Year of Award

2023

Document Type

Dissertation

Degree Type

Doctor of Philosophy (PhD)

Degree Name

Biochemistry & Biophysics

Department or School/College

Department of Chemistry and Biochemistry

Committee Chair

Bruce E. Bowler

Commitee Members

Steve Lodmell, J.B. Alexander Ross, Travis Hughes, Keith Parker

Abstract

The interaction between cytochrome c and cardiolipin is known to be essential for the onset of apoptosis: cytochrome c becomes competent for peroxidase activity due to the presence of reactive oxygen species and oxidizes cardiolipin, ultimately resulting in mitochondrial membrane pores that allow cytochrome c to escape into the cytosol and form the apoptosome complex. As such, understanding this reaction is critical to understanding the mechanisms of programmed cell death. Despite this, many components of this interaction are still under debate. Examples of this include which components of cytochrome c structure are responsible for the large differences in peroxidase activity of the yeast and human cytochrome c homologs, the potential impact of the unique structural properties of cardiolipin, and the nature of the electrostatic binding site between cytochrome c and cardiolipin in vivo. The dynamics of -loop C (residues 40 to 57) of cytochrome c has been suggested to mediate the peroxidase activity of cytochrome c. In the following work, it was discovered that certain residues between yeast iso-1-cytochrome c and human cytochrome c in the Ω-loop C substructure have coevolved (S40/T40, V57/I57, and N63/T63, respectively). In this dissertation, the hypothesis that these residues covaried between the evolution of yeast iso-1-cytochrome c and human cytochrome c to optimize cytochrome c-mediated peroxidase activity in the early stages of apoptosis was tested. The results show that mutations to the human cytochrome c residues in yeast iso-1-cytochrome c (S40T, V57I, and N63T) and vice versa (T40S, I57V, T63N) only produce modest if any changes in global & local stability and peroxidase activity. Therefore, the dynamics that mediate the peroxidase activity of cytochrome c appear to be more complex than has been thought. It was also shown that cardiolipin can produce anomalous lipid structures, even within a relatively small membrane mimic such as a nanodisc. Lastly, it is shown that, in salt concentrations more similar to those in vivo than in previous published studies, positively charged residues other than those canonically considered to be part of the electrostatic binding site are found to play a role in the electrostatic attraction between cytochrome c and cardiolipin in yeast iso-1-cytochrome c.

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