ArticleProteomics2009
Energetic determinants of protein binding specificity: insights into protein interaction networks.
Article in Proteomics, 2009. 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.
- Prediction and Modeling of Protein-Protein Interactions Using "Spotted" Peptides with a Template-Based Approach.Biomolecules · 2022Article
- Molecular basis for protein-protein interactions.Beilstein journal of organic chemistry · 2021Review
- Protein electrostatics: From computational and structural analysis to discovery of functional fingerprints and biotechnological design.Computational and structural biotechnology journal · 2020Review
- The oncogenic potential of small nuclear ribonucleoprotein polypeptide G: a comprehensive and perspective view.American journal of translational research · 2019Review
- Heat shock-induced chaperoning by Hsp70 is enabled in-cell.PloS one · 2019Article
- Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method.PLoS computational biology · 2015Article
- Structural and physico-chemical effects of disease and non-disease nsSNPs on proteins.Current opinion in structural biology · 2015Review
- Minimalistic predictor of protein binding energy: contribution of solvation factor to protein binding.Biophysical journal · 2015Article
- Globular and disordered-the non-identical twins in protein-protein interactions.Frontiers in molecular biosciences · 2015Article
- Druggable orthosteric and allosteric hot spots to target protein-protein interactions.Current pharmaceutical design · 2014Review
- Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles.Journal of chemical theory and computation · 2013Article
- HotRegion: a database of predicted hot spot clusters.Nucleic acids research · 2012Article
- Categorizing biases in high-confidence high-throughput protein-protein interaction data sets.Molecular & cellular proteomics : MCP · 2011Article
- Expanding the proteome: disordered and alternatively folded proteins.Quarterly reviews of biophysics · 2011Article
- On the role of electrostatics in protein-protein interactions.Physical biology · 2011Review
- Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Beauty is in the eye of the beholder: proteins can recognize binding sites of homologous proteins in more than one way.PLoS computational biology · 2010Article
- Why does binding of proteins to DNA or proteins to proteins not necessarily spell function?ACS chemical biology · 2010Article
- Protein-protein interaction networks: how can a hub protein bind so many different partners?Trends in biochemical sciences · 2009Review
- Tradeoff between stability and multispecificity in the design of promiscuous proteins.PLoS computational biology · 2009Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
One of the challenges of the postgenomic era is to provide a more realistic representation of cellular processes by combining a systems biology description of functional networks with information on their interacting components. Here we carried out a systematic large-scale computational study on a structural protein-protein interaction network dataset in order to dissect thermodynamic characteristics of binding determining the interplay between protein affinity and specificity. As expected, interactions involving specific binding sites display higher affinities than those of promiscuous binding sites. Next, in order to investigate a possible role of modular distribution of hot spots in binding specificity, we divided binding sites into modules previously shown to be energetically independent. In general, hot spots that interact with different partners are located in different modules. We further observed that common hot spots tend to interact with partners exhibiting common binding motifs, whereas different hot spots tend to interact with partners with different motifs. Thus, energetic properties of binding sites provide insights into the way proteins modulate interactions with different partners. Knowledge of those factors playing a role in protein specificity is important for understanding how proteins acquire additional partners during evolution. It should also be useful in drug design.
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Registered trials
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