Biology subjects

Tiwari, V. R.

Publications and source records attributed to Tiwari, V. R..

3 recordsLinked to original sources

bioRxiv2024

Syntaxin11 Deficiency Inhibits CRAC Channel Priming To Suppress Cytotoxicity And Gene Expression In FHLH4 Patient T Lymphocytes.

Mutations in Syntaxin11, a Q-SNARE, result in a fatal immune disorder known as familial hemophagocytic lymphohistiocytosis 4 (FHLH4) in human patients. A key diagnostic feature of FHLH4 is defective T and natural killer (NK) cell cytotoxicity. Here we show that Syntaxin11 directly binds and regulates Orai1, the pore forming subunit of calcium release activated calcium (CRAC) channels. CRAC channels enable store-operated calcium entry (SOCE) from the extracellular space and are crucial for granule exocytosis and nuclear factor of activated T cell (NFAT) dependent gene expression in activated lymphocytes. Syntaxin11 depletion strongly inhibited SOCE, CRAC currents, NFAT activation, interleukin-2 gene expression and degranulation in FHLH4 patient T lymphocytes and cell lines without affecting membrane trafficking. Remarkably, defects of cytolytic granule exocytosis as well as interleukin-2 expression could be reversed by ionomycin in patient T lymphocytes and a constitutively active, H134S, mutant of Orai1 rescued calcium entry in Syntaxin11 depleted cells. Further analyses showed that Syntaxin11 primes Orai1 for optimal on-site multimeric assembly which was Stim independent but required for gating. Priming of ion channel pore subunits is, therefore, a primary function of specific SNAREs which may have preceded their role in membrane trafficking and vesicle fusion.

cell biology↗

bioRxiv2022

A Dimer between Monomers and Hexamers - Oligomeric Variations in Glucosamine 6-Phosphate Deaminase Family

In bacteria that live in hosts whose terminal sugar is a sialic acid, Glucosamine 6-phosphate deaminase (NagB) catalyzes the last step in the conversion of sialic acid into Fructose-6-phosphate, which enters the glycolytic pathway. The enzyme exists as a hexamer in Gram-negative bacteria and is shown to be allosterically regulated. In Gram-positive bacteria, it exists as a monomer and lacks allosteric regulation. Our identification of a dimeric Gram-negative bacterial NagB motivated us to characterize the structural basis of the various oligomeric forms. We characterized the crystal structures of NagB from two Gram-negative pathogens, Haemophilus influenzae (Hi) and Pasturella multocida (Pm). The Hi-NagB is active as a hexamer, while Pm-NagB is active as a dimer. We confirm that this is not a crystallographic artifact by cryo-electron microscopy. Both Hi-NagB and Pm-NagB contain the C-terminal helix, and the residues in the interface involved in oligomerization are conserved. The hexamer is described as a dimer of trimers. In the Pm-NagB dimer, the dimeric interface is conserved. This would suggest that the three possible oligomeric forms of NagB are a monomer, a dimer, and a trimer of dimers. Computational modeling and MD simulations indicate that the residues at the trimeric interface have less stabilizing energy of oligomer formation than those in the dimer interface. We propose that Pm-NagB is the evolutionary link between the monomer and the hexamer forms.

biochemistry↗

bioRxiv2019

Computational insights into mechanism of AIM4-mediated inhibition of aggregation of TDP-43 protein implicated in ALS and evidence for in vitro inhibition of liquid-liquid phase separation (LLPS) of TDP-432C-A315T by AIM4.

TDP-43 is an RNA/DNA-binding protein of versatile physiological functions and it is also implicated in the pathogenesis of amyotrophic lateral sclerosis (ALS) disease in addition to several other implicated proteins such as mutant SOD1 and FUS etc. Cytoplasmic mis-localization, liquid-liquid phase separation (LLPS) due to RNA depletion and aggregation of TDP-43 are suggested to be important TDP-43-toxicity causing mechanisms for the ALS manifestation. So far, therapeutic options for ALS are extremely minimal and ineffective therefore, multi-faceted approaches such as treating the oxidative stress and inhibiting the TDP-43s aggregation are being actively pursued. In our recent study, an acridine imidazolium derivative compound, AIM4, has been identified to have anti-TDP-43 aggregation propensity however, its mechanism of inhibition is not deciphered. In this study, we have utilized computational methods to examine binding site(s) of AIM4 in the TDP-43 structure and have also compared its binding efficiency with several other relevant compounds. We find that AIM4 has a binding site in the C-terminal amyloidogenic core region of amino acids aa: 288-319, which coincides with one of the key residue motifs that could potentially mediate liquid-liquid phase separation (LLPS) of TDP-43. Importantly, alike to the previously reported effects exerted by RNA molecules, we found that AIM4 could also inhibit the in vitro LLPS of a recombinantly purified C-terminal fragment TDP-432C bearing an A315T familial mutation. Antagonistic effects of AIM4 towards LLPS which is believed as the precursor process to the TDP-43s aggregation and the in silico prediction of a binding site of AIM4 on TDP-43 occurring in the same region, assert that AIM4 could be an important molecule for further investigations on TDP-43s anti-aggregation effects with relevance to the ALS pathogenesis.

bioinformatics↗