J. Technology and Education, Vol.29, No.1, pp.29-35 (2022)

研究論文

 

AMBERを用いたタンパク質の自己組織化の機構解析

 

佐々 和洋¹*，宮本 貴也¹，後反 克典¹，宇野 健²，林 治尚³

¹福井工業高等専門学校 物質工学科 (〒916-8507 福井県鯖江市下司町)

²県立広島大学 地域創生学部 地域創生学科　(〒734-8558 広島県広島市南区宇品東一丁目1-71)

³兵庫県立大学 学術総合情報センター (〒671-2280 兵庫県姫路市書写2167)

*sasa@fukui-nct.ac.jp

 

Mechanism Analysis of Protein Folding with AMBER

 

Kazuhiro SASA,¹* Takaya MIYAMOTO,¹ Katsunori GOTAN,¹

Takeshi UNO,² Haruhisa HAYASHI³

¹Department of Chemistry and Biology, National Institute of Technology, Fukui College

(Geshi, Sabae, Fukui 916-8507, Japan)

²Department of Regional Developments, Prefectural University of Hiroshima

(1-1-71 Ujinahigashi, Minami-ku, Hiroshima, Hiroshima 734-8558, JAPAN)

³Library and Academic Information Center, University of Hyogo

(2167 Shosha, Himeji, Hyogo 671-2280, JAPAN)

 

(Received April 12, 2022; Accepted May 9, 2022)

 

Abstract

Protein forms a biologically functional steric structure by folding a linear polypeptide consisting of amino acid residues into a three-dimensional structure peculiar to an amino acid sequence. The process of protein self-assembly is called folding, which is said to be assisted by chaperone molecules. However, details have not been confirmed yet. In this study, we performed molecular dynamics simulations of the folding process of tryptophan cage protein (Trp-cage protein), which is a small protein consisting of 20 amino acid residues. Data analysis suggests that the formation of a protein secondary structure is the first step in the folding process, and chaperones may provide energy to overcome the steric energy barrier.

Key words：molecular dynamics simulation, protein folding, chaperone, Trp-cage