ArticlePloS one2011
Bound water at protein-protein interfaces: partners, roles and hydrophobic bubbles as a conserved motif.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 67 citations in OpenAlex.
- How Hydration Weakens Collagen: A Mesoscale Energy Decomposition of Type I and Type II Fibrils.Computational and structural biotechnology journal · 2026Article
- WatCon: A Python Tool for Analysis of Conserved Water Networks Across Protein Families.JACS Au · 2025Article
- Structural convergence and water-mediated substrate mimicry enable broad neuraminidase inhibition by human antibodies.Nature communications · 2025Article
- Statistical analysis of sequential motifs at biologically relevant protein-protein interfaces.Computational and structural biotechnology journal · 2024Article
- Impact of water models on the structure and dynamics of enzyme tunnels.Computational and structural biotechnology journal · 2024Article
- Three-Dimensional Interaction Homology: Deconstructing Residue-Residue and Residue-Lipid Interactions in Membrane Proteins.Molecules (Basel, Switzerland) · 2024Article
- Merging cultures and disciplines to create a drug discovery ecosystem at Virginia commonwealth university: Medicinal chemistry, structural biology, molecular and behavioral pharmacology and computational chemistry.SLAS discovery : advancing life sciences R & D · 2023Review
- HINT, a code for understanding the interaction between biomolecules: a tribute to Donald J. Abraham.Frontiers in molecular biosciences · 2023Review
- Antibody CDR amino acids underlying the functionality of antibody repertoires in recognizing diverse protein antigens.Scientific reports · 2022Article
- Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites.Nature communications · 2021Article
- Rational Design of a User-Friendly Aptamer/Peptide-Based Device for the Detection ofSensors (Basel, Switzerland) · 2020Article
- Local and global anatomy of antibody-protein antigen recognition.Journal of molecular recognition : JMR · 2018Article
- Complex structure of cytochrome c-cytochrome c oxidase reveals a novel protein-protein interaction mode.The EMBO journal · 2017Article
- Conformational selection in amyloid-based immunotherapy: Survey of crystal structures of antibody-amyloid complexes.Biochimica et biophysica acta · 2016Review
- Molecular docking as a popular tool in drug design, an in silico travel.Advances and applications in bioinformatics and chemistry : AABC · 2016Review
- Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures.Acta crystallographica. Section D, Biological crystallography · 2015Article
- Promiscuous and specific recognition among ephrins and Eph receptors.Biochimica et biophysica acta · 2014Article
- IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking.BMC bioinformatics · 2014Article
- Large Scale Chemical Cross-linking Mass Spectrometry Perspectives.Journal of proteomics & bioinformatics · 2013Article
- On the binding affinity of macromolecular interactions: daring to ask why proteins interact.Journal of the Royal Society, Interface · 2013Review
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundThere is a great interest in understanding and exploiting protein-protein associations as new routes for treating human disease. However, these associations are difficult to structurally characterize or model although the number of X-ray structures for protein-protein complexes is expanding. One feature of these complexes that has received little attention is the role of water molecules in the interfacial region. METHODOLOGY: A data set of 4741 water molecules abstracted from 179 high-resolution (≤ 2.30 Å) X-ray crystal structures of protein-protein complexes was analyzed with a suite of modeling tools based on the HINT forcefield and hydrogen-bonding geometry. A metric termed Relevance was used to classify the general roles of the water molecules.
resultsThe water molecules were found to be involved in: a) (bridging) interactions with both proteins (21%), b) favorable interactions with only one protein (53%), and c) no interactions with either protein (26%). This trend is shown to be independent of the crystallographic resolution. Interactions with residue backbones are consistent for all classes and account for 21.5% of all interactions. Interactions with polar residues are significantly more common for the first group and interactions with non-polar residues dominate the last group. Waters interacting with both proteins stabilize on average the proteins' interaction (-0.46 kcal mol(-1)), but the overall average contribution of a single water to the protein-protein interaction energy is unfavorable (+0.03 kcal mol(-1)). Analysis of the waters without favorable interactions with either protein suggests that this is a conserved phenomenon: 42% of these waters have SASA ≤ 10 Å(2) and are thus largely buried, and 69% of these are within predominantly hydrophobic environments or "hydrophobic bubbles". Such water molecules may have an important biological purpose in mediating protein-protein interactions.
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Registered trials
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.