Biology subjects

Chirasani, V. R.

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

7 recordsLinked to original sources

bioRxiv2026

A naturally occurring Tat R52W variant in brain-derived HIV attenuates transcription and may contribute to reservoir persistence

HIV-1 persistence under suppressive antiretroviral therapy (ART) remains a major barrier to eradication, yet the contribution of naturally occurring viral variation to transcriptional regulation is incompletely understood. Here, we identify an HIV-1 Tat variant (R52W) that attenuates viral transcription through the disruption of the Tat-TAR RNA interaction. Full-length HIV-1 genomes derived from the brain microglia of a Last Gift donor, together with peripheral viral sequences obtained during suppressive ART, revealed the presence of the R52W variant in vivo. The same R52W variant was found in another virally suppressed donor within the same cohort. Additional analysis of 3,440 clinical blood isolates from people with HIV identified R52W in 73 sequences (2.12%) of individuals, including three on ART and a therapy controller, and across diverse viral subtypes. Structural modeling demonstrated that R52W destabilizes Tat-TAR binding, while functional assays showed markedly reduced Tat-mediated transcriptional activity, which was restored upon tryptophan-to-arginine reversion (W52R) in Tat. These findings establish a direct molecular mechanism by which a naturally occurring HIV-1 variant modulates viral transcriptional output. Together, our results identify transcriptionally attenuated HIV-1 variants in treated individuals and suggest that modulation of Tat-dependent transcription may represent an underappreciated determinant of viral persistence under suppressive ART.

microbiology↗

bioRxiv2026

APOE interacts with COX-2 on lipid droplets to modulate inflammatory lipid signaling

Alzheimers Disease (AD) is the leading cause of dementia worldwide. Expression of the E4 variant of apolipoprotein E (APOE) greatly increases individuals risk of developing AD. In response to lipogenesis in astrocytes, APOE can escape secretion and traffic to the cytoplasmic surface of lipid droplets (LDs), but protein interactors of APOE at the LD were unknown. Here we find that LD-localized APOE physically interacts with the inflammatory lipid signaling enzyme cyclooxygenase-2 (COX-2). Like APOE, COX-2 can avoid the secretory pathway and traffic to LDs in response to lipogenesis. APOE3, but not APOE4, increases COX-2 localization to LDs. Computational modeling, microscopy-based assays, and targeted lipidomics reveal that APOE3 promotes while APOE4 suppresses COX-2 enzymatic activity at LDs and intracellular prostaglandin production. This work identifies a novel and targetable protein-protein interaction of APOE and provides a mechanistic link between APOE4 and dysregulated inflammatory lipid signaling.

cell biology↗

bioRxiv2025

Structural Interactions of Ankyrin B with NrCAM and β2 Spectrin

Ank2 is a high confidence autism spectrum disorder (ASD) gene encoding the spectrin-actin scaffold protein Ankyrin B (AnkB). The 220 kDal isoform of AnkB has multiple functions including developmental spine pruning through L1 family cell adhesion molecules (L1-CAMs) and class 3 Semaphorins on dendrites of pyramidal neurons to achieve an appropriate excitatory balance in the neocortex. Molecular modeling employing AlphaFold was used to predict the structure and interactions of AnkB with the cytoplasmic domain of Neuron-glial Related L1-CAM (NrCAM), and with {beta}2-Spectrin. The validity of the models was assessed by analyzing protein-protein interactions by co-immunoprecipitation from HEK293 cell lysates after mutating key residues in AnkB predicted to impair these associations. Results revealed a pocket with critical residues in the AnkB membrane-binding domain that engages NrCAM at the conserved cytoplasmic motif FIGQY. Alphafold modeling of the AnkB/{beta}2-Spectrin complex also identified key interactions between the AnkB spectrin-binding domain and {beta}2-Spectrin repeats 14-15. Selected ASD-linked mutations in AnkB predicted to impact binding to NrCAM or {beta}2-Spectrin were then assayed for protein interactions. Maternally inherited ASD missense mutations AnkB A368G located in the NrCAM binding pocket and AnkB R977Q in the Zu51 subdomain disrupted associations with NrCAM and {beta}2-Spectrin, respectively. Moreover, AnkB A368G impaired the neuronal function of 220 kDal AnkB in Semaphorin 3F-induced spine pruning in mouse cortical neuron cultures. These new findings provide structural insights into the L1-CAM/AnkB complex and the molecular basis of ASD etiology associated with AnkB missense mutations.

neuroscience↗

bioRxiv2024

Catestatin improves heart metabolic flexibility by promoting mitochondrial structure and function

Hypertension, a major cause of cardiomyopathy, is one of the most critical risk factors for heart failure and mortality worldwide. Loss of metabolic flexibility of cardiomyocytes is one of the major causes of heart failure. Although Catestatin (CST) treatment is known to be both hypotensive and cardioprotective, its effect on cardiac metabolism is unknown. In this study, we undertook a transcriptomic approach to identify differentially expressed genes that were filtered using Boolean implication relationships to develop a model of gene regulation in saline or CST-supplemented CST knockout (CST-KO) mice. The analysis revealed a set of gene signatures (fibroblast, cardiomyocyte, and macrophage) rescued after CST supplemented CST-KO mice compared to wild-type. Furthermore, we independently validated these gene signature models using publicly available patient datasets. Since the gene signature includes genes related to glucose, fatty acid metabolism, and mitochondrial function, we assessed the glucose and fatty acid uptake after CST treatment. We found that CST treatment can restore the cardiac metabolic inflexibility in CST-KO heart due to the metabolic shift of glucose utilization to fatty acid as energy source. Binding studies after immunoprecipitation and mass spectrometry revealed CST binding with ATP synthase, supported by molecular simulation and computational modeling that predicted CST binding to /{beta} subunit of ATP synthase. Colocalization of CST with mitochondria and increased mitochondrial membrane potential and ATP production upon CST treatment in neonatal cardiomyocytes further exhibit CST as a key regulator of cardiac metabolism and mitochondrial function.

physiology↗

bioRxiv2022

Kinetic and Redox Characterization of KRAS G12C Inhibition

The development of mutant-selective inhibitors for the KRASG12C allele has generated considerable excitement. These KRASG12C inhibitors covalently engage the mutant C12 thiol located within the phosphoryl binding loop of RAS, locking the KRASG12C protein in an inactive state. While clinical trials of these inhibitors have been promising, mechanistic questions regarding the reactivity of this thiol remain, motivating the present studies. Measurement of the C12 thiol pKa by NMR and an independent biochemical assay found a depressed pKa (relative to free cysteine) of 7.6 consistent with its susceptibility to chemical ligation. Using a novel and validated fluorescent KRASY137W variant amenable to stopped-flow spectroscopy, we characterized the kinetics of KRASG12C fluorescence changes upon addition of ARS-853 or AMG 510, noting that ARS-853 addition at 5{degrees}C elicited both a rapid first phase (attributed to binding, yielding a Kd of 36.0 {+/-} 0.7 M), and a second, slower pH-dependent phase taken to represent covalent ligation. Consistent with the lower pKa of the C12 thiol, we found that reversible and irreversible oxidation of KRASG12C occurred readily both in vitro and in the cellular environment, preventing the covalent binding of ARS-853. Moreover, we found that oxidation of the KRASG12C thiol to sulfinic acid alters RAS conformation and dynamics to be more similar to KRASG12D in comparison to the unmodified protein, as assessed by molecular dynamics simulations. Taken together, these findings provide insight for future KRASG12C drug discovery efforts as well as identifying the occurrence of G12C oxidation with currently unknown biological ramifications.

biochemistry↗

bioRxiv2019

Mapping Co-regulation Pathways among Ligand Binding sites in RyR1

Ryanodine receptor 1 (RyR1) is an intracellular calcium (Ca2+) release channel required for skeletal muscle contraction. RyR1 is co-regulated by multiple activators - Ca2+, ATP and caffeine (CFF), yet the mechanism of co-regulation and the action synergy of these activators is unknown. Here, we report the detailed network of allosteric connections between the three ligand sites and the pore region in (i) Ca2+ bound - closed, (ii) ATP/CFF bound - closed, (iii) Ca2+/ATP/CFF bound - closed and (iv) Ca2+/ATP/CFF bound - open RyR1 states. We find that two dominant paths mediate the communication between the Ca2+ binding site and pore region in Ca2+-only state. ATP/CFF-only occupied - closed RyR1 has two additional paths with CFF-but not ATP-occupied path using part of the closed Ca2+-only pathway. In the presence of Ca2+, ATP and CFF, major differences between the open and closed states are identified with both using part of the paths of the closed Ca2+-only and ATP/CFF-only states. We find that the three activators Ca2+, ATP, and CFF propagate their effects to the pore region through a network of partially overlapping pathways. Such coordination of allosteric pathway underlies the molecular basis of synergy of channel regulation by multiple activators.\n\nStatement of SignificanceRyRs are a group of Ca2+ channels that bind to several endogenous modulators and regulate Ca2+ release through closed-to-open gating transition. Despite the high-resolution structural data available for RyR1, the allosteric mechanism of RyR1 gating remains elusive. In this study, we employed graph-theoretical approach to demonstrate the allosteric network of synergistic interaction among various activators in RyR1. To our knowledge, for the first time we were able to identify the co-regulation among ligand sites in RyR1 to regulate the closed-to-open gating transition. The explored allosteric coupling in RyR1 may assist in designing advanced therapeutics for several debilitating diseases. Our findings in this study will assist to design new strategies for controlled allosteric regulation of RyR1 functionality in future.

biophysics↗

bioRxiv2018

Breaking the “unbreakable” ZIKA virus envelope

The rapid spread of zika virus (ZIKV) and its association with microcephaly and Guillain-Barre syndrome have raised major concerns worldwide. Studies have shown that ZIKV can survive in harsh conditions, e.g. high fever; in sharp contrast to the dengue virus (DENV) of same Flaviviridae family. In spite of recent cryo-EM structures that showed similar architecture of the ZIKV and DENV envelopes, little is known of what makes ZIKV envelope so robust and unique. Here, we present a detailed analysis of the constituent raft-raft and protein-protein interactions on ZIKV and DENV envelopes to undermine their differential stability at near-atomic to atomic level using coarse-grained (CG) and all-atom (AA) molecular dynamics simulations. Our results from CG simulations show that, at high temperatures, ZIKV envelope retains its structural integrity, while DENV2 disintegrate through the formation of holes at 5- and 3-fold vertices. Protein structural network from AA simulations shows a stronger inter-raft communications in ZIKV through multiple electrostatic and H-bond interactions. Particularly, the intricate network of interlocking DE-loop and FG-loop among five DIII domains in ZIKA vertices was exceedingly robust that makes this envelope stable, even at high temperatures. Our results are validated by alanine mutations to the CD-loop residues Gln350 and Thr351 that showed no effect on ZIKA stability, in close accordance with a recent mutagenesis study. These detailed information, which were difficult to extract experimentally, broadened our understanding of the flaviviruses and can accelerate the structure-based drug designing processes aiming ZIKA and DENV therapeutics.\n\nIMPORTANCEThe rapid spread of zika virus (ZIKV) and its association with severe birth defects have raised worldwide concern. Recent studies have shown that ZIKV can survive in harsh conditions, e.g. high fever, unlike dengue (DENV) and other flaviviruses. Here, we unravel the molecular basis of ZIKV unprecedented stability over DENV at high temperatures, mimicking fever. Our study, based on coarse-grained and all-atom molecular dynamics simulations, could not only explore the mechanism of DENV envelope breaking at high temperatures, but also captured atomic-level contacts and interactions at raft-raft and protein-protein interfaces that keep ZIKV envelope intact in similar conditions. The obtained results are validated by in-silico and reported in-vitro mutagenesis studies by showing the presence of specific H-bonding and electrostatic interactions among ZIKV E protein residues. At the end, our study was successful to define potential ZIKV epitopes and provide residue-level insights for designing specific ZIKV antibodies and small molecule inhibitors.

biophysics↗