Evaluation of the protein interfaces that form an intermolecular four-helix bundle as studied by computer simulation

Masaki Fukuda*, Yu Komatsu, Hironao Yamada, Ryota Morikawa, Takeshi Miyakawa, Masako Takasu, Satoshi Akanuma, Akihiko Yamagishi

*この研究の対応する著者

研究成果: Article査読

3 被引用数 (Scopus)

抄録

Rational design of protein surface is important for creating higher order protein structures, but it is still challenging. In this study, we designed in silico the several binding interfaces on protein surfaces that allow a de novo protein-protein interaction to be formed. We used a computer simulation technique to find appropriate amino acid arrangements for the binding interface. The protein-protein interaction can be made by forming an intermolecular four-helix bundle structure, which is often found in naturally occurring protein subunit interfaces. As a model protein, we used a helical protein, YciF. Molecular dynamics simulation showed that a new protein-protein interaction is formed depending on the number of hydrophobic and charged amino acid residues present in the binding surfaces. However, too many hydrophobic amino acid residues present in the interface negatively affected on the binding. Finally, we found an appropriate arrangement of hydrophobic and charged amino acid residues that induces a protein-protein interaction through an intermolecular four-helix bundle formation.

本文言語English
ページ(範囲)498-503
ページ数6
ジャーナルMolecular Simulation
40
6
DOI
出版ステータスPublished - 2014 5月 3
外部発表はい

ASJC Scopus subject areas

  • 化学一般
  • 凝縮系物理学
  • 化学工学一般
  • 情報システム
  • 材料科学一般
  • モデリングとシミュレーション

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