Biology subjects

Chakrabarti, S.

Publications and source records attributed to Chakrabarti, S..

4 recordsLinked to original sources

bioRxiv2018

Characterization of α 3 Glycine Receptors with Ginkgolide B and Picrotoxin

Ginkgolide B (GB) and picrotoxin (PTX) are antagonists of the major inhibitory receptors of the central nervous system: GABA and glycine receptors (GlyRs). GlyRs contain one or more of the four alpha subunit isoforms of which 1 and 2 have been extensively studied. This report compares GB and PTX block of 3 GlyRs expressed in HEK 293 cells, using whole-cell patch clamp techniques. In CNS, 3 exists as a heteropentamer in conjunction with beta subunits in a 2:3{beta} ratio. Thus, the nature of block was also tested in 3{beta} heteromeric glycine receptors. GB and PTX blocked 3 GlyRs both in the presence (liganded state) and absence of glycine (unliganded state). This property is unique to 3 subunits; 1 and 2 subunits are only blocked in the liganded state. The GB block of 3 GlyRs is voltage-dependent (more effective when the cell is depolarized) and non-competitive, while the PTX block is competitive and not voltage-dependent. The heteromeric and homomeric 3 GlyRs recovered significantly faster from unliganded GB block compared to liganded GB block, but no such distinction was found for PTX block suggesting more than one binding site for GB. This study sheds light on features of the 3 GlyR that distinguish it from the more widely studied 1 and 2 subunits. Understanding these properties can help decipher the physiological functioning of GlyRs in the CNS and may permit development of subunit specific drugs.

neuroscience↗

bioRxiv2018

Processivity, velocity and universal characteristics of nucleic acidunwinding by helicases

Helicases that act as motors and unwind double stranded nucleic acids are broadly classified as either active or passive, depending on whether or not they directly destabilize the double strand. By using this description in a mathematical framework, we derive analytic expressions for the velocity and run-length of a general model of finitely processive helicases. We show that, in contrast to the helicase unwinding velocity, the processivity exhibits a universal increase in response to external force. We use our results to analyze velocity and processivity data from single molecule experiments on the superfamily-4 ring helicase T7, and establish quantitatively that T7 is a weakly active helicase. We predict that compared to single-strand translocation, there is almost a two orders-of-magnitude increase in the back-stepping probability of T7 while unwinding double-stranded DNA. Our quantitative analysis of T7 suggests that the tendency of helicases to take frequent back-steps may be more common than previously anticipated, as was recently shown for the XPD helicase. Finally, our results suggest the intriguing possibility of a single underlying physical principle governing the experimentally observed increase in unwinding efficiencies of helicases in the presence of force, oligomerization or partner proteins like single strand binding proteins. The clear implication is that helicases may have evolved to maximize processivity rather than speed.

biophysics↗

bioRxiv2018

Acute inflammation sensitizes knee-innervating sensory neurons and decreases mouse digging behavior in a TRPV1-dependent manner.

Ongoing, spontaneous pain is characteristic of inflammatory joint pain and reduces an individuals quality of life. To understand the neural basis of inflammatory joint pain, we made a unilateral knee injection of complete Freunds adjuvant (CFA) in mice, which reduced their natural digging behavior. We hypothesized that sensitization of knee-innervating dorsal root ganglion (DRG) neurons underlies this altered behavior. To test this hypothesis, we performed electrophysiological recordings on retrograde labelled knee-innervating primary DRG neuron cultures and measured their responses to a number of electrical and chemical stimuli. We found that 24-hours after CFA-induced knee inflammation, knee neurons show a decreased action potential generation threshold, as well as increased GABA and capsaicin sensitivity, but have unaltered acid sensitivity. The inflammation-induced sensitization of knee neurons persisted for 24-hours in culture, but was not observed after 48-hours in culture. Through immunohistochemistry, we showed that the increased knee neuron capsaicin sensitivity correlated with enhanced expression of the capsaicin receptor, transient receptor potential vanilloid 1 (TRPV1) in knee-innervating neurons of the CFA-injected side. We also observed an increase in the co-expression of TRPV1 with tropomyosin receptor kinase A (TrkA), which is the receptor for nerve growth factor (NGF), suggesting that NGF partially induces the increased TRPV1 expression. Lastly, we found that systemic administration of the TRPV1 antagonist A-425619 reversed the decrease in digging behavior induced by CFA injection, further confirming the role of TRPV1, expressed by knee neurons, in acute inflammatory joint pain.

neuroscience↗

bioRxiv2017

Molecular chaperones maximize the native state yield per unit time by driving substrates out of equilibrium

Molecular chaperones have evolved to facilitate folding of proteins and RNA in vivo where spontaneous self-assembly is sometimes prohibited. Folding of Tetrahymena ribozyme, assisted by the RNA chaperone CYT-19, surprisingly shows that at physiological Mg2+ ion concentrations, increasing the chaperone concentration reduces the yield of native ribozymes. In contrast, the more extensively investigated protein chaperone GroEL works in exactly the opposite manner--the yield of native substrate increases with the increase in chaperone concentration. Thus, the puzzling observation on the assisted-ribozyme folding seems to contradict the expectation that a molecular chaperone acts as an efficient annealing machine. We suggest a resolution to this apparently paradoxical behavior by developing a minimal stochastic model that captures the essence of the Iterative Annealing Mechanism (IAM), providing a unified description of chaperone mediated-folding of proteins and RNA. Our theory provides a general relation involving the kinetic rates of the system, which quantitatively predicts how the yield of native state depends on chaperone concentration. By carefully analyzing a host of experimental data on Tetrahymena (and its mutants) as well as the protein Rubisco and Malate Dehydrogenase, we show that although the absolute yield of native states decreases in the ribozyme, the rate of native state production increases in both the cases. By utilizing energy from ATP hydrolysis, both CYT-19 and GroEL drive their substrate concentrations far out of equilibrium, in an endeavor to maximize the native yield in a short time. Our findings are consistent with the general expectation that proteins or RNA need to be folded by the cellular machinery on biologically relevant timescales, even if the final yield is lower than what equilibrium thermodynamics would dictate. Besides establishing the IAM as the basis for functions of RNA and protein chaperones, our work shows that cellular copy numbers have been adjusted to optimize the rate of native state production of the folded states of RNA and proteins under physiological conditions.\n\nSignificance statementMolecular chaperones have evolved to assist the folding of proteins and RNA, thus avoiding the deleterious consequences of misfolding. Thus, it is expected that increasing chaperone concentration should lead to an enhancement in native yield. While this has been observed in GroEL-mediated protein folding, experiments on Tetrahymena ribozyme folding assisted by CYT-19, surprisingly show the opposite trend. Here, we reconcile these divergent experimental observations by developing a unified stochastic model of chaperone assisted protein and RNA folding. We show that chaperones drive their substrates out of equilibrium, and in the process maximize the rate of native substrate production rather than the absolute yield or the folding rate. In vivo the number of chaperones is regulated to optimize their functions.

biophysics↗