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure - Part I: Mg2.Nucleic acids research · 2025Article
- Features that matter: Evolutionary signatures can predict viral transmission routes.PLoS pathogens · 2024Article
- Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge.Nature methods · 2024Article
- The Potential of Cyclodextrins as Inhibitors for the BM2 Protein: An In Silico Investigation.Molecules (Basel, Switzerland) · 2024Article
- Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks.Acta crystallographica. Section D, Structural biology · 2022Article
- Prediction of models for ordered solvent in macromolecular structures by a classifier based upon resolution-independent projections of local feature data.Acta crystallographica. Section D, Structural biology · 2019Article
- Hydration Structure and Dynamics of Inhibitor-Bound HIV-1 Protease.Journal of chemical theory and computation · 2018Article
- Influences of lone-pair electrons on directionality of hydrogen bonds formed by hydrophilic amino acid side chains in molecular dynamics simulation.Scientific reports · 2017Article
- Reversible Activation of Halophilic β-lactamase from Methanol-Induced Inactive Form: Contrast to Irreversible Inactivation of Non-Halophilic Counterpart.The protein journal · 2017Article
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2 authors.
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Abstract
Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon-donor hydrogen bonds, OH-π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.
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