Molecular dynamics simulations of a new branched antimicrobial peptide : a comparison of force fields

• Main Authors: Li, Jianguo, Lakshminarayanan, Rajamani, Bai, Yang, Liu, Shouping, Zhou, Lei, Pervushin, Konstantin, Verma, Chandra, Beuerman, Roger W.
• Other Authors: School of Biological Sciences
• Format: Article
• Language: English
• Published: 2014
• Subjects: Biological Sciences
• Online Access: https://hdl.handle.net/10356/101593; http://hdl.handle.net/10220/18700
• Institution: Nanyang Technological University

Branched antimicrobial peptides are promising as a new class of antibiotics displaying high activity and low toxicity and appear to work through a unique mechanism of action. We explore the structural dynamics of a covalently branched 18 amino acid peptide (referred to as B2088) in aqueous and membrane mimicking environments through molecular dynamics (MD) simulations. Towards this, we carry out conventional MD simulations and supplement these with replica exchange simulations. The simulations are carried out using four different force fields that are commonly employed for simulating biomolecular systems. These force fields are GROMOS53a6, CHARMM27 with cMAP, CHARMM27 without cMAP and AMBER99sb. The force fields are benchmarked against experimental data available from circular dichroism and nuclear magnetic resonance spectroscopies, and show that CHARMM27 without cMAP correction is the most successful in reproducing the structural dynamics of B2088 both in water and in the presence of micelles. Although the four force fields predict different structures of B2088, they all show that B2088 stabilizes against the head group of the lipid through hydrogen bonding of its Lys and Arg side chains. This leads us to hypothesize that B2088 is unlikely to penetrate into the hydrophobic region of the membrane owing to the high free energy costs of transfer from water, and possibly acts by carpeting and thus disrupting the membrane.