Paper Citing NAMD - Abstract
Baul, Upayan; Kuroda, Kenichi; Vemparala, Satyavani
Interaction of multiple biomimetic antimicrobial polymers with model bacterial membranes
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 084902, AUG 28 2014
Using atomistic molecular dynamics simulations, interaction of multiple synthetic random copolymers based on methacrylates on prototypical bacterial membranes is investigated. The simulations show that the cationic polymers form a micellar aggregate in water phase and the aggregate, when interacting with the bacterial membrane, induces clustering of oppositely charged anionic lipid molecules to form clusters and enhances ordering of lipid chains. The model bacterial membrane, consequently, develops lateral inhomogeneity in membrane thickness profile compared to polymer-free system. The individual polymers in the aggregate are released into the bacterial membrane in a phased manner and the simulations suggest that the most probable location of the partitioned polymers is near the 1-palmitoyl-2-oleoyl-phosphatidylglycerol (POPG) clusters. The partitioned polymers preferentially adopt facially amphiphilic conformations at lipid-water interface, despite lacking intrinsic secondary structures such as alpha-helix or beta-sheet found in naturally occurring antimicrobial peptides. (C) 2014 AIP Publishing LLC.
