The simulation study of protein-protein interfaces based on the 4-helix bundle structure

Masaki Fukuda*, Yu Komatsu, 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: Conference contribution

2 被引用数 (Scopus)

抄録

Docking of two protein molecules is induced by intermolecular interactions. Our purposes in this study are: designing binding interfaces on the two proteins, which specifically interact to each other; and inducing intermolecular interactions between the two proteins by mixing them. A 4-helix bundle structure was chosen as a scaffold on which binding interfaces were created. Based on this scaffold, we designed binding interfaces involving charged and nonpolar amino acid residues. We performed molecular dynamics (MD) simulation to identify suitable amino acid residues for the interfaces. We chose YciF protein as the scaffold for the protein-protein docking simulation. We observed the structure of two YciF protein molecules (I and II), and we calculated the distance between centroids (center of gravity) of the interfaces' surface planes of the molecules I and II. We found that the docking of the two protein molecules can be controlled by the number of hydrophobic and charged amino acid residues involved in the interfaces. Existence of six hydrophobic and five charged amino acid residues within an interface were most suitable for the protein-protein docking.

本文言語English
ホスト出版物のタイトル4th International Symposium on Slow Dynamics in Complex Systems
ホスト出版物のサブタイトルKeep Going Tohoku
ページ606-609
ページ数4
DOI
出版ステータスPublished - 2013
外部発表はい
イベント4th International Symposium on Slow Dynamics in Complex Systems: Keep Going Tohoku - Sendai, Japan
継続期間: 2012 12 22012 12 7

出版物シリーズ

名前AIP Conference Proceedings
1518
ISSN(印刷版)0094-243X
ISSN(電子版)1551-7616

Other

Other4th International Symposium on Slow Dynamics in Complex Systems: Keep Going Tohoku
国/地域Japan
CitySendai
Period12/12/212/12/7

ASJC Scopus subject areas

  • 物理学および天文学(全般)

フィンガープリント

「The simulation study of protein-protein interfaces based on the 4-helix bundle structure」の研究トピックを掘り下げます。これらがまとまってユニークなフィンガープリントを構成します。

引用スタイル