Biology subjects

Nagaraj, H.

Publications and source records attributed to Nagaraj, H..

4 recordsLinked to original sources

bioRxiv2026

Bacteroidales Secreted Antimicrobial Protein-1 receptor recognition is coupled to protease-activation to form bactericidal pores.

Bacteroidales secreted antimicrobial proteins (BSAPs) are diffusible MACPF-domain toxins that mediate intra-species antagonism in the gut microbiota. Here we define the mechanism of action of BSAP-1 from Bacteroides fragilis, showing how target specificity encoded within the N- and C-terminal domains is coordinated with pore-forming activity of the MACPF. We show that specificity of the toxin for its receptor is mediated by an extended interface comprised of the BSAP-1 C-terminal domain and residues on the receptor that differ from the orthologous protein of BSAP-1 producing strains. On the surface of susceptible cells, BSAP-1 undergoes proteolytic cleavage of an N-terminal regulatory domain, triggering its assembly into oligomeric pores. Cryo-electron microscopy of membrane-inserted BSAP-1 reveals a 13-subunit transmembrane {beta}-barrel pore formed through canonical MACPF rearrangements. Comparative modelling supports a conserved oligomerization mechanism across the BSAP family despite diversification of receptor-binding domains that target either proteins or glycan receptors. Together, these findings establish BSAP-1 as a receptor-targeted, protease-activated antibacterial MACPF toxin and provide a framework for understanding how gut Bacteroidales spatially restrict toxin activation to shape strain-level competition.

microbiology↗

bioRxiv2024

Dichotomous impact of afferent sensory noise on grid-patterned firing and path integration in a continuous attractor network model

The continuous attractor network (CAN) model has been effective in explaining grid-patterned firing in the rodent medial entorhinal cortex, with strong lines of experimental evidence and widespread utilities in understanding path integration. A surprising lacuna in CAN analyses is the lack of quantitative studies assessing the impact of sensory noise in the velocity inputs on the emergence of grid-patterned activity and path integration. In addressing this, we employed an established 2D CAN model which received velocity inputs from a virtual animal traversing a 2D arena to generate grid fields. We introduced different levels of Gaussian noise to the afferent velocity inputs to the model and assessed its impact on the network functions in generating grid fields and performing path-integration. We computed a position estimate at each time step using the network activity and quantified position accuracy using the difference between the real and estimated positions. We performed all simulations using several trajectories for the virtual animal, as computed grid scores and position accuracy showed pronounced trajectory-to-trajectory variability even in noise-free cases. We found that the presence of low levels of sensory noise was beneficial to the generation of grid fields, specifically with trajectories where there was no grid-patterned activity in a no-noise scenario. With trajectories where there was grid-patterned activity in the absence of noise, low levels of noise improved position estimation accuracy. In contrast, high levels of sensory noise impaired position estimates as well as grid-patterned activity, although position estimates were more sensitive to sensory noise compared to grid-patterned activity. Together, these analyses demonstrate the manifestation of stochastic resonance in a 2D CAN model, where low levels of sensory noise were beneficial towards the emergence of grid-patterned firing and in tracking position. Next, motivated by the proposed role of border-cells as an error-correction mechanism, we introduced north and east border cells and connected them to grid cells based on co-activity patterns. For different levels of noise, we computed grid scores and position accuracy in the presence vs. absence of border cells. Interestingly, while border inputs led to grid field formation in cases where grid fields were not generated, their presence only had a marginal impact on position accuracy. Together, our analyses suggest that biological CANs could evolve to yield optimal performance in the presence of noise in biological sensory systems, serving as a stabilizing factor yielding functional robustness through the manifestation of stochastic resonance.

neuroscience↗

bioRxiv2022

Plasticity manifolds and ion-channel degeneracy govern circadian oscillations of neuronal intrinsic properties in the suprachiasmatic nucleus

Motivation and methodsThe suprachiasmatic nucleus (SCN) is the master circadian clock of the mammalian brain that sustains a neural code for circadian time through oscillations in the firing rate of constituent neurons. These cell-autonomous oscillations in intrinsic properties are mediated by plasticity in a subset of ion-channels expressed in SCN neurons and are maintained despite widespread neuron-to-neuron variability in ion channel expression profiles. How do SCN neurons undergo stable transitions and maintain precision in intrinsic properties spanning the day-night cycle if several ion channels change concomitantly in a heterogeneous neuronal population? Here, we address this important question using unbiased stochastic searches on the parametric and the plasticity spaces using populations of SCN models, each explored for multiple valid transitions spanning one complete circadian cycle (day-to-night followed by night-to-day transitions). ResultsOur analyses provided three fundamental insights about the impact of heterogeneities on the circadian oscillations of SCN intrinsic properties. First, SCN neurons could achieve signature electrophysiological characteristics (day-like or night-like) despite pronounced heterogeneity in ion channel conductances, with weak pairwise correlations between their conductance values. This ion-channel degeneracy precluded the need to maintain precise ionchannel expression profiles for achieving characteristic electrophysiological signatures of SCN neurons, thus allowing for parametric heterogeneities despite functional precision. Second, it was not essential that specific conductances had to change by precise values for obtaining valid day-to-night or night-to-day transitions. This plasticity degeneracy, the ability of disparate combinations of ion-channel plasticity to yield the same functional transition, confers flexibility on individual neurons to take one of several routes to achieve valid transitions. Finally, we performed nonlinear dimensionality reduction analyses on the valid plasticity spaces and found the manifestation of a low-dimensional plasticity manifold in day-to-night transitions, but not in night-to-day transitions. These observations demonstrated that the concomitant changes in multiple ion channels are not arbitrary, but follow a structured plasticity manifold that provides a substrate for stability in achieving stable circadian oscillations. ImplicationsOur analyses unveil an elegant substrate, involving a synthesis of the degeneracy and the plasticity manifold frameworks, to effectuate stable circadian oscillations in a heterogeneous population of SCN neurons. Within this framework, the ability of multiple ion channels to change concomitantly provides robustness and flexibility to effectively achieve precise transitions despite widespread heterogeneities in ion-channel expression and plasticity.

neuroscience↗

bioRxiv2021

Identifying SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of nsp5 Main Protease

The coronavirus 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), spread around the world with unprecedented health and socio-economic effects for the global population. While different vaccines are now being made available, very few antiviral drugs have been approved. The main viral protease (nsp5) of SARS-CoV-2 provides an excellent target for antivirals, due to its essential and conserved function in the viral replication cycle. We have expressed, purified and developed assays for nsp5 protease activity. We screened the nsp5 protease against a custom chemical library of over 5,000 characterised pharmaceuticals. We identified calpain inhibitor I and three different peptidyl fluoromethylketones (FMK) as inhibitors of nsp5 activity in vitro, with IC50 values in the low micromolar range. By altering the sequence of our peptidomimetic FMK inhibitors to better mimic the substrate sequence of nsp5, we generated an inhibitor with a subnanomolar IC50. Calpain inhibitor I inhibited viral infection in monkey-derived Vero E6 cells, with an EC50 in the low micromolar range. The most potent and commercially available peptidyl-FMK compound inhibited viral growth in Vero E6 cells to some extent, while our custom peptidyl FMK inhibitor offered a marked antiviral improvement.

biochemistry↗