Discrimination between biological interfaces and crystal-packing contacts

Yuko Tsuchiya, Haruki Nakamura, Kengo Kinoshita

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

A discrimination method between biologically relevant interfaces and artifi cial crystal-packing contacts in crystal structures was constructed. The method evaluates proteinprotein interfaces in terms of complementarities for hydrophobicity, electrostatic potential and shape on the protein surfaces, and chooses the most probable biological interfaces among all possible contacts in the crystal. The method uses a discriminator named as "COMP", which is a linear combination of the complementarities for the above three surface features and does not correlate with the contact area. The discrimination of homo-dimer interfaces from symmetryrelated crystal-packing contacts based on the COMP value achieved the modest success rate. Subsequent detailed review of the discrimination results raised the success rate to about 88.8%. In addition, our discrimination method yielded some clues for understanding the interaction patterns in several examples in the PDB. Thus, the COMP discriminator can also be used as an indicator of the "biological-ness" of protein-protein interfaces.

Original languageEnglish
Pages (from-to)99-113
Number of pages15
JournalAdvances and Applications in Bioinformatics and Chemistry
Volume5
Issue number1
Publication statusPublished - 2012 Aug 17
Externally publishedYes

Keywords

  • Biological interfaces
  • Complementarity analysis
  • Crystal-packing contact
  • Homo-dimer interface
  • Protein-protein interaction

ASJC Scopus subject areas

  • Chemistry (miscellaneous)
  • Biochemistry
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Computer Science Applications

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