ArticlePLoS computational biology2012
Alternative protein-protein interfaces are frequent exceptions.
Article in PLoS computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Graph masked self-distillation learning for prediction of mutation impact on protein-protein interactions.Communications biology · 2024Article
- PPI3D: a web server for searching, analyzing and modeling protein-protein, protein-peptide and protein-nucleic acid interactions.Nucleic acids research · 2024Article
- Assessing the functional impact of protein binding site definition.Protein science : a publication of the Protein Society · 2024Article
- Deep geometric representations for modeling effects of mutations on protein-protein binding affinity.PLoS computational biology · 2021Article
- Improved sequence-based prediction of interaction sites in α-helical transmembrane proteins by deep learning.Computational and structural biotechnology journal · 2021Article
- Performance of computational methods for the evaluation of pericentriolar material 1 missense variants in CAGI-5.Human mutation · 2019Article
- Protein Interaction Z Score Assessment (PIZSA): an empirical scoring scheme for evaluation of protein-protein interactions.Nucleic acids research · 2019Article
- Multiple claudin-claudinCommunications biology · 2018Article
- Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI.Human mutation · 2017Article
- A machine learning approach for ranking clusters of docked protein-protein complexes by pairwise cluster comparison.Proteins · 2017Article
- Great interactions: How binding incorrect partners can teach us about protein recognition and function.Proteins · 2016Article
- Structural and Functional Analysis of a Talin Triple-Domain Module Suggests an Alternative Talin Autoinhibitory Configuration.Structure (London, England : 1993) · 2016Article
- Weak conservation of structural features in the interfaces of homologous transient protein-protein complexes.Protein science : a publication of the Protein Society · 2015Article
- PredictProtein--an open resource for online prediction of protein structural and functional features.Nucleic acids research · 2014Article
- Non-redundant unique interface structures as templates for modeling protein interactions.PloS one · 2014Article
- BioAssemblyModeler (BAM): user-friendly homology modeling of protein homo- and heterooligomers.PloS one · 2014Article
- Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review.Pharmacology & therapeutics · 2013Review
- Characterizing changes in the rate of protein-protein dissociation upon interface mutation using hotspot energy and organization.PLoS computational biology · 2013Article
- Coverage of protein domain families with structural protein-protein interactions: current progress and future trends.Progress in biophysics and molecular biologyReview
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2 authors.
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Abstract
The intricate molecular details of protein-protein interactions (PPIs) are crucial for function. Therefore, measuring the same interacting protein pair again, we expect the same result. This work measured the similarity in the molecular details of interaction for the same and for homologous protein pairs between different experiments. All scores analyzed suggested that different experiments often find exceptions in the interfaces of similar PPIs: up to 22% of all comparisons revealed some differences even for sequence-identical pairs of proteins. The corresponding number for pairs of close homologs reached 68%. Conversely, the interfaces differed entirely for 12-29% of all comparisons. All these estimates were calculated after redundancy reduction. The magnitude of interface differences ranged from subtle to the extreme, as illustrated by a few examples. An extreme case was a change of the interacting domains between two observations of the same biological interaction. One reason for different interfaces was the number of copies of an interaction in the same complex: the probability of observing alternative binding modes increases with the number of copies. Even after removing the special cases with alternative hetero-interfaces to the same homomer, a substantial variability remained. Our results strongly support the surprising notion that there are many alternative solutions to make the intricate molecular details of PPIs crucial for function.
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