Biology subjects

Indurthi, D.

Publications and source records attributed to Indurthi, D..

3 recordsLinked to original sources

bioRxiv2025

Harnessing Protein Unfolding for Thermosensing: Structural Insights from TRPV3

How proteins sense temperature with high precision is a fundamental biological challenge. Here, we structurally elucidate a dynamics-based mechanism for thermoTRPs, termed suicidal gating, in which extreme thermosensitivity arises from intrinsic instability and concerted protein dynamics, coupling channel opening to partial protein unfolding. Using cryo-EM, we directly capture heat-induced partial unfolding within the channels central pore domain, a structural core of gating. Analysis of mutant structures capturing intermediate activated states reveals no large domain shifts despite high temperature dependence, only subtle interfacial changes between domains. Both mutation and heat treatment consistently impact a critical network of thermolabile "latch" interactions along the S6-TRP helix-proximal N-terminus axis, driving receptor activation from a stable closed structure to progressively decoupled states and eventual disintegration. These findings provide direct structural evidence for a new receptor mechanism and establish a broader paradigm in which distributed structural flexibility, rather than localized dedicated sensors, drives extreme biological functions.

physiology↗

bioRxiv2023

Efficiency of an allosteric protein: Multiple affinity-efficacy correlations link agonist binding to nicotinic receptor activation

Receptors signal by switching between resting and active shapes under the influence of agonists. The maximum response produced by an agonist ( efficacy) depends on its relative binding strength ( affinity) to active versus resting conformations. Efficiency, the logcorrelation between these two agonist properties, is the fraction of binding energy converted into energy for the receptors conformational change. In adult muscle nicotinic receptors, efficiencies estimated from 76 concentration-response curves (23 agonists, 53 mutations) segregate into 5 discrete classes (%): 0.56 (17), 0.51(32), 0.45(13), 0.41(26) and 0.31(12). There is a strong linear correlation between affinity and efficacy within each class, but the multiplicity of classes precludes the appearance of any overall relationship. The efficiency class distribution indicates that there are at least 5 resting versus active binding site structural pairs. We discuss efficiency as a quantitative measure of energy coupling between agonist binding and protein conformational change that is fundamental to receptor operation.

biophysics↗

bioRxiv2020

Agonist efficiency estimated from concentration-response curves

Agonists are evaluated by a concentration-response curve (CRC), with a midpoint (EC50) that indicates potency, a high-concentration asymptote that indicates efficacy and a low-concentration asymptote that indicates constitutive activity. A third agonist attribute, efficiency ({eta}), is the fraction of binding energy that is applied to the conformational change that activates the receptor. We show that {eta} can be calculated from EC50 and the asymptotes of a CRC derived from either single-channel or whole-cell responses. For 20 agonists of skeletal muscle nicotinic receptors, the distribution of {eta} values is bimodal with population means at 51% (including ACh, nornicotine and DMPP) and 40% (including epibatidine, varenicline and cytisine). The value of {eta} is related inversely to the size of the agonists head-group, with high-versus low-efficiency ligands having an average volume of 70 [A]3 versus 102 [A]3. Most binding site mutations have only a small effect on ACh efficiency except for Y190A (35%), W149A (60%) and those at G153 (42%). If {eta} is known, the midpoint and high-concentration asymptote can be calculated from each other. Hence, an entire CRC can be estimated from the response to a single agonist concentration, and efficacy can be estimated from EC50 of a CRC that has been normalized to 1. Given {eta}, the level of constitutive activity can be estimated from a single CRC. Statement of significanceReceptors are molecular machines that convert chemical energy from agonist binding into mechanical energy of a global conformational change that generates a cell response. Agonists are distinguished by their potency (proportional to affinity) and efficacy, but also by the efficiency at which their binding energy is applied to receptor activation. Here we show that agonist efficiency can be estimated from a single concentrationresponse curve, and estimate efficiencies of 20 nicotinic receptor agonists. These have a bimodal distribution with larger agonists belonging to the lower-efficiency population. We further show that mutations of some binding site residues alter efficiency, and that knowledge of agonist efficiency simplifies and extends dose-response curve analysis.

biophysics↗