Molecular dynamics study on the ligand recognition by tandem SH3 domains of p47phox, regulating NADPH oxidase activity

Yoko Watanabe, Hideyuki Tsuboi, Michihisa Koyama, Momoji Kubo, Carlos A. Del Carpio, Ewa Broclawik, Eiichiro Ichiishi, Masahiro Kohno, Akira Miyamoto

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6 Citations (Scopus)


The phagocyte NADPH oxidase complex plays a crucial role in host defense against microbial infection through the production of superoxides. Chronic granulomatous disease (CGD) is an inherited immune deficiency caused by the absence of certain components of the NADPH oxidase. Key to the activation of the NADPH oxidase is the cytoplasmic subunit p47phox, which includes the tandem SH3 domains (N-SH3 and C-SH3). In active phagocytes, p47phox forms a stable complex with the cytoplasmic region of membrane subunit p22phox that forms a left-handed polyproline type-II (PPII) helix conformation. In this report, we have analyzed the conformational changes of p47phox-p22phox complexes of wild-type and three mutants, which have been detected in CGD patients, using molecular dynamics simulations. We have found that in the wild-type, two basal planes of PPII prism in cytoplasmic region of p22phox interacted with N-SH3 and C-SH3. In contrast, in the modeled mutants, the residue at the ape of PPII helix, which interacts simultaneously with both of the tandem SH3 domains in the wild-type, moved toward C-SH3. Furthermore, interaction energies of the cytoplasmic region of p22phox with C-SH3 tend to decrease in these mutants. All these findings led us to conclude that interactions between N-SH3 of p47phox and PPII helix, which is formed by cytoplasmic region of p22phox, may play a significant role in the activation of the NADPH oxidase.

Original languageEnglish
Pages (from-to)303-312
Number of pages10
JournalComputational Biology and Chemistry
Issue number4
Publication statusPublished - Aug 2006
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry
  • Organic Chemistry
  • Computational Mathematics


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