ArticleBMC bioinformatics2015
Decomposing the space of protein quaternary structures with the interface fragment pair library.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed.
- Computational Assessment of Protein-protein Binding Affinity by Reversely Engineering the Energetics in Protein Complexes.Genomics, proteomics & bioinformatics · 2021Article
- A fragment-based protein interface design algorithm for symmetric assemblies.Protein engineering, design & selection : PEDS · 2021Article
- Protein structural motifs in prediction and design.Current opinion in structural biology · 2017Review
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4 authors.
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Abstract
backgroundThe physical interactions between proteins constitute the basis of protein quaternary structures. They dominate many biological processes in living cells. Deciphering the structural features of interacting proteins is essential to understand their cellular functions. Similar to the space of protein tertiary structures in which discrete patterns are clearly observed on fold or sub-fold motif levels, it has been found that the space of protein quaternary structures is highly degenerate due to the packing of compact secondary structure elements at interfaces. Therefore, it is necessary to further decompose the protein quaternary structural space into a more local representation.
resultsHere we constructed an interface fragment pair library from the current structure database of protein complexes. After structural-based clustering, we found that more than 90% of these interface fragment pairs can be represented by a limited number of highly abundant motifs. These motifs were further used to guide complex assembly. A large-scale benchmark test shows that the native-like binding is highly likely in the structural ensemble of modeled protein complexes that were built through the library.
conclusionsOur study therefore presents supportive evidences that the space of protein quaternary structures can be represented by the combination of a small set of secondary-structure-based packing at binding interfaces. Finally, after future improvements such as adding sequence profiles, we expect this new library will be useful to predict structures of unknown protein-protein interactions.
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