Biology subjects

Sahoo, B.

Publications and source records attributed to Sahoo, B..

At least 19 recordsLinked to original sources

bioRxiv2026

Structural Mechanisms of SAMD9 Autoinhibition and Pathogenic Dysregulation

SAMD9 and SAMD9L (SAMD9/9L) are large cytosolic proteins essential for hematopoietic homeostasis and antiviral defense1-3. Germline gain-of-function (GoF) mutations in SAMD9/9L cause severe multisystem disorders and predisposition to leukemia, yet the mechanisms that regulate SAMD9/9L activity and how pathogenic mutations disrupt these processes, remain poorly understood. Here, we determine cryo-electron microscopy structures of human SAMD9 in multiple conformational and oligomeric states. We show that SAMD9 predominantly adopts a closed, autoinhibited conformation stabilized by a central ATP-bound nucleotide-binding oligomerization domain (NOD) and an extensive network of intramolecular interactions. Recurrent patient-derived GoF mutations localize to and destabilize these intramolecular interfaces, and restoring the disrupted interactions through compensatory mutations reinstates autoinhibition. We further identify low-abundance asymmetric SAMD9 dimers in which one protomer undergoes large conformational changes and establishes intermolecular interactions that are essential for SAMD9 activation. Together, these findings define the structural basis of SAMD9 autoinhibition and explain how human GoF mutations subvert this regulatory mechanism to drive disease.

biophysics↗

bioRxiv2025

Hypothalamic Vasopressin Neurons Enable Maternal Thermoregulatory Behaviors

Newborns of many mammalian species are partial poikilotherms and require adult thermoregulatory care for survival. In mice, pup survival in cold and cool ambient temperature depends on the ability of adult caregivers to huddle pups and bring them into a high-quality nest. It is therefore essential that adult mice adjust parental care as a function of changes in ambient temperature. Here, we investigated how mouse maternal care adapts to a range of temperatures, from cold to warm. We show that changes in ambient temperature affect several individual and co-parenting maternal behaviors in both dams and virgin female mice, and modulate activity of vasopressin neurons. Furthermore, we establish that the effects of ambient temperature on both maternal care and the activity of vasopressin neurons depend in part on thermosensation, specifically on the TRPM8 sensor. Using trans-synaptic anterograde tracing and whole-brain activity mapping, we find that vasopressin neurons from the paraventricular hypothalamic nucleus connect synaptically with temperature-responsive brain structures implicated in maternal care. We then show that optogenetic activation of vasopressin projections to the central amygdala, a structure activated by cold ambient temperature, recapitulates the effects of cold on co-parenting behaviors. Our data provide a biological mechanism for maternal thermoregulatory behavior in mice with translational relevance to the reported association between ecosystem temperature fluctuations and variations in human child neglect cases.

neuroscience↗

bioRxiv2024

Distractor anticipation during working memory is associated with theta and beta oscillations across spatial scales

Anticipating distractors during working memory maintenance is critical to reduce their disruptive effects. In this study, we aimed to identify the oscillatory correlates of this process across different spatial scales of neural activity. We simultaneously recorded local field potentials (LFP) from the LPFC and electroencephalograms (EEG) from the scalp of monkeys performing a modified memory-guided saccade (MGS) task. The monkeys were required to remember the location of a target visual stimulus while anticipating distracting visual stimulus, flashed at 50% probability during the delay period. We found significant theta-band activity across spatial scales during anticipation of a distractor, closely linked with underlying working memory dynamics, through decoding and cross-temporal generalization analyses. EEG particularly reflected reactivation of memory around the anticipated time of a distractor, even in the absence of stimuli. During this anticipated time, beta-band activity exhibited transiently enhanced intrahemispheric communication between the LPFC and occipitoparietal brain areas. These oscillatory phenomena were observed only when the monkeys successfully performed the task, implicating their possible functional role in mitigating anticipated distractors. Our results demonstrate that distractor anticipation recruits multiple oscillatory processes across the brain during working memory maintenance, with a key activity observed predominantly in the theta and beta bands.

neuroscience↗

bioRxiv2024

Neural Dynamics Underlying False Alarms in Extrastriate Cortex

The unfolding of neural population activity can be approximated as a dynamical system. Stability in the latent dynamics that characterize neural population activity has been linked with consistency in animal behavior, such as motor control or value-based decision-making. However, whether similar dynamics characterize perceptual activity and decision-making in the visual cortex is not well understood. To test this, we recorded V4 populations in monkeys engaged in a non-match-to-sample visual change-detection task that required sustained engagement. We measured how the stability in the latent dynamics in V4 might affect monkeys perceptual behavior. Specifically, we reasoned that unstable sensory neural activity around dynamic attractor boundaries may make animals susceptible to taking incorrect actions when withholding action would have been correct ("false alarms"). We made three key discoveries: 1) greater stability was associated with longer trial sequences; 2) false alarm rate decreased (and reaction times slowed) when neural dynamics were more stable; and, 3) low stability predicted false alarms on a single-trial level, and this relationship depended on the elapsed time during the trial, consistent with the latent neural state approaching an attractor boundary. Our results suggest the same outward false alarm behavior can be attributed to two different potential strategies that can be disambiguated by examining neural stability: 1) premeditated false alarms that might lead to greater stability in population dynamics and faster reaction time and 2) false alarms due to unstable sensory activity consistent with misperception.

neuroscience↗

bioRxiv2023

Genome organization in double-stranded DNA viruses observed by cryoET

Double-stranded DNA (dsDNA) viruses package their genetic material into protein cages with diameters usually a few hundred times smaller than the length of their genome. Compressing the relatively stiff and highly negatively charged dsDNA into a small volume is energetically costly and mechanistically enigmatic. Multiple models of dsDNA packaging have been proposed based on various experimental evidence and simulation methods, but direct observation of any viral genome organization is lacking. Here, using cryoET and an improved data processing scheme that utilizes information from the encaging protein shell, we present 3D views of dsDNA genome inside individual viral particles at resolution that densities of neighboring DNA duplexes are readily separable. These cryoET observations reveal a "rod-and-coil" fold of the dsDNA that is conserved among herpes simplex virus type 1 (HSV-1) with a spherical capsid, bacteriophage T4 with a prolate capsid, and bacteriophage T7 with a proteinaceous core inside the capsid. Finally, inspired by the genome arrangement in partially packaged T4 particles, we propose a mechanism for the genome packaging process in dsDNA viruses.

molecular biology↗

bioRxiv2023

Effects of protein G-quadruplex interactions on phase transitions and protein aggregation

The SERF family of proteins were originally discovered for their ability to accelerate amyloid formation. Znf706 is an uncharacterized protein whose N-terminus is homologous to SERF proteins. We show here that human Znf706 can promote protein aggregation and amyloid formation. Unexpectedly, Znf706 specifically interacts with stable, non-canonical nucleic acid structures known as G-quadruplexes. G-quadruplexes can affect gene regulation and suppress protein aggregation; however, it is unknown if and how these two activities are linked. We find Znf706 binds preferentially to parallel G-quadruplexes with low micromolar affinity, primarily using its N-terminus, and upon interaction, its dynamics are constrained. G-quadruplex binding suppresses Znf706s ability to promote protein aggregation. Znf706 in conjunction with G-quadruplexes therefore may play a role in regulating protein folding. RNAseq analysis shows that Znf706 depletion specifically impacts the mRNA abundance of genes that are predicted to contain high G-quadruplex density. Our studies give insight into how proteins and G-quadruplexes interact, and how these interactions affect both partners and lead to the modulation of protein aggregation and cellular mRNA levels. These observations suggest that the SERF family of proteins, in conjunction with G-quadruplexes, may have a broader role in regulating protein folding and gene expression than previously appreciated.

biochemistry↗

bioRxiv2023

How NINJ1 mediates plasma membrane rupture and why NINJ2 cannot

NINJ1 is a recently identified active executioner of plasma membrane rupture (PMR), a process previously thought to be a passive osmotic lysis event in lytic cell death. NINJ2 is a close paralog of NINJ1 but it failed to mediate PMR. By cryoEM, we found that both NINJ1 and NINJ2 were able to assemble into linear filament that binds strongly to lipids on one side but is water-soluble on the other side. The more-or-less straight NINJ1 filament was able to wrap around a membrane bleb and solubilize it from the plasma membrane to induce PMR; however, the intrinsically curved NINJ2 filament failed to do so, explaining its incapability of mediating PMR. We further demonstrated that binding to cholesterol at the inner leaflet of the lipid bilayer was responsible for the curving of the NINJ2 filament, while strong lipid binding at the outer leaflet was contributing to NINJ1s capability of mediating PMR.

immunology↗

bioRxiv2021

SARS-CoV-2 genome sequences from Lucknow, Uttar Pradesh, India by Nanopore Sequencing

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has emerged as a significant challenge worldwide. Rapid genome sequencing of SARS-CoV-2 is going on across the globe to detect mutations and genomic modifications in SARS-CoV-2. In this study, we have sequenced twenty-three SARS-CoV-2 positive samples collected during the first pandemic from the state of Uttar Pradesh, India. We observed a range of already reported mutations (2-22), including; D614G, L452R, Q613H, Q677H, T1027I in the S gene; S194L in the N gene; Q57H, L106F, T175I in the ORF3. Few unreported mutations such as P309S in the ORF1ab gene; T379I in the N gene; and L52F, V77I in the ORF3a gene were also detected. Phylogenetic genome analysis showed similarity with other SARS-CoV-2 viruses reported from Uttar Pradesh. The observed mutations may be associated with SARS-CoV-2 virus pathogenicity or disease severity.

genomics↗

bioRxiv2021

From Alpha to Zeta: Identifying variants and subtypes of SARS-CoV-2 via clustering

The availability of millions of SARS-CoV-2 sequences in public databases such as GISAID and EMBL-EBI (UK) allows a detailed study of the evolution, genomic diversity and dynamics of a virus like never before. Here we identify novel variants and sub-types of SARS-CoV-2 by clustering sequences in adapting methods originally designed for haplotyping intra-host viral populations. We asses our results using clustering entropy -- the first time it has been used in this context. Our clustering approach reaches lower entropies compared to other methods, and we are able to boost this even further through gap filling and Monte Carlo based entropy minimization. Moreover, our method clearly identifies the well-known Alpha variant in the UK and GISAID datasets, but is also able to detect the much less represented (< 1% of the sequences) Beta (South Africa), Epsilon (California), Gamma and Zeta (Brazil) variants in the GISAID dataset. Finally, we show that each variant identified has high selective fitness, based on the growth rate of its cluster over time. This demonstrates that our clustering approach is a viable alternative for detecting even rare subtypes in very large datasets.

bioinformatics↗

bioRxiv2021

Probable omnigenic effect and evolutionary insights of aerobic adaptation allele OsNCED2T on qDTY12.1 effecting grain yield under reproductive stage drought stress in rice

Yield associated quantitative trait loci (qDTY) under drought stress provides significant advantage for grain yield in rice. The major, stable qDTY12.1 was identified in a mapping population developed from upland cultivars Vandana and Way Rarem. Further, introgression line comprising of qDTY12.1 genomic region was characterized to have multiple genes (NAM, DECUSSATE) regulating the drought tolerance under severe drought stress substantiated through recently proposed omnigenic model for complex traits. Recently, plastid localized NCED2T allele present within the qDTY12.1 genomic region was characterized for conferring aerobic adaptation in lowland varieties. Since, NCED2T is evolutionary fixed in upland cultivars and Vandana was found to have the favorable allele of NCED2T, we hypothesized that this favorable allele might confer omnigenic effect on qDTY12.1 genes. Our evolutionary analysis using non synonymous SNPs present in genes namely NCED, NAM, and DECUSSATE and qDTY12.1 genomic regions showed specific grouping of Vandana with upland cultivars only for NCED gene and its adjoining genomic regions. However, non synonymous SNPs in NAM and DECUSSATE genes and its adjoining genomic regions of drought tolerant varieties were closely related and grouped together in the phylogenetic analysis. Moreover, ecotype specific differentiation and greater nucleotide difference with wild relatives was also observed for DECUSSATE gene in rice. This finding indicates differential evolution of qDTY12.1 regions for upland and drought tolerance and omnigenic effect of NCED2T gene in qDTY12.1. Further, we propose a breeding model for enhancing genetic gain for yield under severe drought stress by incorporation of NCEDT, qDTY12.1 and other drought tolerant QTLs for membrane stability in rice.

plant biology↗

bioRxiv2020

Natural-abundance 17O NMR spectroscopy of magnetically aligned lipid nanodiscs

Natural-abundance 17O NMR experiments are used to investigate the hydrated water in magnetically alligned synthetic polymer based lipid-nanodiscs. Residual quadrupole couplings (RQCs) measured from the observed five 17O (central and satellite) transitions, and molecular dynamics simulations, are used to probe the ordering of water moecules across the lipid bilayer.

biophysics↗

bioRxiv2020

Conformational Tuning of Amylin by Charged SMA Copolymers

Human amylin forms structurally heterogeneous amyloids that have been linked to type-2 diabetes. Thus, understanding the molecular interactions governing amylin aggregation can provide mechanistic insights in its pathogenic formation. Here, we demonstrate that fibril formation of amylin is altered by synthetic amphipathic copolymer derivatives of the styrene- maleic-acid (SMAQA and SMAEA). High-speed AFM is used to follow the real-time aggregation of amylin by observing the rapid formation of de novo globular oligomers and arrestment of fibrillation by the positively-charged SMAQA. We also observed an accelerated fibril formation in the presence of the negatively-charged SMAEA. These findings were further validated by fluorescence, SOFAST-HMQC, DOSY and STD NMR experiments. Conformational analysis by CD and FT-IR revealed that the SMA copolymers modulate the conformation of amylin aggregates. While the species formed with SMAQA are -helical, the ones formed with SMAEA are rich in {beta}-sheet structure. The interacting interfaces between SMAEA or SMAQA and amylin are mapped by NMR and microseconds all-atom MD simulation. SMAEA displayed {pi}-{pi} interaction with Phe23, electrostatic {pi}-cation interaction with His18 and hydrophobic packing with Ala13 and Val17; whereas SMAQA showed a selective interaction with amylins C-terminus (residues 31-37) that belongs to one of the two {beta}-sheet regions (residues 14-19 and 31-36) involved in amylin fibrillation. Toxicity analysis showed both SMA copolymers to be non-toxic in vitro and the amylin species formed with the copolymers showed minimal deformity to zebrafish embryos. Together, this study demonstrates that chemical tools, such as copolymers, can be used to modulate amylin aggregation, alter the conformation of species.

biophysics↗

bioRxiv2020

Degradation of Alzheimers Amyloid-beta by a Catalytically Inactive Insulin Degrading Enzyme

It is known that insulin-degrading-enzyme (IDE) plays a crucial role in the clearance of Alzheimers amyloid-{beta} (A{beta}). The cysteine-free IDE mutant (cf-E111Q-IDE) is catalytically inactive against insulin, but its effect on A{beta} degradation is unknown that would help in the allosteric modulation of the enzyme activity. Herein, the degradation of A{beta}(1-40) by cf-E111Q-IDE via a non-chaperone mechanism is demonstrated by NMR and LC-MS, and the aggregation of fragmented peptides is characterized using fluorescence and electron microscopy. cf-E111Q-IDE presented a reduced effect on the aggregation kinetics of A{beta}(1-40) when compared with the wild-type IDE. Whereas LC-MS and diffusion ordered NMR spectroscopy revealed the generation of A{beta} fragments by both wild-type and cf-E111Q-IDE. The aggregation propensities and the difference in the morphological phenotype of the full-length A{beta}(1-40) and its fragments are explained using multi-microseconds molecular dynamics simulations. Notably, our results reveal that zinc binding to A{beta}(1-40) inactivates cf-E111Q-IDEs catalytic function, whereas zinc removal restores its function as evidenced from high-speed AFM, electron microscopy, chromatography, and NMR results. These findings emphasize the catalytic role of cf-E111Q-IDE on A{beta} degradation and urge the development of zinc chelators as an alternative therapeutic strategy that switches on/off IDEs function.

biophysics↗

bioRxiv2020

Hsp70 inhibits aggregation of Islet amyloid polypeptide by binding to the heterogeneous prenucleation oligomers

Molecular chaperone Hsp70 plays important roles in the pathology of amyloid diseases by inhibiting aberrant aggregation of proteins. However, mechanism of the interactions of Hsp70 with the amyloidogenic intrinsically disordered proteins (IDPs) is not clear. Here, we use Hsp70 from different organisms to show that it inhibits aggregation of Islet amyloid polypeptide (IAPP) at substoichiometric concentrations even in absence of ATP. The effect is found to be the strongest if Hsp70 is added in the beginning of aggregation but progressively less if added later, indicating role of Hsp70 in preventing primary nucleation possibly via interactions with the prefibrillar oligomers of IAPP. Fluorescence Correlation Spectroscopy (FCS) measurements of the solutions containing fluorescently labelled Hsp70 and IAPP exhibit fluorescence bursts suggesting formation of heterogeneous complexes of oligomeric IAPP binding to multiple molecules of Hsp70. Size exclusion chromatography and field flow fractionation are then used to fractionate the smaller complexes. Multiangle light scattering and FCS measurements suggest that these complexes comprise of monomers of Hsp70 and small oligomers of IAPP. However, concentration of the complexes is measured to be a few nanomolar amidst several molar of free Hsp70 and IAPP. Hence, our results indicate that Hsp70 interacts poorly with the monomers but strongly with oligomers of IAPP. This is likely a common feature of the interactions between the chaperones and the amyloidogenic IDPs. While strong interactions with the oligomers prevent aberrant aggregation, poor interaction with the monomers avert interference with the functions of the IDPs.

biophysics↗

bioRxiv2019

High Throughput Screening at the Membrane Interface Reveals New Inhibitors of Amyloid-β

Amyloid-{beta} aggregation at the cell-membrane of neruonal cells is implicated as a source of toxicity for Alzheimers disease. Small molecules have been studied for their ability to supress amyloid aggregation and toxicity, but the presence of membranes negate their activity. Here, we have identified 5 small molecules that are active at the membrane interface.

biochemistry↗

bioRxiv2019

Apolipoprotein A-I Mimetic 4F Peptide Generates Amyloid Cytotoxins by Forming Hetero-oligomers with β-amyloid

Apolipoproteins are involved in pathological conditions of Alzheimers disease (AD), truncated apolipoprotein fragments and {beta}-amyloid (A{beta}) peptides coexist as neurotoxic heteromers within the plaques. Therefore, it is important to investigate these complexes at the molecular level to better understand their properties and roles in the pathology of AD. Here, we present a mechanistic insight into such heteromerization using a structurally homologue apolipoprotein fragment of apoA-I (4F) complexed with A{beta}(M1-42) and characterize their toxicity. The 4F peptide slows down the aggregation kinetics of A{beta}(M1-42) by constraining its structural plasticity. NMR and CD experiments identified 4F-A{beta}(M1-42) heteromers as being comprised of unstructured A{beta}(M1-42) and helical 4F. A uniform {approx}2-fold reduction in A{beta}42 15N/1H NMR signal intensities with no observable chemical shift perturbation indicated the formation of a large complex, which was further confirmed by diffusion NMR experiments. Microsecond scale atomistic molecular dynamics simulations showed that 4F interaction with A{beta}(M1-42) is electrostatically driven and induces unfolding of A{beta}(M1-42). Neurotoxicity profiling of A{beta}(M1-42) complexed with 4F confirms a significant reduction in cell-viability and neurite growth. The molecular architecture of heteromerization between 4F and A{beta}(M1-42) discovered in this study provides evidence towards our understanding of the role of apolipoproteins or their truncated fragments in exacerbating AD pathology.

biophysics↗

bioRxiv2019

High resolution structure of a partially folded insulin aggregation intermediate

Insulin has long served as a model for protein aggregation, both because of the importance of aggregation in insulin manufacture and because the structural biology of insulin has been extensively characterized. Despite intensive study, details about the initial triggers for aggregation have remained elusive at the molecular level. We show here that at acidic pH, the aggregation of insulin is likely initiated by a partially folded monomeric intermediate whose concentration is controlled by an off-pathway micellar species. High resolution structures of the partially folded intermediate show that it is coarsely similar to the initial monomeric structure but differs in subtle details - the A chain helices on the receptor interface are more disordered and the B chain helix moves away from C-terminal A chain helix. The result of these movements is the creation of a hydrophobic cavity in the center of the protein that may serve as nucleation site for oligomer formation. Knowledge of this transition may aid in the engineering of insulin variants that retain the favorable pharamacokinetic properties of monomeric insulin but are more resistant to aggregation.

biophysics↗

bioRxiv2018

Lifespan driven reorganization of the global network dynamics unfold on a multifrequency landscape

Healthy ageing is accompanied by changes to spontaneous electromagnetic oscillations. At the macroscopic scale, previous studies have quantified the basic features, e.g., power and frequencies in rhythms of interest from the perspective of attention, perception, learning and memory. On the other hand, signatures and modes of neural communication have recently been argued to be identifiable from global measures applied on neuro-electromagnetic data such as global coherence that quantifies the degree of togetherness of distributed neural oscillations and metastability that parametrizes the transient dynamics of the network switching between successive stable states. Here, we demonstrate that global coherence and metastability can be informative measures to track healthy ageing dynamics over lifespan and together with the traditional spectral measures provides an attractive explanation of neuronal information processing. Finding normative patterns of brain rhythms in resting state MEG would naturally pave the way for tracking task relevant metrics that could crucially determine cognitive flexibility and performance. While previously reported observations of a reduction in peak alpha frequency and increased beta power in older adults are reflective of changes at individual sensors (during rest and task), global coherence and metastability truly pinpoint the underlying coordination dynamics over multiple brain areas across the entire lifespan. In addition to replication of the previous observations in a substantially larger lifespan cohort than what was previously reported, we also demonstrate, for the first time to the best of our knowledge, age related changes in coherence and metastability in signals over time scales of neuronal processing. Furthermore, we observed a marked frequency dependence in changes in global coordination dynamics, which, coupled with the long held view of specific frequency bands sub-serving different aspects of cognition, hints at differential functional processing roles for slower and faster brain dynamics.

neuroscience↗