Date of Graduation

2023

Document Type

Dissertation

Degree Type

PhD

College

Eberly College of Arts and Sciences

Department

Chemistry

Committee Chair

Blake Mertz

Committee Co-Chair

Justin Legleiter

Committee Member

Mark McLaughlin

Committee Member

Brian Popp

Committee Member

Peng Li

Abstract

Cell membranes are crowded environments which can modulate protein structure-function relationships through interaction with lipids, other proteins, carbohydrate structures and so on. This work focuses the impact of the membrane environment on two varieties of peptides: Microbial rhodopsin proteins, and cyclic peptides.

Life on Earth is dependent on the ability of plants and microbes to harness sunlight for energy production. Their ability to transform light into carbohydrates requires tailor-made machinery, and for a wealth of microorganisms, microbial rhodopsin proteins (MR) are critical for maintaining the concentration gradients used to produce the energy molecule Adenosine triphosphate (ATP). The central retinal molecule covalently attached to the transmembrane protein can absorb light, triggering a conformational change in the retinal backbone. As the photon's energy dissipates through a sequence of ion transfers, residue rearrangements, and alterations in the tertiary structure, the protein returns to its ground state conformation, resulting in an ion passing through the protein. Applications of MR proteins for light-based technologies require total control of the photocycle of a protein and the ability to create useful mutations of desired absorbance. To reduce wet lab cost, we have demonstrated the ability of molecular dynamics (MD) simulations to capture the retinal dynamics of the photointermediate structures of Bacteriorhodopsin, which can create a linear regression model that can predict both bR photocycle intermediates and spectral absorption of pocket mutant bR structures within $+/-$ 18 nm. We have also used longer time scale equilibrium MD simulations to gather detailed knowledge of structural alterations between photointermediates with greater resolution, as shown in the M state simulation of blue proton-proteorhodopsin(BPR).

Cyclic peptides are ringed peptides that, despite their large size, are able to penetrate cell membranes. Their large scaffolding is an ideal method to target G-coupled protein receptors, such as BPR and bR. In this work, we show that solvent simulations of lariat peptides are able to capture conformational change and can be used to create a high through-put screening method, which in forgoing the need to model a bilayer, will provide significant speed in filtering out peptides with low likelihood of penetration of the cell membrane.

Download

Share

COinS