ArticleThe Journal of chemical physics2015
Are protein-protein interfaces special regions on a protein's surface?
Article in The Journal of chemical physics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Quantitative Characterization of the Impact of Protein-Protein Interactions on Ligand-Protein Binding: A Multi-Chain Dynamics Perturbation Analysis Method.International journal of molecular sciences · 2024Article
- Predicting therapeutic and side effects from drug binding affinities to human proteome structures.iScience · 2024Article
- Assessing the functional impact of protein binding site definition.Protein science : a publication of the Protein Society · 2024Article
- Cold Spot SCANNER: Colab Notebook for predicting cold spots in protein-protein interfaces.BMC bioinformatics · 2024Article
- Origins of life: first came evolutionary dynamics.QRB discovery · 2023Review
- Discovery of small molecule inhibitors that effectively disrupt IQGAP1-Cdc42 interaction in breast cancer cells.Scientific reports · 2022Article
- Cold spots are universal in protein-protein interactions.Protein science : a publication of the Protein Society · 2022Article
- Implications of the Essential Role of Small Molecule Ligand Binding Pockets in Protein-Protein Interactions.The journal of physical chemistry. B · 2022Article
- AlphaFold 2: Why It Works and Its Implications for Understanding the Relationships of Protein Sequence, Structure, and Function.Journal of chemical information and modeling · 2021Article
- Article
- Computational characterization of the binding mode between oncoprotein Ets-1 and DNA-repair enzymes.Proteins · 2018Article
- A model for hydrophobic protrusions on peripheral membrane proteins.PLoS computational biology · 2018Article
- Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Perspective: On the importance of hydrodynamic interactions in the subcellular dynamics of macromolecules.The Journal of chemical physics · 2016Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Protein-protein interactions (PPIs) are involved in many cellular processes. Experimentally obtained protein quaternary structures provide the location of protein-protein interfaces, the surface region of a given protein that interacts with another. These regions are termed half-interfaces (HIs). Canonical HIs cover roughly one third of a protein's surface and were found to have more hydrophobic residues than the non-interface surface region. In addition, the classical view of protein HIs was that there are a few (if not one) HIs per protein that are structurally and chemically unique. However, on average, a given protein interacts with at least a dozen others. This raises the question of whether they use the same or other HIs. By copying HIs from monomers with the same folds in solved quaternary structures, we introduce the concept of geometric HIs (HIs whose geometry has a significant match to other known interfaces) and show that on average they cover three quarters of a protein's surface. We then demonstrate that in some cases, these geometric HI could result in real physical interactions (which may or may not be biologically relevant). The composition of the new HIs is on average more charged compared to most known ones, suggesting that the current protein interface database is biased towards more hydrophobic, possibly more obligate, complexes. Finally, our results provide evidence for interface fuzziness and PPI promiscuity. Thus, the classical view of unique, well defined HIs needs to be revisited as HIs are another example of coarse-graining that is used by nature.
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Registered trials
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