Biology subjects

Jha, K.

Publications and source records attributed to Jha, K..

9 recordsLinked to original sources

bioRxiv2026

Phosphoinositides protonation states dictate AKT1 binding with membrane

Phosphoinositides are key regulators of membrane-associated signaling, yet their electrostatic properties are commonly represented by a single nominal charge in molecular simulations and structural models. Using the essential protein kinase AKT1 as a model system, we show that phosphoinositide protonation microstates, both the degree and positional placement of protons, govern peripheral membrane-protein recognition. By integrating quantum-mechanics-derived headgroup parameters, microsecond-scale all-atom molecular dynamics, and umbrella-sampling free-energy calculations with the available solid-state NMR-derived lipid populations via Bayesian/Maximum Entropy reweighting, we account explicitly for the thermodynamic ensemble of phosphoinositide proto-nation states. This population-weighted free-energy framework provides a quantitative mechanistic rationale for the strict specificity of wild-type AKT1 toward PI(3, 4, 5)P3 and elucidates how the oncogenic sentry mutation (E17K) alters this specificity to enable high-affinity PIP2 binding. Furthermore, Proximity-based Labeling of Membrane Associated Proteins (PLiMAP) assays experimentally confirm that AKT1 pleckstrin homology domain binding to distinct phosphoinositide species is differentially sensitive to pH. Together, our findings establish a direct connection between phosphoinositide protonation equilibria, binding energetics, and AKT1 lipid specificity. Beyond AKT1, these results demonstrate that the dynamic protonation microstates of anionic phospholipids act as a functional regulatory layer governing peripheral membrane-protein recruitment across diverse cellular microenvironments.

biophysics↗

bioRxiv2025

Deep Learning-coupled Proximity Proteomics to Deconvolve Kinase Signaling In Vivo

Deconvolving the substrates of hundreds of kinases linked to phosphorylation networks driving cellular behavior is a fundamental, unresolved biological challenge, largely due to the poorly understood interplay of kinase selectivity and substrate proximity. We introduce KolossuS, a deep learning framework leveraging protein language models to decode kinase-substrate specificity. KolossuS achieves superior prediction accuracy and sensitivity across mammalian kinomes, enabling proteome-wide predictions and evolutionary insights. By integrating KolossuS with CRISPR-based proximity proteomics in vivo, we capture kinase-substrate recognition and spatial context, obviating prior limitations. We show this combined framework identifies kinase substrates associated with physiological states such as sleep, revealing both known and novel Sik3 substrates during sleep deprivation. This novel integrated computational-experimental approach promises to transform systematic investigations of kinase signaling in health and disease.

cell biology↗

bioRxiv2025

C. elegans SAS-1 ensures centriole integrity and ciliary function, and operates with SSNA-1

Centrioles are microtubule-based organelles critical for signaling, motility and division. The microtubule-binding protein SAS-1 is homologous to the human ciliopathy component C2CD3 and contributes to centriole integrity in C. elegans, but how this function is exerted is incompletely understood. Here, through the generation of a null allele and analysis with U-Ex-STED, we establish that SAS-1 is dispensable for the onset of centriole assembly, but essential for organelle integrity during oogenesis, spermatogenesis and in the early embryo. Additionally, we uncover that SAS-1 is present at the transition zone of sensory neurons, where it contributes in a partially redundant manner to ciliary function. Furthermore, we investigate the relationship between SAS-1 and the C. elegans Sjogren Syndrome Nuclear Antigen 1 protein SSNA-1, establishing that SSNA-1 localizes next to the SAS-1 C-terminus in the centriole architecture. Moreover, through molecular epistasis experiments with null alleles of both components, we reveal that SAS-1 is essential for SSNA-1 localization to centrioles during oogenesis and to the transition zone during ciliogenesis. Moreover, using a heterologous human cell assay, we establish that SAS-1 recruits SSNA-1 to microtubules. Overall, our findings help clarify how SAS-1, together with SSNA-1, ensures centriole integrity and reveals that it contributes to cilium function.

cell biology↗

bioRxiv2025

Sirtuin 2 controls global protein synthesis by regulating Rheb-GTPase

Upregulated global protein synthesis is associated with the development and progression of several diseases and disorders. Strategies like calorie restriction and pharmacological inhibition of protein synthesis, have exhibited health-promoting effects. However, the complex molecular events that regulate global protein synthesis are not completely understood. Here, we report that SIRT2, a histone deacylase, negatively regulates global protein synthesis by inhibiting the mTORC1 pathway via deacetylating Rheb and promoting Rheb degradation. Our in vitro results suggest that SIRT2 deficiency increases protein synthesis, whereas SIRT2 overexpression suppresses protein synthesis. SIRT2-deficient mice exhibit age-associated and neurohormone-induced cardiac hypertrophy. Here, we report increased global protein synthesis in the hearts of young SIRT2-deficient mice, which may contribute to the development of cardiac hypertrophy. Conversely, cardiac-specific overexpression of SIRT2 reduces global protein synthesis in mice hearts. Mechanistically, SIRT2 binds to and deacetylates Rheb at K151 residue to enhance ubiquitin-proteosome-mediated degradation of Rheb. Depletion of Rheb rescues the increased protein synthesis in SIRT2-inhibited conditions. Our findings suggest that SIRT2 activation can be a potential therapeutic for treating diseases associated with increased protein synthesis.

cell biology↗

bioRxiv2024

Determining the Youngs Modulus of the Bacterial Cell Envelope

Bacteria experience substantial physical forces in their natural environment including forces caused by osmotic pressure, growth in constrained spaces, and fluid shear. The cell envelope is the primary load-carrying structure of bacteria, but the mechanical properties of the cell envelope are poorly understood; reports of Youngs modulus of the cell envelope of E. coli are widely range from 2 MPa to 18 MPa. We have developed a microfluidic system to apply mechanical loads to hundreds of bacteria at once and demonstrated the utility of the approach for evaluating whole-cell stiffness. Here we extend this technique to determine Youngs modulus of the cell envelope of E. coli and of the pathogens V. cholerae and S. aureus. An optimization-based inverse finite element analysis was used to determine the cell envelope Youngs modulus from observed deformations. The Youngs modulus of the cell envelope was 2.06 {+/-} 0.04 MPa for E. coli, 0.84 {+/-} 0.02 MPa for E. coli treated with a chemical known to reduce cell stiffness, 0.12 {+/-} 0.03 MPa for V. cholerae, and 1.52 {+/-} 0.06 MPa for S. aureus (mean {+/-} SD). The microfluidic approach allows examining hundreds of cells at once and is readily applied to Gram-negative and Gram-positive organisms as well as rod-shaped and cocci cells, allowing further examination of the structural causes of differences in cell envelope Youngs modulus among bacteria species and strains.

bioengineering↗

bioRxiv2023

Centriole elimination during C. elegans oogenesis initiates with loss of the central tube protein SAS-1

Centrioles are lost during oogenesis in most metazoans, ensuring that the zygote is endowed with the correct number of two centrioles, which are paternally contributed. How centriole architecture is dismantled during oogenesis is not understood. Here, we analyze with unprecedent detail the ultrastructural and molecular changes during oogenesis centriole elimination in C. elegans. Centriole elimination begins with loss of the so-called central tube and organelle widening, followed by microtubule disassembly. The resulting cluster of centriolar proteins then disappears gradually, usually moving in a microtubule- and dynein-dependent manner to the plasma membrane. Moreover, we find that neither Polo-like kinases nor the PCM, which modulate oogenesis centriole elimination in Drosophila, do so in C. elegans. Furthermore, we demonstrate that the central tube protein SAS-1 normally departs first from the organelle, which loses integrity earlier in sas-1 mutants. Overall, our work provides novel mechanistic insights regarding the fundamental process of oogenesis centriole elimination.

cell biology↗

bioRxiv2022

Bridging The Evolving Semantics: A Data Driven Approach to Knowledge Discovery In Biomedicine

Recent progress in biological, medical and health-care technologies, and innovations in wearable sensors provide us with unprecedented opportunities to accumulate massive data to understand disease prognosis and develop personalized treatments and interventions. These massive data supplemented with rapid growth in computing infrastructure has enabled bio-medical researchers to perform more comprehensive experiments and detailed case-studies. At the same time, performing these experiments are not only monetarily expensive but also time consuming. Thus, there is a growing need to provide tools to the researchers that will allow them to pose queries that will assist them in focusing on interesting "hypotheses". However, such a tool would require capabilities to derive inferences based on existing known relationship between medical concepts. In this paper, we tackle this problem as one of non-factoid question answering wherein we try to answer the user-post questions by leveraging both authoritative as well as social media posts. While the former provides us with well knowledge on well researched topics, the latter provides us with real-time feedback on variety of topics like adverse drug effect (ADE), symptoms-drug relationship, etc. The challenge with leveraging the authoritative sources to infer answers for non-factoid question lies in: (a) The effective navigation of the answer search-space for timely response to the queries, (b) Ranking the candidate answers derived in step-(a) to enable non-trivial and novel discoveries, and (c) Being robust to perform confirmatory as well as discovery type of tasks.

bioinformatics↗

bioRxiv2022

Molecular architecture of the C. elegans centriole

Uncovering organizing principles of organelle assembly is a fundamental pursuit in the life sciences. C. elegans was key in identifying evolutionary conserved components governing assembly of the centriole organelle. However, localizing these components with high precision has been hampered by the minute size of the worm centriole, thus impeding understanding of underlying assembly mechanisms. Here, we used Ultrastructure Expansion coupled with STimulated Emission Depletion microscopy (U-Ex-STED), as well as electron microscopy (EM) and tomography (ET), to decipher the molecular architecture of the worm centriole. Achieving an effective lateral resolution of [~]14 nm, we localize centriolar and PeriCentriolar Material (PCM) components in a comprehensive manner with utmost spatial precision. We uncovered that the procentriole assembles from a location on the centriole margin characterized by SPD-2 and ZYG-1 accumulation. Moreover, we found that SAS-6 and SAS-5 are present in the nascent procentriole, with SAS-4 and microtubules recruited thereafter. We registered U-Ex-STED and EM data using the radial array of microtubules, thus allowing us to map each centriolar and PCM protein to a specific ultrastructural compartment. Importantly, we discovered that SAS-6 and SAS-4 exhibit a radial symmetry that is offset relative to microtubules, leading to a chiral centriole ensemble. Furthermore, we establish that the centriole is surrounded by a region from which ribosomes are excluded and to which SAS-7 localizes. Overall, our work uncovers the molecular architecture of the C. elegans centriole in unprecedented detail and establishes a comprehensive framework for understanding mechanisms of organelle biogenesis and function.

cell biology↗

bioRxiv2019

Flexible pivoting of the pleckstrin domain domain in dynamin catalyzes fission by affecting membrane properties: Insights into the molecular degrees of freedom

The neuronal dynamin1 functions in the release of synaptic vesicles by orchestrating the process of GTPase-dependent membrane fission. Dynamin1 associates with the plasma membrane-localized phosphatidylinositol-4,5-bisphosphate (PIP2) with its centrally-located pleckstrin homology domain (PHD). The PHD is dispensable as fission can be managed, albeit at much slower rates, even when the PHD-PIP2 interaction is replaced by a generic polyhistidine- or polylysine-lipid interaction. However, even when the PHD is present, the length of the dynamin scaffold and in turn the membrane remodeling and fission rates are severely restricted with mutations such as I533A on membrane-interacting variable loop 1 (VL1) of PHD. These observations suggest that PIP2-containing membrane interactions of PHD could have evolved to expedite fission to fulfill the requirement of rapid kinetics of synaptic vesicle recycling. Here, we use a suite of multiscale modeling approaches that combine atomistic molecular dynamics simulations, mixed resolution membrane mimetic models, coarse-grained molecular simulations and advanced free-energy sampling methods (metadynamics and umbrella sampling) to explore PHD-membrane interactions. Our results reveal that: (a) the binding of PHD to PIP2-containing membranes modulates the lipids towards fission-favoring conformations and softens the membrane, (b) that PHD engages another loop (VL4) for membrane association, which acts as an auxiliary pivot and modulates the orientation flexibility of PHD on the membrane - a mechanism we believe may be important for high fidelity dynamin collar assembly on the membrane. (c) Through analyses of our trajectories data and free-energy calculations on membrane-bound WT and mutant systems, we also identify key residues on multiple VLs that stabilizes PHD membrane association. And we suggest experiments to explore the ability of PHD to associate with membrane in orientations that favors faster fission. Together, these insights provide a molecular-level understanding of the "catalytic" role of the PHD in dynamin-mediated membrane fission. SIGNIFICANCEDynamin, a large multi-domain GTPase, remodels the membrane by self-assembling onto the neck of a budding vesicle and induces fission by its energy driven conformational changes. In this work, we use multi-scale molecular simulations to probe the role of dynamins pleckstrin-homology domain (PHD), which facilitates membrane interactions. Notably, PHD is dispensable for fission as is the case with extant bacterial and mitochondrial dynamins. However, reconstitution experiments suggest that the functional role of PHD in neuronal-membrane goes beyond that of an adaptor domain as it possibly expedites the fission reaction during synaptic vesicle recycling. We provide a molecular-dynamics picture of how PHDs make membranes more pliable for fission and suggest new insights into the molecular-level processes driving the expedited fission behavior.

biophysics↗