Biology subjects

Sannigrahi, A.

Publications and source records attributed to Sannigrahi, A..

9 recordsLinked to original sources

bioRxiv2026

Lipid-Protein Reciprocal Coupling: A Quantitative Analysis of Membrane Curvature, Architecture, and Protein Association

Cellular membranes are dynamic molecular landscapes in which lipid composition, transbilayer asymmetry, membrane curvature, thickness and mechanics collectively shape protein organization and function, while proteins can in turn remodel lipid organization and membrane architecture. Yet lipid-protein interactions are often treated as discrete binding events, obscuring the extent to which the physical organization of the membrane itself constitutes an active determinant of protein conformational states and cellular activity. Here, we investigate lipid-protein reciprocal coupling by integrating quantitative analyses of curvature-dependent protein-membrane association and hydrophobic-run organization with established structural, lipidomic and biochemical evidence. Our analysis reveals substantial variation in protein association with curved versus flat membrane environments and highlights how membrane curvature, together with lipid composition, cholesterol and asymmetry, can regulate protein structure and function, including in disease-associated systems. We further examine emerging lipid sensors, spatial proteomics and advanced biomimetic membrane platforms that are beginning to bridge molecular mechanisms with protein-lipid organization in cells. In particular, suspended membranes, pore-spanning systems and nanopillar architectures offer opportunities to independently control lipid composition, leaflet asymmetry, curvature and mechanics while directly interrogating protein behaviour. Together, these findings support a model in which membrane architecture encodes physical information that is read by proteins and reciprocally reshaped by protein activity to regulate cellular function.

biophysics↗

bioRxiv2026

Sphingomyelin-Cholesterol Synergy as a Lipid Chaperone Driving Cytolysin A Pore Formation

Bacterial pathogens rely on pore-forming toxins (PFTs) to breach host barriers, a feat that requires water-soluble monomers to spontaneously metamorphose into membrane-inserted pores. In the extracellular milieu, these toxins must navigate complex folding landscapes without ATP-dependent chaperones. Here, we show that the synergistic interplay of host sphingomyelin (SM) and cholesterol (CHOL) acts as an intrinsic "lipid chaperone" that drives the conformational maturation of the bacterial toxin Cytolysin A (ClyA). Using leakage assays on vesicles and suspended lipid bilayer (SuLBs) arrays, atomistic molecular dynamics (MD) simulations, cell membrane permeabilization assays and biophysical measurements, we demonstrate that SM-CHOL synergy accelerates the rate-limiting unfolding of the toxins membrane bound {beta}-tongue motif into a reactive "molten globule" intermediate and guides its subsequent refolding into functional -helical conformation crucial for pore formation. We identify conserved lysine residues (K175 and K206) as critical molecular sensors that detect this specific lipid signature to drive productive transformation. This assembly process reciprocally remodels the host membrane and dismantling liquid-ordered domains, suggesting a mechanical coupling between toxin folding and the disruption of host lipid homeostasis. Our findings establish a paradigm of lipid-mediated chaperoning, revealing how pathogens co-evolve to exploit host lipid complexity to overcome the energetic barriers of membrane insertion.

biophysics↗

bioRxiv2025

Dengue virus suppression by 25-hydroxycholesterol is mediated by a combination of membrane fusion inhibition, innate immune activation and cholesterol biosynthesis dysregulation

Physicochemical properties and composition of cellular membranes are crucial for regulating broad cellular responses including signaling and defense against pathogens. Dengue virus (DENV) exploits cholesterol-rich membranes and host lipid pathways, such as cholesterol biosynthesis, lipid raft organization, and lipid droplet formation, for entry, replication, and assembly. Additionally, lipid-based plasma membrane signaling can trigger innate immune responses that attenuate viral growth, underscoring the dual role of lipids in facilitating and restricting DENV infection. Here, we demonstrate that 25-hydroxycholesterol (25-HC), an oxidized cholesterol metabolite, inhibits DENV infection through a multifaceted mechanism. 25-HC disrupts viral membrane fusion by altering cholesterol distribution and lipid raft organization, impairing the binding and fusion of the DENV envelope (E) protein with host membranes. Additionally, 25-HC modulates host cholesterol metabolism by suppressing biosynthesis pathways essential for viral replication while enhancing lipid droplet formation and stress-response pathways. Transcriptomic analyses reveal that 25-HC primes innate immune responses, activating proinflammatory pathways such as the NLRP3 inflammasome and MAPK signaling, while selectively modulating interferon-stimulated gene expression. Notably, 25-HC exhibits synergistic antiviral effects when combined with direct-acting antivirals like Remdesivir, underscoring its potential in combination therapies. These findings establish 25-HC as a promising candidate for host-directed antiviral strategies against DENV and other enveloped viruses.

cell biology↗

bioRxiv2024

Mechanism of host cell invasion by Leishmania through KMP-11 mediated cholesterol-transport and membrane phase transition

The first step of successful infection by any intracellular pathogen relies on its ability to invade its host cell membrane. However, the detailed structural and molecular understanding underlying lipid membrane modification during pathogenic invasion remains unclear. In this study, we show that a specific Leishmania donovani (LD) protein, KMP-11, forms oligomers that bridge LD and host macrophage (M{Phi}) membranes. This KMP-11 induced interaction between LD and M{Phi} depends on the variations in cholesterol (CHOL) and ergosterol (ERG) contents in their respective membranes. These variations are crucial for the subsequent steps of invasion, including (a) the initial attachment, (b) CHOL transport from M{Phi} to LD, and (c) detachment of LD from the initial point of contact through a liquid ordered (Lo) to liquid disordered (Ld) membrane-phase transition. To validate the importance of KMP-11, we generated KMP-11 depleted LD, which failed to attach and invade host M{Phi}. Through tryptophan-scanning mutagenesis and synthesized peptides, we developed a generalized mathematical model, which demonstrates that the hydrophobic moment and the symmetry sequence code at the membrane interacting protein domain are key factors in facilitating the membrane phase transition and, consequently, the host cell infection process by Leishmania parasites.

biophysics↗

bioRxiv2024

Conformational switch of a peptide provides a novel strategy to design peptide loaded porous organic polymer for Pyroptosis pathway mediated cancer therapy

While peptide-based drug development is now extensively explored, this strategy does have limitations, which come from their rapid excretion from the body (or shorter half-life in the body), and vulnerability to protease-mediated degradation. To overcome these limitations, here we introduce a novel strategy for the development of a peptide-based anticancer agent using the conformation switch property of a chameleon sequence stretch, which we derived from a mycobacterium secretory protein, MPT63. Then, we loaded this peptide in a new porous organic polymer (PG-DFC-POP) synthesized using phloroglucinol and acresolderivative via condensation reaction for delivering the peptide selectively to the cancer cells. Employing an ensemble and single molecule approaches, we demonstrate that this peptide undergoes a disordered to alpha-helical conformational transition, which is triggered by a low pH environment inside cancer cells. This adopted alpha-helical conformation results in the formation of proteolysis-resistant oligomers, which show efficient membrane pore-forming activity selectively for negatively charged phospholipid which is accumulated in cancer cell membrane. Our in vitro and in vivo experimental results demonstrate that the peptide-loaded nanomaterial PG-DFC-POP-PEP 1 exhibits significant cytotoxicity in cancer cells, leading to cell death through the Pyroptosis pathway that is confirmed by monitoring numerous associated events starting from lysosome membrane damage to GSDMD-induced cell membrane demolition. We believe that this novel conformational switch-based drug design strategy has great potential in endogenous environment-responsive cancer therapy and the development of future drug candidates to mitigate cancers.

biochemistry↗

bioRxiv2021

In vitro reconstitution demonstrates the amyloid-beta mediated myelin membrane deformation

Amyloid-beta (A{beta}) aggregation mediated neuronal membrane deformation, although poorly understood, is implicated in Alzheimers Disease (AD). Particularly, whether A{beta} aggregation can induce neuronal demyelination remains unknown. Here we show that A{beta}-40 binds and induces extensive tubulation in the myelin membrane in vitro. The binding of A{beta}-40 depends predominantly on the lipid packing defect densities and electrostatic interactions and results in rigidification of the myelin membrane in the early time scales. Furthermore, elongation of A{beta}-40 into higher oligomeric and fibrillar species leads to eventual fluidization of the myelin membrane followed by extensive membrane tubulation observed in the late phase. Taken together, our results capture mechanistic insights into snapshots of temporal dynamics of A{beta}-40 - myelin membrane interaction and demonstrate how short timescale, local phenomena of binding, and fibril mediated load generation manifests into long timescale, global phenomena of myelin tubulation and demonstrates the ability of A{beta}-40 to demyelinate.

biophysics↗

bioRxiv2020

Membrane composition and lipid to protein ratio modulate amyloid kinetics of yeast prion protein

Understanding of prion aggregation in membrane environment may help to ameliorate neurodegenerative complications caused by the amyloid forms of prions. Here, we investigated the membrane binding induced aggregation of yeast prion protein Sup35. Using the combination of fluorescence correlation spectroscopy (FCS) at single molecule resolution and other biophysical studies, we establish that lipid composition and lipid/protein ratio are key modulators of the aggregation kinetics of Sup35. In the presence of zwitterionic membrane, Sup35 exhibited a novel biphasic aggregation kinetics at lipid/protein ratio ranging between 20:1 and 70:1 (termed here as the Optimum Lipid Concentration, OLC). In ratios below (Low Lipid Concentration, LLC) and above (ELC, Excess Lipid Concentration) that range, the aggregation was found to be monophasic. In contrast, in the presence of negatively charged membrane, we did not observe any bi-phasic aggregation kinetics in the entire range of protein to lipid ratios. The toxicity of the aggregates formed within OLC range was found to be greater. Our results provide a mechanistic description of the role that membrane-concentration/composition-modulated-aggregation may play in neurodegenerative diseases.

biophysics↗

bioRxiv2020

The metal cofactor zinc and interacting membranes modulate SOD1 conformation-aggregation landscape in an in vitro ALS Model

Aggregation of Cu-Zn superoxide dismutase (SOD1) is implicated in the motor neuron disease, ALS. Although more than 140 disease mutations of SOD1 are available, their stability or aggregation behaviors in membrane environment are not correlated with disease pathophysiology. Here, we use multiple mutational variants of SOD1 to show that the absence of Zn, and not Cu, significantly impacts membrane attachment of SOD1 through two loop regions facilitating aggregation driven by lipid induced conformational changes. These loop regions influence both the primary (through Cu intake) and the gain of function (through aggregation) of SOD1 presumably through a shared conformational landscape. Combining experimental and theoretical frameworks using representative ALS disease mutants, we develop a co-factor derived membrane association model wherein mutational stress closer to the Zn (but not to the Cu) pocket is responsible for membrane association mediated toxic aggregation and survival time scale after ALS diagnosis.

biophysics↗

bioRxiv2020

Protein induced membrane phase transition facilitates leishmania infection

Although host membrane is known to play critical roles in the internalization of leishmania parasites inside macrophages (M{phi}), any detailed mechanistic understanding is missing. We show here that KMP-11, a small immunogenic protein of Leishmania Donovani (LD) facilitates the infection process by binding to M{phi} membrane through its N-terminal domain (1-19AA). This binding results in a membrane phase transition that occurs at a threshold protein/lipid ratio, which is linked to the change in membrane tension. KMP-11 induced phase transition is also associated with lipid raft disruption and T-cell deactivation. Finally, using a combination of tryptophan-scanning mutagenesis and synthesized peptides, we develop a mathematical exposition, which demonstrates that hydrophobic moment (H) and the number of residues involved in a mirror sequence (N) at the interacting N-terminal are governing factors for the membrane phase transition, which facilitates infection process.

biophysics↗