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JKMRS Volume 22, No 4, pp 139, Molecular dynamics simulation o...
2018년 12월 20일 / 조회수: 572

Molecular dynamics simulation of short peptide in DPC micelle using explicit water solvent parameters


Ji-Hun Kim1,ǂ, Jong-Jae Yi2,ǂ, Hyung-Sik Won3,ǂ, and Woo Sung Son2,*


1 College of Pharmacy, Chungbuk National University, Cheongju, Chungbuk 28160, Republic of Korea
2 College of pharmacy and Institute of Pharmaceutical Sciences, CHA University, 120 Haeyong-ro, Pocheon-si, Gyeonggi-do 11160, Republic of Korea
3 Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungju, Chungbuk 27478, Republic of Korea


Received Dec 06, 2018; Revised Dec 15, 2018; Accepted Dec 17, 2018


Abstract

Short antimicrobial peptide, A4W, have been studied by molecular dynamics (MD) simulation in an explicit dodecylphosphocholine (DPC) micelle. Peptide was aligned with DPC micelle and transferred new peptide-micelle coordinates within the same solvent box using specific micelle topology parameters. After initial energy minimization and equilibration, the conformation and orientation of the peptide were analyzed from trajectories obtained from the RMD (restrained molecular dynamics) or the subsequent free MD. Also, the information of solvation in the backbone and the side chain of the peptide, hydrogen bonding, and the properties of the dynamics were obtained. The results showed that the backbone residues of peptide are either solvated using water or in other case, they relate to hydrogen bonding. These properties could be a critical factor against the insertion mode of interaction. Most of the peptide-micelle interactions come from the hydrophobic interaction between the side chains of peptide and the structural interior of micelle system. The interaction of peptide-micelle, electrostatic potential and hydrogen bonding, between the terminal residues of peptide and the headgroups in micelle were observed. These interactions could be effect on the structure and flexibility of the peptide terminus.


ǂ These authors contributed equally.
* Address correspondence to: Woo Sung Son, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, 120 Haeryong-ro, Pocheon-si, Gyeonggi-do 11160, Republic of Korea, Tel: 82-31-850-9398; Fax: 82-31-850-
9398; E-mail: wson@cha.ac.kr

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