Folding simulation of small proteins by dissipative particle dynamics (DPD) with non-empirical interaction parameters based on fragment molecular orbital calculations

Koji Okuwaki, Hideo Doi, Kaori Fukuzawa, Yuji Mochizuki

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Recently, we have developed a new simulation scheme with dissipative particle dynamics (DPD) based on non-empirical interaction parameters derived from a series of fragment molecular orbital (FMO) calculations. This approach (FMO-DPD) was applied to folding simulations of Chignolin and Superchignolin mini-proteins. Their characteristic hairpin structure was obtained from an elongated form within short computation time. Essential residue-residue interactions such as hydrogen bonding and CH/π were observed at the final form. FMO-DPD should have a potential applicability to nano-bio systems involving proteins.

Original languageEnglish
Article number017002
JournalApplied Physics Express
Volume13
Issue number1
DOIs
Publication statusPublished - 2020 Jan 1
Externally publishedYes

ASJC Scopus subject areas

  • Engineering(all)
  • Physics and Astronomy(all)

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