Biology subjects

Bayne, A. N.

Publications and source records attributed to Bayne, A. N..

7 recordsLinked to original sources

bioRxiv2026

GBAviewer: a structural database of GBA1 variants in Parkinson's disease

Background: GBA1 variants are common risk factors for Parkinson's disease (PD), yet the structural consequences of most variants remain uncharacterized. No centralized resource currently integrates the growing number of GCase structures, compounds, and PD-associated variants. Objectives: To develop an interactive tool mapping GBA1-PD missense variants onto GCase structures, alongside interactors and therapeutic compounds. Methods: We built GBAviewer, an R/Shiny web server integrating GBA1-PD Browser variants with crystal structures, cryo-EM complexes, AlphaFold3 models, and AlphaMissense scores. We also modelled a putative GCase-Saposin C-glucosylceramide ternary complex using AlphaFold3. Results: GBAviewer maps variants in 3D across the GCase active site, LIMP-2 and SapC surfaces, chaperone pockets, and dimerization interface. Our ternary model corroborates SapC binding to the GCase active site entrance, where several variants of unknown significance cluster. Conclusions: GBAviewer is a freely accessible platform for structural analysis of GBA1 variants, supporting mechanistic studies and therapeutic development. Available at: https://g-can.shinyapps.io/GBAviewer/

neuroscience↗

bioRxiv2025

Conformational flexibility of tubulin dimers regulates the transitions of microtubule dynamic instability

Microtubules are highly conserved polymers of {beta}-tubulin dimers that undergo dynamic instability. While dynamic instability is conserved across eukaryotes, many of its associated conformational changes, like lattice compaction and twist, are not. Tubulin dimers sample multiple conformations in solution and undergo conformational changes during polymerization; the rate and extent of these changes describes their "conformational flexibility." Here, we investigate the relationship between the conformational flexibility of tubulins and the dynamic phenotypes of the microtubules they produce with a comparative study of Drosophila melanogaster tubulin (Dm-Tb) and Bos taurus brain tubulin (Bt-Tb). While these tubulins share high sequence and structural similarity, their microtubules display divergent dynamic phenotypes in vitro, with altered transition frequencies between phases of growth and shrinkage. Dm-Tb microtubules showed drastically longer lifetimes, lower barriers to nucleation, and a high rescue frequency, while maintaining a similar growth rate to Bt-Tb microtubules. 3D reconstruction of mature Dm-Tb microtubules showed high structural conservation with mammalian microtubules. However, when we performed molecular dynamics simulations of free tubulin dimers, we found Dm-Tb to be more rigid and adopt fewer conformational states than Bt-Tb. Biochemical characterizations experimentally confirmed this finding, leading us to hypothesize that differences in the conformational flexibility of tubulins may tune the frequency of transitions between the dynamic phases of microtubules, thereby altering their stability and overall dynamic phenotypes.

biophysics↗

bioRxiv2025

Substrate recognition by the human mitochondrial processing peptidase and its processing of PINK1

Nuclear-encoded mitochondrial proteins rely on N-terminal targeting sequences (N-MTS) for their import. These N-MTSs interact with the translocation machinery and are cleaved in the matrix by the mitochondrial processing peptidase (MPP), a heterodimeric zinc metalloprotease which is essential for the maturation of imported proteins. Import and cleavage of PINK1, a kinase implicated in Parkinsons disease, govern its ability to sense mitochondrial damage, but the MPP cleavage site and its role in PINK1s function remains cryptic. MPP typically cleaves a unique motif in N-MTSs with an arginine in the P2 position, but how MPP recognizes this motif is unclear. Here, we show that recombinant human MPP cleaves PINK1 between Ala28 and Tyr29 yet is turned over slowly compared to other canonical N-MTSs. While MPP cleavage is not required for downstream PARL processing or PINK1 accumulation in cells, the PINK1 N-MTS binds potently to MPP and inhibits the cleavage of other N-MTSs by glueing the regulatory () and catalytic ({beta}) subunits. Finally, we utilize hydrogen-deuterium exchange mass spectrometry to reveal the binding site of the PINK1 N-MTS on MPP. Taken together, our work provides key insight into both the PINK1 import pathway and the mechanisms of MPP processing.

biochemistry↗

bioRxiv2021

MTSviewer: a database to visualize mitochondrial targeting sequences, cleavage sites, and mutations on protein structures

SummaryMitochondrial dysfunction is implicated in a wide array of human diseases ranging from neurodegenerative disorders to cardiovascular defects. The coordinated localization and import of proteins into mitochondria are essential processes that ensure mitochondrial homeostasis and consequently cell survival. The localization and import of most mitochondrial proteins are driven by N-terminal mitochondrial targeting sequences (MTSs), which interact with import machinery and are removed by the mitochondrial processing peptidase (MPP). The recent discovery of internal MTSs - those which are distributed throughout a protein and act as import regulators or secondary MPP cleavage sites - has expanded the role of both MTSs and MPP beyond conventional N-terminal regulatory pathways. Still, the global mutational landscape of MTSs remains poorly characterized, both from genetic and structural perspectives. To this end, we have integrated a variety of tools into one harmonized R/Shiny database called MTSviewer (https://neurobioinfo.github.io/MTSvieweR/) which combines MTS predictions, cleavage sites, genetic variants, pathogenicity predictions, and N-terminomics data with structural visualization using AlphaFold models of human and yeast mitochondrial proteomes. Availability and ImplementationMTSviewer is freely available on the web at https://neurobioinfo.github.io/MTSvieweR/. Source code is available at https://github.com/neurobioinfo/MTSvieweR. Contacteanfrancois.trempe@mcgill.ca; sali.farhan@mcgill.ca

bioinformatics↗

bioRxiv2021

An Approach to Measuring Protein Turnover in Human Induced Pluripotent Stem Cell Organoids by Mass Spectrometry

Patient-derived organoids from induced pluripotent stem cells have emerged as a model for studying human diseases beyond conventional two-dimensional (2D) cell culture. Briefly, these three-dimensional organoids are highly complex, capable of self-organizing, recapitulate cellular architecture, and have the potential to model diseases in complex organs, such as the brain. For example, the hallmark of Parkinsons disease - proteostatic dysfunction leading to the selective death of neurons in the substantia nigra - present a subtle distinction in cell type specificity that is simply lost in 2D cell culture models. As such, the development of robust methods to study global proteostasis and protein turnover in organoids will remain a critical need as organoid models evolve. To solve this problem, we have designed a workflow to extract proteins from organoids and measure global protein turnover using mass spectrometry and stable isotope labeling using amino acids in cell culture (SILAC). This allowed us to measure the turnover rates of 844 proteins and compare protein turnover to previously reported data in primary cell cultures and in vivo models. Taken together, this method will facilitate the study of proteostasis in organoid models of human disease and will provide an analytical and statistical framework to measure protein turnover in organoids of all cell types.

neuroscience↗

bioRxiv2020

Proteomic profiling of mitochondrial-derived vesicles in brain reveals enrichment of respiratory complex sub-assemblies and small TIM chaperones

The generation of mitochondrial-derived vesicles (MDVs) is implicated in a plethora of vital cell functions, from mitochondrial quality control to peroxisomal biogenesis. The discovery of distinct subtypes of MDVs has revealed the selective inclusion of mitochondrial cargo in response to varying stimuli. However, the true scope and variety of MDVs is currently unclear, and unbiased approaches have yet to be used to understand their biology. Furthermore, as mitochondrial dysfunction has been implicated in many neurodegenerative diseases, it is essential to understand MDV pathways in the nervous system. To address this, we sought to identify the cargo in brain MDVs. We used an in vitro budding assay and proteomic approach to identify proteins selectively enriched in MDVs. 72 proteins were identified as MDV enriched, of which 31% were OXPHOS proteins. Interestingly, the OXPHOS proteins localized to specific modules of the respiratory complexes, hinting at the inclusion of sub-assemblies in MDVs. Small TIM chaperones were also highly enriched in MDVs, linking mitochondrial chaperone-mediated protein transport to MDV formation. As the two Parkinsons disease genes PINK1 and Parkin have been previously implicated in MDV biogenesis in response to oxidative stress, we compared the MDV proteomes from the brains of wild-type mice with those of PINK1-/- and Parkin-/- mice. No significant difference was found, suggesting that PINK1- and Parkin-dependent MDVs make up a small proportion of all MDVs in the brain. Our findings demonstrate a previously uncovered landscape of MDV complexity and provide a foundation from which to discover further novel MDV functions.

biochemistry↗

bioRxiv2019

The E3 ubiquitin ligase TRAF6 is a novel interacting protein of amyotrophic lateral sclerosis-linked misfolded SOD1

Amyotrophic lateral sclerosis (ALS) is a fatal disease, characterized by the selective loss of motor neurons leading to paralysis. Mutations in the gene encoding superoxide dismutase 1 (SOD1) are the second most common cause of familial ALS, and considerable evidence suggests that these mutations result in an increase in toxicity due to protein misfolding. We previously demonstrated in the SOD1G93A rat model that misfolded SOD1 exists as distinct conformers and forms deposits on mitochondrial subpopulations. Here, using SOD1G93A rats and conformation-restricted antibodies specific for misfolded SOD1 (B8H10 and AMF7-63), we identified the interactomes of the mitochondrial pools of misfolded SOD1. This strategy identified binding proteins that uniquely interacted with either AMF7-63 or B8H10-reactive SOD1 conformers as well as with a high proportion of interactors common to both conformers. Of this latter set, we identified the E3 ubiquitin ligase TNF receptor-associated factor 6 (TRAF6) as a SOD1 interactor and determined that exposure of the SOD1 functional loops facilitates this interaction. Of note, this conformational change was not universally fulfilled by all SOD1 variants and differentiated TRAF6-interacting from TRAF6 non-interacting SOD1 variants. Functionally, TRAF6 stimulated polyubiquitination and aggregation of the interacting SOD1 variants. TRAF6 E3 ubiquitin ligase activity was required for the former, but was dispensable for the latter, indicating that TRAF6-mediated polyubiquitination and aggregation of the SOD1 variants are independent events. We propose that the interaction between misfolded SOD1 and TRAF6 may be relevant to the etiology of ALS.

neuroscience↗