A coarse-grained model of the effective interaction for charged amino acid residues and its application to formation of GCN4-pLI tetramer |
| |
| Authors: | Kazutomo Kawaguchi Satoshi Nakagawa Isman Kurniawan Koichi Kodama Muhammad Saleh Arwansyah Hidemi Nagao |
| |
| Affiliation: | 1. Institute of Science and Engineering, Kanazawa University, Kanazawa, Japankkawa@wriron1.s.kanazawa-u.ac.jp;3. Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan |
| |
| Abstract: | ABSTRACTWe 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. |
| |
| Keywords: | Coarse-grained model effective interaction electrostatic interaction charged amino acid GCN4 |
|
|
