A detailed unfolding pathway of a (β/α)8-barrel protein as studied by molecular dynamics simulations

Satoshi Akanuma, Hiroh Miyagawa, Kunihiro Kitamura, Akihiko Yamagishi

研究成果: Article査読

8 被引用数 (Scopus)

抄録

The (β/α)8-barrel is the most common protein fold. Similar structural properties for folding intermediates of (β/α) 8-barrel proteins involved in tryptophan biosynthesis have been reported in a number of experimental studies; these intermediates have the last two β-strands and three α-helices partially unfolded, with other regions of the polypeptide chain native-like in conformation. To investigate the detailed folding/unfolding pathways of these (β/α) 8-barrel proteins, temperature-induced unfolding simulations of N-(5′-phosphoribosyl)anthranilate isomerase from Escherichia coli were carried out using a special-purpose parallel computer system. Unfolding simulations at five different temperatures showed a sequential unfolding pathway comprised of several events. Early events in unfolding involved disruption of the last two strands and three helices, producing an intermediate ensemble similar to those detected in experimental studies. Then, denaturation of the first two βα units and separation of the sixth strand from the fifth took place independently. The remaining central βαβαβ module persisted the longest during all simulations, suggesting an important role for this module as the incipient folding scaffold. Our simulations also predicted the presence of a nucleation site, onto which several hydrophobic residues condensed forming the foundation for the central βαβ αβ module.

本文言語English
ページ(範囲)538-546
ページ数9
ジャーナルProteins: Structure, Function and Genetics
58
3
DOI
出版ステータスPublished - 2005 2 15
外部発表はい

ASJC Scopus subject areas

  • 構造生物学
  • 生化学
  • 分子生物学

フィンガープリント

「A detailed unfolding pathway of a (β/α)<sub>8</sub>-barrel protein as studied by molecular dynamics simulations」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