Dynamic features of homodimer interfaces calculated by normal-mode analysis

Yuko Tsuchiya, Kengo Kinoshita, Shigeru Endo, Hiroshi Wako

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Knowledge of the dynamic features of protein interfaces is necessary for a deeper understanding of protein-protein interactions. We performed normal-mode analysis (NMA) of 517 nonredundant homodimers and their protomers to characterize dimer interfaces from a dynamic perspective. The motion vector calculated by NMA for each atom of a dimer was decomposed into internal and external motion vectors in individual component subunits, followed by the averaging of time-averaged correlations between these vectors over atom pairs in the interface. This averaged correlation coefficient (ACC) was defined for various combinations of vectors and investigated in detail. ACCs decrease exponentially with an increasing interface area and r-value, that is, interface area divided by the entire subunit surface area. As the r-value reflects the nature of dimer formation, the result suggests that both the interface area and the nature of dimer formation are responsible for the dynamic properties of dimer interfaces. For interfaces with small or medium r-values and without intersubunit entanglements, ACCs are found to increase on dimer formation when compared with those in the protomer state. In contrast, ACCs do not increase on dimer formation for interfaces with large r-values and intersubunit entanglements such as in interwinding dimers. Furthermore, relationships between ACCs for intrasubunit atom pairs and for intersubunit atom pairs are found to significantly differ between interwinding and noninterwinding dimers for external motions. External motions are considered as an important factor for characterizing dimer interfaces.

Original languageEnglish
Pages (from-to)1503-1513
Number of pages11
JournalProtein Science
Volume21
Issue number10
DOIs
Publication statusPublished - 2012 Oct 1

Keywords

  • Correlative atomic fluctuations
  • External motion
  • Homodimer interfaces
  • Interface dynamics
  • Internal motion
  • Interwinding interfaces
  • Normal-mode analysis
  • Protein-protein interaction

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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