Biology subjects

Rana, J. K.

Publications and source records attributed to Rana, J. K..

5 recordsLinked to original sources

bioRxiv2025

A painless nerve growth factor variant uncouples nociceptive and neurotrophic TrkA signaling

Nerve growth factor (NGF) binding to the receptor tyrosine kinase, TrkA, drives neurotrophic signaling essential for neuronal development and survival. This interaction simultaneously drives peripheral pain, making this pathway an attractive but complicated therapeutic target for chronic pain. By integrating single-molecule microscopy, structural and electrophysiology analyses, with a human NGF variant, NGFpainless, which retains neurotrophic effects but abolishes pain, we delineate the molecular mechanisms that bias TrkA signaling towards neurotrophic functions without triggering nociception. We show that, unlike wild-type NGF, NGFpainless fails to sensitize TRPV1 channels to capsaicin, thus disengaging TrkA from the nociceptive pathway. We further show that this selective loss of nociceptive TrkA signaling by NGFpainless results from its reduced ability to activate PLC{gamma}1 and trigger calcium release compared to NGF, while still preserving the ERK and AKT signaling essential for neurotrophic functions. This biased signaling arises from reduced electrostatic complementarity at the TrkA:NGFpainless complex interface, which shortens the lifetime of this functional complex on native membranes. Mutations in TrkA that restore the electrostatic complementarity at the TrkA:NGFpainless interface eliminate biased signaling. This mechanistic understanding of TrkA binding by NGFpainless, and how it differs from NGF, will spur the development of two therapeutic classes of molecules - one that selectively suppresses nociceptive signaling while preserving neurotrophic functions in chronic pain, and another that enhances neurotrophic activity without evoking peripheral pain in neurodegenerative conditions.

neuroscience↗

bioRxiv2025

CTE-Type Tau Filaments in Alzheimer's Disease with Co-morbid LATE-NC

Alzheimers disease (AD), the most common neurodegenerative disease, is defined by {beta}-amyloid plaques and tau neurofibrillary tangles. Tau filaments in AD adopt the "Alzheimers fold", which is distinct from other tauopathies and highly conserved across sporadic and familial AD. However, to date, structural studies have focused on pure AD, despite the high prevalence of comorbid pathologies. In particular, up to half of AD patients harbor limbic-predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC). This co-pathology-- consisting of mislocalized and aggregated TDP-43, mainly restricted to the medial temporal lobe--is associated with accelerated clinical decline and more severe tau pathology. Whether there is a structural basis for this clinical synergy remains unknown. Here, using cryo-electron microscopy, we determine the structure of tau filaments from three AD patients with LATE-NC. We show that in addition to the expected Alzheimers fold tau filaments, all cases exhibit a distinct fibril morphology identical to chronic traumatic encephalopathy (CTE) fold tau. Additional sampling revealed CTE neuropathology in one patient, suggestive features without definitive CTE in the second, and no evidence of CTE in the third. These findings raise questions about the relationship between LATE-NC and CTE, the effect of TDP-43 on tau conformation, and the etiology of LATE-NC.

molecular biology↗

bioRxiv2024

Structure of the CABIT2 domain of THEMIS reveals a novel protein fold with an inserted SH3-like domain

Maturation of thymocytes into T cells is critical for proper function of the adaptive immune system. During this developmental process, thymocytes undergo a highly-regulated selection process regulated by the signaling characteristics of the T cell receptor (TCR) pathway. Thymocyte-Expressed Molecule Involved in Selection (THEMIS) is an essential protein for T cell development. THEMIS regulates phosphatases downstream of the T cell receptor to ensure signaling thresholds are met during selection. Important features of THEMIS are its two uncharacterized CABIT (Cysteine-containing All-Beta In THEMIS) domains, which are intriguing because they have been proposed to participate in important protein-protein interactions (PPIs) that modulate immunological signals. Here, we report the 2.9 [A] crystal structure of the THEMIS CABIT2 domain determined via heavy atom phasing. The structure revealed a novel protein domain fold comprised mainly of {beta}-sheets with two distinct subdomains. This domain appears to have a different C-terminal boundary than predicted or found in previously used experimental constructs. Inclusion of the proline rich segment enables GRB2 to bind CABIT2. Isolated CABIT2 domain is unable to bind or modulate the function of SHP1 phosphatase. This structure will provide the foundation for future structure-function studies of CABIT domains and THEMIS.

biochemistry↗

bioRxiv2023

Structure of the human systemic RNAi defective transmembrane protein 1 (hSIDT1) reveals the conformational flexibility of its lipid binding domain

In C. elegans, inter-cellular transport of the small non-coding RNA causing systemic RNA interference (RNAi) is mediated by the transmembrane protein SID1, encoded by the sid1 gene in the systemic RNA interference-defective (sid) loci. SID1 shares structural and sequence similarity with cholesterol uptake protein 1 (CHUP1) and is classified as a member of the cholesterol uptake family (ChUP). Although systemic RNAi is not an evolutionarily conserved process, the sid gene products are found across the animal kingdom, suggesting the existence of other novel gene regulatory mechanisms mediated by small non-coding RNAs. Human homologs of sid gene products - hSIDT1 and hSIDT2 - mediate contact-dependent lipophilic small non-coding dsRNA transport. Here, we report the structure of recombinant human SIDT1. We find that the extra- cytosolic domain (ECD) of hSIDT1 adopts a double jelly roll fold, and the transmembrane domain (TMD) exists as two modules - a flexible lipid binding domain (LBD) and a rigid TMD core. Our structural analyses provide insights into the inherent conformational dynamics within the lipid binding domain in cholesterol uptake (ChUP) family members.

biophysics↗

bioRxiv2022

Structural analysis of the macrocyclic inhibitor BI-4020 binding to EGFR kinase

A novel macrocyclic inhibitor of mutant EGFR (BI-4020) has shown promise in pre-clinical studies of T790M and C797S drug-resistant non-small cell lung cancer. To better understand the molecular basis for BI-4020 selectivity and potency, we have carried out biochemical activity assays and structural analysis with X-ray crystallography. Biochemical potencies agree with previous studies indicating that BI-4020 is uniquely potent against drug-resistant L858R/T790M and L858R/T790M/C797S variants. Structures show that BI-4020 is likely rendered selective due to interactions with the kinase domain hinge region as well as T790M, akin to Osimertinib. Additionally, BI-4020 is also rendered more potent due to its constrained macrocycle geometry as well as additional H-bonds to conserved K745 and T845 residues in both active and inactive conformations. These findings taken together show how this novel macrocyclic inhibitor is both highly potent and selective for mutant EGFR in a reversible mechanism and motivate structure-inspired approaches to developing targeted therapies in medicinal oncology.

pharmacology and toxicology↗