Discrimination between biological interfaces and crystal-packing contacts

Yuko Tsuchiya, Haruki Nakamura, Kengo Kinoshita

研究成果: Article査読

6 被引用数 (Scopus)

抄録

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.

本文言語English
ページ(範囲)99-113
ページ数15
ジャーナルAdvances and Applications in Bioinformatics and Chemistry
5
1
出版ステータスPublished - 2012 8 17
外部発表はい

ASJC Scopus subject areas

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

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