Interaction between a Single-Stranded DNA and a Binding Protein Viewed by the Fragment Molecular Orbital Method

Yuto Komeiji, Yoshio Okiyama, Yuji Mochizuki, Kaori Fukuzawa

研究成果: Article査読

4 被引用数 (Scopus)

抄録

The interaction between a single-stranded DNA (ssDNA) and a binding protein (Sulfolobus solfataricus ssDNA binding protein, SSB) were investigated by the ab initio fragment molecular orbital (FMO) method in explicit solvent. The calculated overall energy change upon complexation suggested that the ssDNA/SSB association is not strong. Nonetheless, more detailed analysis of interfragment interaction energy (IFIE) and pair interaction energy decomposition analysis (PIEDA) indicated that the ssDNA/SSB association is based upon a minute balance of various contributions of local structural parts of the molecules. The most stabilizing contribution was that by the electrostatic interaction between the sugarphosphate backbone of ssDNA and charged side chains of SSB, and the second was that by the stacking interaction between bases of ssDNA and aromatic side chains of SSB. Thus, though the overall association energy change was small, the local interactions were suggested to contribute to the association.

本文言語English
ページ(範囲)1596-1605
ページ数10
ジャーナルBulletin of the Chemical Society of Japan
91
11
DOI
出版ステータスPublished - 2018
外部発表はい

ASJC Scopus subject areas

  • 化学 (全般)

フィンガープリント

「Interaction between a Single-Stranded DNA and a Binding Protein Viewed by the Fragment Molecular Orbital Method」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