A coarse-grained model of the effective interaction for charged amino acid residues and its application to formation of GCN4-pLI tetramer. (19th March 2018)

• Record Type: Journal Article
• Authors: Kawaguchi, Kazutomo; Nakagawa, Satoshi; Kurniawan, Isman; Kodama, Koichi; Arwansyah, Muhammad Saleh; Nagao, Hidemi
• Is Part Of: Molecular physics. Volume 116:Number 5/6(2018)
• Page Start: 649
• Page End: 657
• Publication Date: 2018-03-19
• Subjects: Coarse-grained model -- effective interaction -- electrostatic interaction -- charged amino acid -- GCN4; Molecules -- Periodicals; Chemistry, Physical and theoretical -- Periodicals; Molécules -- Périodiques; Chimie physique et théorique -- Périodiques; 539.6.05
• DOI: 10.1080/00268976.2017.1393574
• Languages: English
• ISSNs: 0026-8976

Abstract

ABSTRACT: We present a simple coarse-grained model of the effective interaction for charged amino acid residues, such as Glu and Lys, in a water solvent. The free-energy profile as a function of the distance between two charged amino acid side-chain analogues in an explicit water solvent is calculated with all-atom molecular dynamics simulation and thermodynamic integration method. The calculated free-energy profile is applied to the coarse-grained potential of the effective interaction between two amino acid residues. The Langevin dynamics simulations with our coarse-grained potential are performed for association of a small protein complex, GCN4-pLI tetramer. The tetramer conformation reproduced by our coarse-grained model is similar to the X-ray crystallographic structure. We show that the effective interaction between charged amino acid residues stabilises association and orientation of protein complex. We also investigate the association pathways of GCN4-pLI tetramer. Abstract :