Dissertations, Theses, and Capstone Projects

Date of Degree

9-2017

Document Type

Dissertation

Degree Name

Ph.D.

Program

Chemistry

Advisor

Themis Lazaridis

Committee Members

Lei Xie

Marta Filizola

Emilio Gallicchio

Subject Categories

Biophysics | Chemistry | Computational Biology

Keywords

Antimicrobial peptides, Protegrin, Implicit Membrane Model 1, Effective Energy Function 1, Molecular dynamics

Abstract

β-hairpin antimicrobial peptides (AMPs) are small, usually cationic peptides that provide innate biological defenses against multiple agents. They have been proposed as the basis for novel antibiotics, but their pore formation has not been directly observed on a molecular level. We review previous computational studies of peptide-induced membrane pore formation and report several new molecular dynamics simulations of β-hairpin AMPs to elucidate their pore formation mechanism. We simulated β-barrels of various AMPs in anionic implicit membranes, finding that most of the AMPs’ β-barrels were not as stable as those of protegrin. We also performed an optimization study of protegrin β-barrels in implicit membranes, finding that nonamers were the most stable, but that multiplicities 7–13 were almost equally favorable. This indicated the possibility of a diversity of pore states consisting of various numbers of protegrin peptides. Finally, we used the Anton 2 supercomputer to perform multimicrosecond, all-atom molecular dynamics simulations of various protegrin-1 oligomers on the membrane surface and in transmembrane topologies. We also considered an octamer of the β-hairpin AMP tachyplesin. The simulations on the membrane surface indicated that protegrin dimers are stable, while trimers and tetramers break down because they assume a bent, twisted β-sheet shape. Tetrameric arcs remained stably inserted, but the pore water was displaced by lipid molecules. Unsheared protegrin β-barrels opened into long, twisted β-sheets that surrounded stable aqueous pores, whereas tilted barrels with sheared hydrogen bonding patterns were stable in most topologies. A third type of observed pore consisted of multiple small oligomers surrounding a small, partially lipidic pore. The octameric tachyplesin bundle resulted in small pores surrounded by 6 peptides as monomers and dimers. The results imply that multiple protegrin configurations may produce aqueous pores and illustrate the relationship between topology and pore formation steps. However, these structures’ long-term stability requires further investigation.

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