MOLECULAR SIMULATION OF ANTIMICROBIAL PEPTIDE WLBU2-MOD BINDING WITH GRAM-NEGATIVE INNER MEMBRANE MIMIC

Abstract

Since the discovery of Penicillin in 1928 by Sir Alexander Fleming, antibiotics have been

one of the most important technologies in modern medicine. Due to the lack of novel

innovative methods and the gross abuse of antibiotics both in human use and agriculture,

we currently face an antibiotic resistance crisis. In the last fifty years only a handful of new

class of antibiotics that target gram-positive bacteria have been introduced and, in that time,

no new class of antibiotics that target gram-negative bacteria have been introduced. This

thesis focuses on the molecular dynamic simulations involving the cationic α-helical

antibacterial peptide, WLBU2-mod (RRWVRRVRRVWRRVVRVVRRWVRR), binding

with a gram-negative bacterial inner membrane (IM) mimic composed of palmitoyloleoyl

PE (POPE), palmitoyloleoyl PG (POPG), and 1,1’,2,2’-tetraoctadecenoyl CL (TOCL2) in

a 7:2:1 ratio respectively. The structure of WLBU2-mod was predicted using Robetta to be

either a single extended α-helical structure or a bent α-helical structure. Replica exchange

with solute tempering with an improved Hamiltonian acceptance protocol (REST2) was

performed on WLBU2-mod to relax the peptide to an unstructured conformation in an

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explicit aqueous solution. WLBU2-mod relaxed with REST2 consists of mainly random

coil and β-sheet secondary structure which matches experimental circular dichroism (CD)

results collected by Aria Salyapongse and Dr. Tristram-Nagle. Experimental CD results

with the IM predicted the peptide to be structured with majority α-helical secondary

structure, contrary to the unstructured results of the peptide in water. Both structured and

unstructured WLBU2-mod were placed in parallel 10 Å above the IM mimic and molecular

dynamics (MD) was performed to observe the binding mechanism. Simulations failed to

see significant bilayer thinning or penetration into the hydrophobic core but there is strong

indication that our simulations represent in intermediate state toward the final binding

mechanism. In order to observe more substantial binding to the IM, future projects should

consider increasing the length of the simulations and flipping the orientation of the peptide

to have the hydrophobic components face inward toward the bilayer. Future projects in

combination with the groundwork laid out here will hopefully provide insight into how

antibacterial peptides can become the answer to the resistance crisis we face today.