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

Author:

Okuwaki KojiORCID,Doi HideoORCID,Fukuzawa KaoriORCID,Mochizuki YujiORCID

Abstract

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.

Funder

Rikkyo SFR

Grant-in-Aid for Scientific Research

Social and scientific priority issue #6 (Accelerated Development of Innovative Clean Energy Systems) to be tackled by using post-K computer

Publisher

IOP Publishing

Subject

General Physics and Astronomy,General Engineering

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