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Mass Spectrometric Investigations of Hidden Post-Translational Modifications and the Inevitable Fate of Long-Lived Proteins

  • Author(s): Lyon, Yana Alexandra
  • Advisor(s): Julian, Ryan R
  • et al.
Abstract

Protein turnover is essential for the vitality of a functional proteome, as it allows for old and damaged proteins to be destroyed and replaced with newly synthesized copies. However, there is a growing class of proteins that escape this process and are classified as long-lived proteins (LLPs). The intrinsic instability of LLPs makes them susceptible to damage through the accumulation of unwanted post-translational modifications (PTMs), and mounting evidence suggests that this plays a critical role in aging and disease. It is known that crystallin turnover essentially stops in the mature lens fiber cells of the eye which makes it an ideal target for understanding damage due to aging, however mapping out the ensuing degradation has proven to be a formidable challenge. There are a myriad of spontaneous PTMs that accrue in the lens, including isomerization and epimerization, both of which are invisible to many traditional analytical techniques. Such small perturbations to individual amino acids may appear to be innocuous, but in fact, these hidden modifications impact protein structure, function, and solubility, all of which are crucial for lens transparency. The details of protein aging are examined herein by employing a novel mass spectrometric dissociation technique that utilizes radical chemistry to detect sites of isomerization and epimerization. Studies on young animal eye lenses reveal how the degree of these modifications change as a function of protein solubility and shows that specific structural motifs and amino acid repeats serve as isomerization hotspots. Investigations on human donor lenses expose an increased presence of isoAspartyl residues in the nucleus of the lens compared to the cortex, suggesting decreased activity of a specific repair enzyme. Delving deeper into the structural and functional consequences of these modifications required the use of native mass spectrometry, enzyme assays, and molecular dynamics calculations, all of which help show that proper crystallin oligomerization can be disrupted by these PTMs. An alternative approach to RDD utilizing electron transfer dissociation (ETD) was also developed to detect epimerized residues in peptide models. Collectively, this work serves to better our understanding of how isomerization and epimerization contribute to the inevitable fate of LLPs.

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