title: Exploring protein domain organization by recognition of secondary structure packing interfaces.
abstract: BACKGROUND
  Protein domains are fundamental units of protein structure, function and evolution; thus, it is critical to gain a deep understanding of protein domain organization. Previous works have attempted to identify key residues involved in organization of domain architecture. Because one of the most important characteristics of domain architecture is the arrangement of secondary structure elements (SSEs), here we present a picture of domain organization through an integrated consideration of SSE arrangements and residue contact networks.
  
  
  RESULTS
  In this work, by representing SSEs as main-chain scaffolds and side-chain interfaces and through construction of residue contact networks, we have identified the SSE interfaces well packed within protein domains as SSE packing clusters. In total, 17 334 SSE packing clusters were recognized from 9015 Structural Classification of Proteins domains of <40% sequence identity. The similar SSE packing clusters were observed not only among domains of the same folds, but also among domains of different folds, indicating their roles as common scaffolds for organization of protein domains. Further analysis of 14 small single-domain proteins reveals a high correlation between the SSE packing clusters and the folding nuclei. Consistent with their important roles in domain organization, SSE packing clusters were found to be more conserved than other regions within the same proteins.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Key Laboratory of Protein & Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and University of the Chinese Academy of Sciences, Beijing 100049, China Key Laboratory of Protein & Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and University of the Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Lizong
authors.initials: L
authors.lastname: Deng
authors.affiliation: Key Laboratory of Protein & Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and University of the Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Aiping
authors.initials: A
authors.lastname: Wu
authors.affiliation: Key Laboratory of Protein & Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and University of the Chinese Academy of Sciences, Beijing 100049, China Key Laboratory of Protein & Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and University of the Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Wentao
authors.initials: W
authors.lastname: Dai
authors.affiliation: Key Laboratory of Protein & Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and University of the Chinese Academy of Sciences, Beijing 100049, China Key Laboratory of Protein & Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and University of the Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Tingrui
authors.initials: T
authors.lastname: Song
authors.affiliation: Key Laboratory of Protein & Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and University of the Chinese Academy of Sciences, Beijing 100049, China Key Laboratory of Protein & Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and University of the Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Ya
authors.initials: Y
authors.lastname: Cui
authors.affiliation: Key Laboratory of Protein & Peptide Pharmaceuticals, National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101 and University of the Chinese Academy of Sciences, Beijing 100049, China.
authors.forename: Taijiao
authors.initials: T
authors.lastname: Jiang
mesh_terms: D019295:Computational Biology / Q000379:methods; D006801:Humans; D008958:Models, Molecular; D011494:Protein Kinases / Q000737:chemistry; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
chemical_list: D011494:Protein Kinases