Date of Graduation

12-2022

Document Type

Dissertation

Degree Name

Doctor of Philosophy in Cell & Molecular Biology (PhD)

Degree Level

Graduate

Department

Biological Sciences

Advisor/Mentor

Mahmoud Moradi

Committee Member

Bob Beitle Jr.

Second Committee Member

Suresh Thallapuranam

Third Committee Member

Yong Wang

Keywords

Conformational dynamics, Membrane proteins, Molecular dynamics simulations, Nanoparticles, Peptides, Protein mechanism

Abstract

Researchers in chemistry and biology often utilize computer simulations, in conjunction with experimental data, to model and predict the structures, energies, kinetics, processes, and functions of the systems that are their focus of study, ranging from single molecules to whole viruses. Here, we use molecular dynamics (MD) techniques to gain a deeper understanding of biomolecular processes in biology and biotechnology-oriented applications. Using a mixture of equilibrium and non-equilibrium MD simulations, this work describes the insertion process of YidC at the atomic level. In order to better comprehend the insertion process, several docking models of YidC-Pf3 in the lipid bilayer were created. We employed conventional molecular dynamics simulations combined with a non-equilibrium approach to undertake a thorough analysis of the conformational difference between the two docking models produced. Our results show that this high-affinity association requires the YidC transmembrane (TM) groove, and that the hydrophilic YidC groove is crucial for protein trafficking through the cytoplasmic membrane bilayer to the periplasmic side. The Pf3 coat protein is mechanistically affected by conformational changes in the YidC TM domain and membrane core at various phases of the insertion process. The hydration and dehydration of the YidC's hydrophilic groove are also crucial throughout the insertion phase. These findings show that during insertion, Pf3's coat protein interacts with the membrane and YidC in a variety of conformational states. Finally, the thorough investigation directly supports YidC's role as a independent insertase. We have performed the first comprehensive analysis of the gram-negative bacterial YidC protein using microsecond-level all-atom MD simulations. By using equilibrium MD simulations, this study clarifies the relevance of many domains in the YidC structure at the atomic level. The purpose of this study was to describe the crucial function of the C2 loop and the periplasmic domain found in gram-negative YidC, which is lacking in its gram-positive counterpart. Various models of YidC embedded in the lipid bilayer were created. According to our findings, the C2 loop stabilizes the protein overall, especially in the transmembrane region, and it also has an allosteric effect on the periplasmic domain. Important intra- and inter-domain interactions that support the protein's stability and functionality have been identified. Lastly, we also provide a unique computational method for predicting the trend of the size and activity of peptide-directed nanoparticles by calculating the peptide's binding affinity to a single ion. To examine how the solitary, Green Fluorescent Protein (GFP)-fused peptides behave differently from one another, we used MD simulations. The usual nanoparticle sizes observed from images taken with a transmission electron microscope are in line with the binding free energies we estimated for palladium (Pd). Additionally, computationally estimated Pd binding affinities match Stille coupling and Suzuki-Miyaura reaction turnover frequencies (TOF). The findings demonstrate that although employing Pd4 and its two known variations (A6 and A11) alone results in nanoparticles of various sizes, fusing these peptides to the GFPuv protein results in nanoparticles with comparable sizes and activity. To put it another way, the GFPuv makes the nanoparticles less sensitive to the peptide sequence. In this study, a computational framework for making peptides that are both free and attached to proteins is shown. This makes it easier to make nanoparticles with well-defined properties.

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