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

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.