Decomposing the space of protein quaternary structures with the interface fragment pair library

Zhong Ru Xie, Jiawen Chen, Yilin Zhao, Yinghao Wu

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Background: The 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. Results: Here 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. Conclusions: Our 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.

Original languageEnglish (US)
Article number14
JournalBMC Bioinformatics
Volume16
Issue number1
DOIs
StatePublished - Jan 16 2015

Fingerprint

Quaternary Protein Structure
Protein Structure
Libraries
Fragment
Proteins
Protein
Secondary Structure
Packing
Fold
Biological Phenomena
Protein-protein Interaction
Benchmarking
Protein Databases
Tertiary Protein Structure
Ensemble
Likely
Cluster Analysis
Clustering
Benchmark
Decompose

ASJC Scopus subject areas

  • Applied Mathematics
  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications

Cite this

Decomposing the space of protein quaternary structures with the interface fragment pair library. / Xie, Zhong Ru; Chen, Jiawen; Zhao, Yilin; Wu, Yinghao.

In: BMC Bioinformatics, Vol. 16, No. 1, 14, 16.01.2015.

Research output: Contribution to journalArticle

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