Shape complementarity and hydrogen bond preferences in protein-protein interfaces: Implications for antibody modeling and protein-protein docking

Daisuke Kuroda, Jeffrey J Gray

Research output: Contribution to journalArticle

Abstract

Motivations: Characterizing protein-protein interfaces and the hydrogen bonds is a first step to better understand proteins' structures and functions toward high-resolution protein design. However, there are few large-scale surveys of hydrogen bonds of interfaces. In addition, previous work of shape complementarity of protein complexes suggested that lower shape complementarity in antibody-antigen interfaces is related to their evolutionary origin. Results: Using 6637 non-redundant protein-protein interfaces, we revealed peculiar features of various protein complex types. In contrast to previous findings, the shape complementarity of antibody-antigen interfaces resembles that of the other interface types. These results highlight the importance of hydrogen bonds during evolution of protein interfaces and rectify the prevailing belief that antibodies have lower shape complementarity. Contact: Supplementary Information: Supplementary data are available at Bioinformatics online.

Original languageEnglish (US)
Pages (from-to)2451-2456
Number of pages6
JournalBioinformatics
Volume32
Issue number16
DOIs
StatePublished - Aug 15 2016

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Medicine(all)
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

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