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Journal of Biosciences

, Volume 32, Issue 1, pp 101–111 | Cite as

Peptide segments in protein-protein interfaces

  • Arumay Pal
  • Pinak Chakrabarti
  • Ranjit Bahadur
  • Francis Rodier
  • Joël Janin
Article

Abstract

An important component of functional genomics involves the understanding of protein association. The interfaces resulting from protein-protein interactions — (i) specific, as represented by the homodimeric quaternary structures and the complexes formed by two independently occurring protein components, and (ii) non-specific, as observed in the crystal lattice of monomeric proteins — have been analysed on the basis of the length and the number of peptide segments. In 1000 Å2 of the interface area, contributed by a polypeptide chain, there would be 3.4 segments in homodimers, 5.6 in complexes and 6.3 in crystal contacts. Concomitantly, the segments are the longest (with 8.7 interface residues) in homodimers. Core segments (likely to contribute more towards binding) are more in number in homodimers (1.7) than in crystal contacts (0.5), and this number can be used as one of the parameters to distinguish between the two types of interfaces. Dominant segments involved in specific interactions, along with their secondary structural features, are enumerated.

Keywords

Binding site interfacial peptides peptide inhibitor protein-protein interactions specific and non-specific interactions 

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Copyright information

© Indian Academy of Sciences 2007

Authors and Affiliations

  • Arumay Pal
    • 1
  • Pinak Chakrabarti
    • 1
  • Ranjit Bahadur
    • 1
    • 2
  • Francis Rodier
    • 3
  • Joël Janin
    • 2
    • 3
  1. 1.Department of BiochemistryBose InstituteCalcuttaIndia
  2. 2.Institut de Biochimie et Biologie Moléculaire et CellulaireUniversité Paris-SudOrsayFrance
  3. 3.Laboratoire d’Enzymologie et de Biochimie StructuralesUPR9063 CNRSGif-sur-YvetteFrance

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