UCLA

Coenzyme Q (CoQ) is a redox-active lipid functioning at the intersection of diverse metabolic processes. Its unique chemical and physical properties enable it to function both as a mitochondrial electron carrier and as a chain-breaking antioxidant, supporting cellular respiration and inhibiting lipid peroxidation within the lipid bilayer. In eukaryotes, CoQ is synthesized by nuclear-encoded polypeptides that assemble into a lipid-rich complex, termed the CoQ synthome, peripherally associated with the matrix face of the inner mitochondrial membrane. Defects in CoQ biosynthesis cause primary CoQ deficiency, a condition with diverse clinical manifestations. Supplementation with CoQ10, the native human form, has shown inconsistent efficacy due to poor bioavailability, underscoring the need for a comprehensive understanding of CoQ biosynthesis. Chapter 1 of this work provides an overview of CoQ’s essential roles in metabolism, as well as current functional and structural evidence supporting our understanding of the CoQ biosynthetic polypeptides. Chapter 2 examines the genetic underpinnings of primary CoQ deficiency by classifying missense single nucleotide variants (SNVs) affecting functional regions of core synthome subunits. Building on this analysis, Chapters 3 and 4 focus on biochemical validation of functional regions in the C-methyltransferase COQ5/Coq5 in Saccharomyces cerevisiae. Chapter 3 combines liquid chromatography–tandem mass spectrometry (LC-MS/MS) with molecular dynamics (MD) simulations and other computational approaches to identify catalytic residues and proposes a mechanism for aromatic carbon nucleophile activation and methyl transfer. Chapter 4 builds on this work by linking Coq5 dimerization to catalytic activity through an SNV in the dimer interface that disrupts both oligomerization and CoQ biosynthesis. Appendices I–III extend beyond CoQ biosynthesis, addressing C-methyltransferase substrate selectivity, methylation as a post-translational modification, and mechanistic organic chemistry. Additional supporting data are provided as supplementary files: Files 1–5 relate to Chapter 3 and include an AlphaFold-predicted COQ5 structure, a table summarizing analyses of COQ5 SNVs, and representative MD structures; Files 6–7, associated with Appendix II, contain interaction energies and structural analyses of methylarginine-containing complexes. Together, this work provides insights into how genetic variation, active-site chemistry, and protein–protein interactions shape CoQ biosynthesis and highlights a broader interest in the functionally diverse family of methyltransferases.