Biology subjects

Beaudoin, C. A.

Publications and source records attributed to Beaudoin, C. A..

7 recordsLinked to original sources

bioRxiv2026

Reduced entropy of subthalamic beta bursts predicts freezing of gait in Parkinsons disease

BackgroundFreezing of gait (FOG) in Parkinsons disease is associated with abnormal beta activity in the subthalamic nucleus (STN), but the temporal structure of burst dynamics remains poorly understood. ObjectivesTo determine whether temporal features of STN beta bursts distinguish pre-freeze from stable gait and predict freezing onset. MethodsSTN recordings during gait from four individuals were analyzed. Temporal features of burst timing, including entropy and variability, were computed across behavioral states. Predictive performance was assessed using leave-one-patient-out classifiers. ResultsEntropy of inter-burst intervals was reduced prior to freezing (p < 0.01), with strong predictive performance (AUC = 0.825; threshold AUC = 0.858). During freezing, variability measures decreased and temporal structure increased, while entropy did not differ from pre-freeze. Phase-amplitude coupling showed frequency-specific but heterogeneous effects across comparisons. ConclusionsReduced temporal variability of STN beta burst timing precedes and predicts freezing, suggesting a transition to constrained neural dynamics.

neuroscience↗

bioRxiv2026

HANSEN: An Integrated Structural and Functional Proteome Resource for Structure-Guided Drug Discovery in Mycobacterium leprae

Leprosy remains a leading infectious cause of preventable disability, yet its causative agent, Mycobacterium leprae (M. leprae), is structurally under-characterised. Only ten Protein Data Bank (PDB) entries represent seven of its 1,603 protein-coding genes. We present HANSEN, a proteome-wide structural and functional resource for M. leprae. Monomeric and oligomeric models were generated with AlphaFold 3, Boltz-1, Boltz-2 and Chai-1, and annotated with per-residue confidence, predicted aligned error and, for assemblies, interface confidence. Ligand-binding pockets were predicted with AF2BIND, P2Rank and fpocket, template-derived ligands were modelled within oligomeric complexes, residue-level B-cell epitope propensity was estimated with DiscoTope-3.0, and gene essentiality was transferred from Mycobacterium tuberculosis transposon-sequencing labels. These features are integrated in a relational database with interactive visualisation and combined into a calibrated Target Priority Score that ranks all 1,603 proteins into four tiers and recovers established antimycobacterial targets. HANSEN (https://hansen-leprosy.medschl.cam.ac.uk/home) provides a practical basis for target prioritisation and structure-guided drug discovery in leprosy.

bioinformatics↗

bioRxiv2026

Pathological cortico-STN beta coupling in Parkinson's disease is confined to beta bursts

Abnormal beta-band activity (13-30 Hz) within the cortico-basal ganglia network is a hallmark of Parkinsons disease (PD) and is closely linked to motor impairment. Pathological beta activity in the subthalamic nucleus (STN) occurs predominantly as brief, high-amplitude bursts rather than continuous oscillations. Although beta-band coherence between the STN and cortex increases during bursts, it remains unclear whether cortico-STN beta coupling persists outside these bursts. Using intraoperative STN local field potentials and simultaneous cortical electrocorticography from seven patients undergoing deep brain stimulation implantation surgery, cortico-STN beta coupling during burst and non-burst epochs was compared. Coupling was assessed using magnitude-squared coherence and the debiased weighted phase lag index (dwPLI) and compared against surrogate distributions generated by circular time-shifting. Both coupling metrics were significantly elevated during burst epochs relative to non-burst periods. During non-burst epochs, coupling collapsed to surrogate levels, indicating no evidence of sustained synchronization. Time-resolved analyses further demonstrated that elevated coupling was confined to burst epochs. Although a subset of motor cortical contacts exhibited elevated baseline coherence, coupling was less evident using dwPLI. These findings suggest that pathological cortico-STN beta coupling in PD is preferentially expressed during beta bursts rather than sustained across non-burst epochs, with implications for adaptive neuromodulation strategies.

neuroscience↗

bioRxiv2025

Structural implications of glycosylation on the voltage-gated sodium channel β3-subunit

Voltage-gated sodium (NaV) channel -subunits are modulated by associated {beta}-subunits that affect their localization, trafficking and gating behaviour. The {beta}-subunits are members of the immunoglobulin (Ig) domain family of cell-adhesion molecules and the interactions between their extracellular Ig-domains may modify channel clustering. The full-length {beta}3-subunit can form cis trimers on the plasma membrane. The atomic resolution structure of a deglycosylated trimeric {beta}3-subunit Ig-domain has been solved by X-ray crystallography. However, it is not clear whether this particular trimeric Ig-domain structure is plausible for cell-expressed, glycosylated {beta}3-subunits. Here we use glycan profiling to confirm an extensive and heterogeneous pattern of {beta}3-subunit glycosylation, with the majority of glycans being bi- and tri-antennary structures with one or two terminal sialic acids. Two tryptic peptides of the {beta}3 Ig-domain are predicted to contain potential N-linked glycosylation sites. When the isolated, glycosylated full-length {beta}3-subunit was trypsin-digested and analysed by LC-MS/MS, only one of these peptides - containing an N-linked glycosylation site at residue N95 and located close to the trimer interface - was identified in its unmodified form, suggesting that residue N95 is under-glycosylated. All-atom molecular dynamics simulations of the glycosylated, membrane-bound full-length {beta}3 trimer confirmed that glycans can be accommodated with the Ig-domain trimer and indeed, may contribute to protein-membrane and inter-protomer interactions within the full-length, membrane-embedded trimer. Further biochemical studies are warranted to explore the interactions between oligomeric {beta}-subunits with corresponding -subunit sodium channels.

biochemistry↗

bioRxiv2024

Isoform-specific N-linked glycosylation of voltage-gated sodium channel alpha-subunits alters beta-subunit binding sites

HighlightsO_LIThree N-linked glycosylation sites conserved among all Nav channels C_LIO_LIGlycan modelling and molecular dynamics simulations highlight 3D landscape C_LIO_LIUnique Nav1.5 N-linked glycans may prevent binding to Ig-domains of {beta}1 and {beta}3 C_LIO_LIUnique Nav1.8 N-linked glycan may prevent binding to Ig-domains of {beta}2 and {beta}4 C_LIO_LIN-linked glycans likely contribute to supra-molecular clustering of Nav channels C_LI Voltage-gated sodium channel -subunits (Nav1.1-1.9) initiate and propagate action potentials in neurons and myocytes. The Nav {beta}-subunits ({beta}1-4) have been shown to modulate -subunit properties. Homo-oligomerization of {beta}-subunits on neighboring or opposing plasma membranes has been suggested to facilitate cis or trans interactions, respectively. The interactions between several Nav channel isoforms and {beta}-subunits have been determined using cryogenic electron microscopy (cryo-EM). Interestingly, the Nav cryo-EM structures reveal the presence of N-linked glycosylation sites. However, only the first glycan moieties are typically resolved at each site due to the flexibility of mature glycan trees. Thus, existing cryo-EM structures may risk de-emphasizing the structural implications of glycans on the Nav channels. Herein, molecular modelling and all-atom molecular dynamics simulations were applied to investigate the conformational landscape of N-linked glycans on Nav channel surfaces. The simulations revealed that negatively-charged sialic acid residues of two glycan sites may interact with voltage-sensing domains. Notably, two Nav1.5 isoform-specific glycans extensively cover the -subunit region that, in other Nav channel -subunit isoforms, corresponds to the binding site for the {beta}1-(and likely {beta}3-) subunit immunoglobulin (Ig) domain. Nav1.8 contains a unique N-linked glycosylation site that likely prevents its interaction with the {beta}2 and {beta}4-subunit Ig domain. These isoform-specific glycans may have evolved to facilitate specific functional interactions, for example by redirecting {beta}-subunit Ig-domains outwards to permit cis or trans supra-clustering within specialized cellular compartments such as the cardiomyocyte perinexal space. Further experimental work is necessary to validate these predictions.

biochemistry↗

bioRxiv2024

Similarity of drug targets to human microbiome metaproteome promotes pharmacological promiscuity

Similarity between candidate drug targets and human proteins is commonly assessed to minimize the occurrence of side effects. Although numerous drugs have been found to disrupt the health of the human microbiome, no comprehensive comparison between established drug targets and the human microbiome metaproteome has yet been conducted. Therefore, herein, sequence and structure alignments between human and pathogen drug targets and representative human gut, oral, and vaginal microbiome metaproteomes were performed. Both human and pathogen drug targets were found to be similar in sequence, function, structure, and drug binding capacity to proteins in diverse pathogenic and non-pathogenic bacteria from all three microbiomes. The gut metaproteome was identified as particularly susceptible overall to off-target effects. Certain symptoms, such as infections and immune disorders, may be more common among drugs that non-selectively target host microbiota. These findings suggest that similarities between human microbiome metaproteomes and drug target candidates should be routinely checked.

bioinformatics↗

bioRxiv2021

Predicted structural mimicry of spike receptor-binding motifs from highly pathogenic human coronaviruses

Viruses often encode proteins that mimic host proteins in order to facilitate infection. Little work has been done to understand the potential mimicry of the SARS-CoV-2, SARS-CoV, and MERS-CoV spike proteins, particularly the receptor-binding motifs, which could be important in determining tropism of the virus. Here, we use structural bioinformatics software to characterize potential mimicry of the three coronavirus spike protein receptor-binding motifs. We utilize sequence-independent alignment tools to compare structurally known or predicted three-dimensional protein models with the receptor-binding motifs and verify potential mimicry with protein docking simulations. Both human and non-human proteins were found to be similar to all three receptor-binding motifs. Similarity to human proteins may reveal which pathways the spike protein is co-opting, while analogous non-human proteins may indicate shared host interaction partners and overlapping antibody cross-reactivity. These findings can help guide experimental efforts to further understand potential interactions between human and coronavirus proteins. HighlightsO_LIPotential coronavirus spike protein mimicry revealed by structural comparison C_LIO_LIHuman and non-human protein potential interactions with virus identified C_LIO_LIPredicted structural mimicry corroborated by protein-protein docking C_LIO_LIEpitope-based alignments may help guide vaccine efforts C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/441187v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@1f09454org.highwire.dtl.DTLVardef@19a5557org.highwire.dtl.DTLVardef@158d3fdorg.highwire.dtl.DTLVardef@c59511_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗