Biology subjects

Julian, R. R.

Publications and source records attributed to Julian, R. R..

3 recordsLinked to original sources

bioRxiv2024

Unusually Rapid Isomerization of Aspartic Acid in Tau

Spontaneous chemical modifications in long-lived proteins can potentially change protein structure in ways that impact proteostasis and cellular health. For example, isomerization of aspartic acid interferes with protein turnover and is anticorrelated with cognitive acuity in Alzheimers disease. However, few isomerization rates have been determined for Asp residues in intact proteins. To remedy this deficiency, we used protein extracts from SH-SY5Y neuroblastoma cells as a source of a complex, brain-relevant proteome with no baseline isomerization. Cell lysates were aged in vitro to generate isomers, and extracted proteins were analyzed by data-independent acquisition (DIA) liquid chromatography-mass spectrometry (LC-MS). Although no Asp isomers were detected at Day 0, isomerization increased across time and was quantifiable for 105 proteins by Day 50. Data analysis revealed that isomerization rate is influenced by both primary sequence and secondary structure, suggesting that steric hindrance and backbone rigidity modulate isomerization. Additionally, we examined lysates extracted under gentle conditions to preserve protein complexes and found that protein-protein interactions often slow isomerization. Base catalysis was explored as a means to accelerate Asp isomerization due to findings of accelerated asparagine deamidation. However, no substantial rate enhancement was found for isomerization, suggesting fundamental differences in acid-base chemistry. With an enhanced understanding of Asp isomerization in proteins in general, we next sought to better understand Asp isomerization in tau. In vitro aging of monomeric and aggregated recombinant tau revealed that tau isomerizes significantly faster than any similar protein within our dataset, which is likely related to its correlation with cognition in Alzheimers disease. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/626870v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@1f57a5borg.highwire.dtl.DTLVardef@13405fcorg.highwire.dtl.DTLVardef@751a60org.highwire.dtl.DTLVardef@16a753_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2021

Lysosomal proteolysis of amyloid beta is impeded by fibrils grown in both acidic and neutral pH environments

Aggregation of amyloid-beta (A{beta}) into extracellular plaques is a well-known hallmark of Alzheimers disease (AD). Similarly, autophagic vacuoles, autophagosomes, and other residual bodies within dystrophic neurites, though more difficult to detect, are characteristic features of AD. To explore the potential intersection between these observations, we conducted experiments to assess whether A{beta} fibril formation disrupts lysosomal proteolysis. Fibrils constituted from either A{beta} 1-40 or A{beta} 1-42 were grown under both neutral and acidic pH. The extent of proteolysis by individual cathepsins (L, D, B, and H) was monitored by both thioflavin T fluorescence and liquid-chromatography combined with mass spectrometry. The results show that all A{beta} fibrils are resistant to cathepsin digestion, with significant amounts of undigested material remaining for samples of fibrils grown in both neutral and acidic pH. Further analysis revealed that the neutral-grown fibrils are proteolytically resistant throughout the sequence, while the acid-grown fibrils prevented digestion primarily in the C-terminal portion of the sequence. Fibrils grown from A{beta} 1-42 are generally more resistant to degradation compared to A{beta} 1-40. Overall, the results indicate that A{beta} fibrils formed in the neutral pH environments found in intracellular or extracellular spaces may pose the greatest difficulty for complete digestion by the lysosome, particularly when the fibrils are comprised of A{beta} 1-42.

biochemistry↗

bioRxiv2021

Spontaneous Isomerization of Asp387 in Tau is Diagnostic for Alzheimer's Disease: An Endogenous Indicator of Reduced Autophagic Flux

Amino acid isomerization is a spontaneous chemical modification potentially related to the underlying causes of Alzheimers disease (AD). We demonstrate that data-independent acquisition mass spectrometry can be used to characterize isomerization in complex protein mixtures. Examination of a large cohort of brain tissue samples revealed a striking relationship between isomerization of tau and AD status. Surprisingly, isomerization was found to be more abundant in both autosomal dominant and sporadic AD samples relative to controls. We hypothesize that lower autophagic flux in AD brains accounts for these results. Additional data, including quantitative analysis of proteins related to autophagy, strongly support this hypothesis. For example, isomerization of tau is positively correlated with levels of p62, a recognized indicator of autophagic inhibition. In sum, the data suggest strong ties between isomerization and autophagic flux, which may therefore represent a promising target for future investigations into the therapy and prevention of AD.

neuroscience↗