Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Relaxation Times of Ligand-Receptor Complex Formation Control T Cell Activation.

ABSTRACT: One of the most important functions of immune T cells is to recognize the presence of the pathogen-derived ligands and to quickly respond to them while at the same time not responding to its own ligands. This is known as absolute discrimination, and it is one of the most challenging phenomena to explain. The effectiveness of pathogen detection by T cell receptor is limited by chemical similarity of foreign and self-peptides and very low concentrations of foreign ligands. We propose a new mechanism of how absolute discrimination by T cells might function. It is suggested that the decision to activate or not to activate the immune response is controlled by the time to reach the stationary concentration of the T-cell-receptor-ligand-activated complex, which transfers the signal to downstream cellular biochemical networks. Our theoretical method models T cell receptor phosphorylation events as a sequence of stochastic transitions between discrete biochemical states, and this allows us to explicitly describe the dynamical properties of the system. It is found that the proposed criterion on the relaxation times is able to explain available experimental observations. In addition, we suggest that the level of stochastic noise might be an additional factor in the activation mechanisms. Furthermore, our theoretical approach explicitly analyzes the relationships between speed, sensitivity, and specificity of T cell functioning, which are the main characteristics of the process. Thus, it clarifies the molecular picture of T cell activation in immune response.

SUBMITTER: Teimouri H

PROVIDER: S-EPMC7335936 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Short relaxation times but long transient times in both simple and complex reaction networks.

Project description:When relaxation towards an equilibrium or steady state is exponential at large times, one usually considers that the associated relaxation time ?, i.e. the inverse of the decay rate, is the longest characteristic time in the system. However, that need not be true, other times such as the lifetime of an infinitesimal perturbation can be much longer. In the present work, we demonstrate that this paradoxical property can arise even in quite simple systems such as a linear chain of reactions obeying mass action (MA) kinetics. By mathematical analysis of simple reaction networks, we pin-point the reason why the standard relaxation time does not provide relevant information on the potentially long transient times of typical infinitesimal perturbations. Overall, we consider four characteristic times and study their behaviour in both simple linear chains and in more complex reaction networks taken from the publicly available database 'Biomodels'. In all these systems, whether involving MA rates, Michaelis-Menten reversible kinetics, or phenomenological laws for reaction rates, we find that the characteristic times corresponding to lifetimes of tracers and of concentration perturbations can be significantly longer than ?.

| S-EPMC4971225 | biostudies-literature

Ligand-specific endocytic dwell times control functional selectivity of the cannabinoid receptor 1.

Project description:G protein-coupled receptors (GPCRs) are the major transducers of external stimuli and key therapeutic targets in many pathological conditions. When activated by different ligands, one receptor can elicit multiple signalling cascades that are mediated by G proteins or β-arrestin, a process defined as functional selectivity or ligand bias. However, the dynamic mechanisms underlying β-arrestin signalling remain unknown. Here by studying the cannabinoid receptor 1 (CB1R), we identify ligand-specific endocytic dwell times, that is, the time during which receptors are clustered into clathrin pits together with β-arrestins before endocytosis, as the mechanism controlling β-arrestin signalling. Agonists inducing short endocytic dwell times produce little or no β-arrestin signalling, whereas those eliciting prolonged dwell times induce robust signalling. Remarkably, extending CB1R dwell times by preventing endocytosis substantially increased β-arrestin signalling. These studies reveal how receptor activation translates into β-arrestin signalling and identify a mechanism to control this pathway.

| S-EPMC4227836 | biostudies-literature

Single cell analysis of ligand binding and complex formation of interleukin-4 receptor subunits.

Project description:Interleukin-4 (IL-4) is an important class I cytokine involved in adaptive immunity. IL-4 binds with high affinity to the single-pass transmembrane receptor IL-4R?. Subsequently, IL-4R?/IL-4 is believed to engage a second receptor chain, either IL-2R? or IL-13R?1, to form type I or II receptor complexes, respectively. This ternary complex formation then triggers downstream signaling via intracellular Janus kinases bound to the cytoplasmic receptor tails. Here, we study the successive steps of complex formation at the single cell level with confocal fluorescence imaging and correlation spectroscopy. We characterize binding and signaling of fluorescently labeled IL-4 by flow cytometry of IL-4-dependent BaF3 cells. The affinity to ectopically expressed IL-4R? was then measured by single-color fluorescence correlation spectroscopy in adherent HEK293T cells that express the components of the type II IL-4R but not type I. Finally, IL-4-induced complex formation was tested by dual-color fluorescence cross-correlation spectroscopy. The data provide evidence for codiffusion of IL-4-A647 bound IL-4R? and the type II subunit IL-13R?1 fused to enhanced green fluorescent protein, whereas type I complexes containing IL-2R? and JAK3 were not detected at the cell surface. This behavior may reflect hitherto undefined differences in the mode of receptor activation between type I (lymphoid) and type II (epithelial) receptor expressing cells.

| S-EPMC3218321 | biostudies-literature

Ligand Control of 59Co Nuclear Spin Relaxation Thermometry.

Project description:Studying the correlation between temperature-driven molecular structure and nuclear spin dynamics is essential to understanding fundamental design principles for thermometric nuclear magnetic resonance spin-based probes. Herein, we study the impact of progressively encapsulating ligands on temperature-dependent 59Co T1 (spin-lattice) and T2 (spin-spin) relaxation times in a set of Co(III) complexes: K3[Co(CN)6] (1); [Co(NH3)6]Cl3 (2); [Co(en)3]Cl3 (3), en = ethylenediamine); [Co(tn)3]Cl3 (4), tn = trimethylenediamine); [Co(tame)2]Cl3 (5), tame = triaminomethylethane); and [Co(dinosar)]Cl3 (6), dinosar = dinitrosarcophagine). Measurements indicate that 59Co T1 and T2 increase with temperature for 1-6 between 10 and 60 °C, with the greatest ΔT1/ΔT and ΔT2/ΔT temperature sensitivities found for 4 and 3, 5.3(3)%T1/°C and 6(1)%T2/°C, respectively. Temperature-dependent T2* (dephasing time) analyses were also made, revealing the highest ΔT2*/ΔT sensitivities in structures of greatest encapsulation, as high as 4.64%T2*/°C for 6. Calculations of the temperature-dependent quadrupolar coupling parameter, Δe2qQ/ΔT, enable insight into the origins of the relative ΔT1/ΔT values. These results suggest tunable quadrupolar coupling interactions as novel design principles for enhancing temperature sensitivity in nuclear spin-based probes.

| S-EPMC8174815 | biostudies-literature

T cell receptor dwell times control the kinase activity of Zap70.

Project description:Kinase recruitment to membrane receptors is essential for signal transduction. However, the underlying regulatory mechanisms are poorly understood. We investigated how conformational changes control T cell receptor (TCR) association and activity of the kinase Zap70. Structural analysis showed that TCR binding or phosphorylation of Zap70 triggers a transition from a closed, autoinhibited conformation to an open conformation. Using Zap70 mutants with defined conformations, we found that TCR dwell times controlled Zap70 activity. The closed conformation minimized TCR dwell times and thereby prevented activation by membrane-associated kinases. Parallel recruitment of coreceptor-associated Lck kinase to the TCR ensured Zap70 phosphorylation and stabilized Zap70 TCR binding. Our study suggests that the dynamics of cytosolic enzyme recruitment to the plasma membrane regulate the activity and function of receptors lacking intrinsic catalytic activity.

| S-EPMC4605427 | biostudies-literature

Measurement of Ligand-Target Residence Times by <sup>1</sup>H Relaxation Dispersion NMR Spectroscopy.

Project description:A ligand-observed 1H NMR relaxation experiment is introduced for measuring the binding kinetics of low-molecular-weight compounds to their biomolecular targets. We show that this approach, which does not require any isotope labeling, is applicable to ligand-target systems involving proteins and nucleic acids of variable molecular size. The experiment is particularly useful for the systematic investigation of low affinity molecules with residence times in the micro- to millisecond time regime.

| S-EPMC5150660 | biostudies-literature

Ligand mobility modulates immunological synapse formation and T cell activation.

Project description:T cell receptor (TCR) engagement induces clustering and recruitment to the plasma membrane of many signaling molecules, including the protein tyrosine kinase zeta-chain associated protein of 70 kDa (ZAP70) and the adaptor SH2 domain-containing leukocyte protein of 76 kDa (SLP76). This molecular rearrangement results in formation of the immunological synapse (IS), a dynamic protein array that modulates T cell activation. The current study investigates the effects of apparent long-range ligand mobility on T cell signaling activity and IS formation. We formed stimulatory lipid bilayers on glass surfaces from binary lipid mixtures with varied composition, and characterized these surfaces with respect to diffusion coefficient and fluid connectivity. Stimulatory ligands coupled to these surfaces with similar density and orientation showed differences in their ability to activate T cells. On less mobile membranes, central supramolecular activation cluster (cSMAC) formation was delayed and the overall accumulation of CD3? at the IS was reduced. Analysis of signaling microcluster (MC) dynamics showed that ZAP70 MCs exhibited faster track velocity and longer trajectories as a function of increased ligand mobility, whereas movement of SLP76 MCs was relatively insensitive to this parameter. Actin retrograde flow was observed on all surfaces, but cell spreading and subsequent cytoskeletal contraction were more pronounced on mobile membranes. Finally, increased tyrosine phosphorylation and persistent elevation of intracellular Ca(2+) were observed in cells stimulated on fluid membranes. These results point to ligand mobility as an important parameter in modulating T cell responses.

| S-EPMC3284572 | biostudies-literature

Allosteric activation of T cell antigen receptor signaling by quaternary structure relaxation.

Project description:The mechanism of T cell antigen receptor (TCR-CD3) signaling remains elusive. Here, we identify mutations in the transmembrane region of TCRβ or CD3ζ that augment peptide T cell antigen receptor (pMHC)-induced signaling not explicable by enhanced ligand binding, lateral diffusion, clustering, or co-receptor function. Using a biochemical assay and molecular dynamics simulation, we demonstrate that the gain-of-function mutations loosen the interaction between TCRαβ and CD3ζ. Similar to the activating mutations, pMHC binding reduces TCRαβ cohesion with CD3ζ. This event occurs prior to CD3ζ phosphorylation and at 0°C. Moreover, we demonstrate that soluble monovalent pMHC alone induces signaling and reduces TCRαβ cohesion with CD3ζ in membrane-bound or solubilised TCR-CD3. Our data provide compelling evidence that pMHC binding suffices to activate allosteric changes propagating from TCRαβ to the CD3 subunits, reconfiguring interchain transmembrane region interactions. These dynamic modifications could change the arrangement of TCR-CD3 boundary lipids to license CD3ζ phosphorylation and initiate signal propagation.

| S-EPMC8293630 | biostudies-literature

Regulation of nitric oxide signaling by formation of a distal receptor-ligand complex.

Project description:The binding of nitric oxide (NO) to the heme cofactor of heme-nitric oxide/oxygen binding (H-NOX) proteins can lead to the dissociation of the heme-ligating histidine residue and yield a five-coordinate nitrosyl complex, an important step for NO-dependent signaling. In the five-coordinate nitrosyl complex, NO can reside on either the distal or proximal side of the heme, which could have a profound influence over the lifetime of the in vivo signal. To investigate this central molecular question, we characterized the Shewanella oneidensis H-NOX (So H-NOX)-NO complex biophysically under limiting and excess NO conditions. The results show that So H-NOX preferably forms a distal NO species with both limiting and excess NO. Therefore, signal strength and complex lifetime in vivo will be dictated by the dissociation rate of NO from the distal complex and the rebinding of the histidine ligand to the heme.

| S-EPMC5698159 | biostudies-literature

Hyperpolarized nanodiamond with long spin-relaxation times.

Project description:The use of hyperpolarized agents in magnetic resonance, such as (13)C-labelled compounds, enables powerful new imaging and detection modalities that stem from a 10,000-fold boost in signal. A major challenge for the future of the hyperpolarization technique is the inherently short spin-relaxation times, typically <60 s for (13)C liquid-state compounds, which limit the time that the signal remains boosted. Here we demonstrate that 1.1% natural abundance (13)C spins in synthetic nanodiamond can be hyperpolarized at cryogenic and room temperature without the use of free radicals, and, owing to their solid-state environment, exhibit relaxation times exceeding 1 h. Combined with the already established applications of nanodiamonds in the life sciences as inexpensive fluorescent markers and non-cytotoxic substrates for gene and drug delivery, these results extend the theranostic capabilities of nanoscale diamonds into the domain of hyperpolarized magnetic resonance.

| S-EPMC4633625 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data