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At least 19 recordsLinked to original sources
PubMed1978

Conformational change and cooperative ligand binding in hemoglobin.

Although many studies have been carried out on the cooperativityly of ligand binding to hemoglobin, its molecular mechanism is not yet completely confirmed. Various models have been proposed on one hand, but on the other hand the direct judgement of the validity of each model is confronted with experimental difficulties. With this situation in mind, we re-examine carefully various kinds of experimental data, with the intention of finding any hints for future studies on the molecular mechanism of the cooperativity of ligand binding not only to hemoglobin but also to other allosteric proteins composed of subunits. As a result of these re-examinations most of the experimental data can be consistently explained from the viewpoint that the strain due to ligation is transmitted to the interfaces of the subunits and the degree of the strain stored in the interfaces between the subunits controls the cooperativity of of ligand binding. The subjects selected to the present study are molecular structural differences between the deoxy- and oxy-hemoglobin, temperature dependence of oxygen equilibrium constants, and recombination curves of carbon monoxide in flash photolysis experiments. In the first section, the difference of the interfaces of the subunits between deoxy- and oxy-hemoglobin is investigated on the basis of the atomic coordinates determined by Perutz et al. and we examine energetically which of the segment's pairs contributes mainly to the difference in the molecular structure between the two forms. On the basis of this investigation, it is shown in the next section that the oxygen equilibrium constants of human adult hemoglobin under normal physiological conditions are well explained by the following sequence of the conformational changes. The local changes in the interfaces of the subunits are reflected directly on the small differences among the first three Adair constants and the succeeding rearrangement to the four subunits causes the outstandingly larger value of the fourth Adair constant. In more alkaline pH, this rearrangement begins to occur at the earlier stages of ligation. In the succeeding section, it is pointed out that the property of this rearrangement can be studied in more detail through the recombination curves followed by flash photolysis under special conditions.

Allosteric Regulation↗
PubMed2025

Mass spectrometry-based ligand binding assays in biomedical research.

INTRODUCTION: Ligand binding assays combining immunoaffinity enrichment steps with mass spectrometry (MS) readout have gained attention as a highly specific and sensitive tool for protein quantification. These techniques typically combine enzymatic fragmentation of the sample or enriched protein with capture on the protein or peptide-level for quantification. Antibodies ensure specific target recognition, while MS offers quantitative accuracy with isotopically labeled internal standards. This dual approach supports a broad dynamic range, enabling protein measurements from picomolar to nanomolar levels. These methods have diverse applications, from quantifying signaling proteins in basic research to biomarker monitoring in clinical trials and analyzing the pharmacokinetics of therapeutic proteins. AREAS COVERED: This review delves into the diverse workflows of immunoaffinity-MS, shedding light on the innovative strategies employed, their practical applications, efficacy, and inherent limitations in the realm of protein quantification. EXPERT OPINION: Immunoaffinity-MS has transformed protein analysis, but widespread adoption is hindered by complex workflows, high instrument costs, and limited capture molecule availability. Efforts to enhance automation, standardize workflows, and advance technological innovation aim to overcome these barriers. Improvements in mass spectrometer sensitivity, advances in recombinant capture technologies, and support from public initiatives are poised to further improve the reliability and accessibility of this method.

Mass Spectrometry↗
PubMed1976

Estimation of protein-ligand binding parameters from contiuous ultrafiltration results.

A method of analyzing the result of continuous ultrafiltration experiments to obtain protein-ligand binding parameters is presented. This method employs a nonlinear least-squares regression algorithm coupled with a model of protein-ligand binding which alloww the computation of free ligand concentrations, and a second-order Runge-Kutta method to integrate free concentrations with respect to collected ultrafiltrate. The approach is general and effectively removes the constraints on maximum fraction size imposed by other methods.

Adenosine Triphosphatases↗
PubMed1975

Ligand binding properties of hemoglobin 3 of the trout, Salmo gairdneri. The occurrence of an acid Bohr effect in the absence of heme-heme interaction.

The four components of hemoglobin from the rainbow trout (Salmo gairdneri) have been isolated. The oxygen affinities of the first two components eluted from the DEAE-cellulose column have much smaller pH dependencies than the last two components. These components have very low O2 affinities at low pH. The effect of pH on the equilibrium and kinetics of ligand binding to the third fraction, the pH-dependent component present in greatest amounts, has been studied. Measurements of ligand binding equilibria demonstrate the presence of both an alkaline and an acid Bohr effect. In the region of the alkaline Bohr effect the value of n in the Hill equation is a function of ligand affinity. For CO binding n decreases as the pH is decreased until at pH 6, the minimum ligand affinity is reached. At this pH there is also a complete loss of cooperative ligand binding. Decreasing the pH further results in an increase of ligand affinity, but this acid Bohr effect is not associated with a reappearance of cooperativity. This suggests that Fraction 3 of S. gairdneri is frozen in the low affinity, deoxygenated conformation at low pH and that the quaternary structure does not change even when fully liganded. However, the properties of the low affinity conformation of this hemoglobin are pH-dependent.

Animals↗
PubMed1977

Production of BALB/c anti-idiotypic antibodies against the BALB/c myeloma protein 315 does not require an intact ligand-binding site.

To determine whether the ligand-binding site of the BALB/c myeloma protein 315 is essential for the anti-idiotypic response in syngeneic animals, 17 BALB/c mice were immunized with M315 that had been affinity-labeled with bromo-acetyl-DNP-L-lysine (BADL). Essentially all the active sites of M315 were blocked by the affinity label. Fourteen mice produced antibodies that reacted with an idiotypic determinant localized in the Fv fragment of M315, but this idiotype was not part of the DNP-lysine-binding site, and it was absent from L315 and H315 chains. Two groups of BALB/c mice were immunized with nonaffinity-labeled M315, to determine whether the same idiotype was recognized with this immunogen. All animals in the group that received the most prolonged immunization produced antibodies that could be divided in two populations: about 75% were directed against the site-associated idiotype, and the rest reacted with the nonsite idiotype. The other group produced antibodies exclusively specific for the site. Thus, the site-associated idiotype of M315 is not essential for the antibody response of BALB/c mice against M315, and M315 carries at least two different idiotypes that can be recognized by B cells of syngeneic animals.

Animals↗
PubMed1977

Distinctions between the two-state and sequential models for cooperative ligand binding.

The two-state and sequential models for positive cooperativity in ligand binding can produce significantly different theoretical binding curves when presented in a Scatchard plot. The conditions that produce the greatest differences have been examined. The theoretical differences have been used to select the two-state model as the best model for describing the binding of acetylcholine to acetylcholine receptors that have been solubilized by Triton X-100 and sodium cholate.

Acetylcholine↗
PubMed2025

An image-based protein-ligand binding representation learning framework via multi-level flexible dynamics trajectory pre-training.

MOTIVATION: Accurate prediction of protein-ligand binding (PLB) relationships plays a crucial role in drug discovery, which helps identify drugs that modulate the activity of specific targets. Traditional biological assays for measuring PLB relationships are time consuming and costly. In addition, models for predicting PLB relationships have been developed and widely used in drug discovery tasks. However, learning more accurate PLB representations is essential to meet the stringent standards required for drug discovery. RESULTS: We propose an image-based PLB representation learning framework, called ImagePLB, which equips ligand representation learner (LRL) and protein representation learner (PRL) to accept 3D multi-view ligand images and protein graphs as input, respectively, and learns rich interaction information between ligand and protein through a binding representation learner (BRL). Considering the scarcity of protein-ligand pairs, we further propose a multi-level next trajectory prediction (MLNTP) task to pre-train ImagePLB on the 4D flexible dynamics trajectory of 16 972 complexes, including ligand level, protein level, and complex level, to learn information related to trajectories. Besides, by introducing trajectory regularization (TR), we effectively alleviate the problem of high (even almost identical) feature similarity caused by adjacent trajectories. Compared with the current state-of-the-art methods, ImagePLB has achieved competitive improvements on PLB-related prediction tasks, including protein-ligand affinity and efficacy prediction tasks. This study opens the door to the image-based PLB learning paradigm. AVAILABILITY AND IMPLEMENTATION: All data and implementation details of code can be obtained from https://github.com/HongxinXiang/ImagePLB.

Ligands↗
PubMed1976

Effects of formylation of vinyl side chains of heme on optical and ligand binding properties of horse heart ferric myoglobin.

Effects of substitution of vinyl groups of hemin with formyl groups on the optical and ligand binding properties of horse heart ferric myoglobin were investigated. The peak positions as well as the line shapes of the absorption spectra of the ferric derivatives of three kinds of formylmyoglobin, 2-vinyl-4-formyl-, 2-formyl-4-vinyl-, and 2,4-diformylmyoglobins depend on the number and the position of the formyl groups. Absorption maxima in the Soret region of the acid forms of these ferric formylmyoglobins in 0.1 M potassium phosphate buffer, pH 6.0, at 20 degrees were 415.2, 422, and 429 nm, respectively. The acid forms of these formylmyoglobins exhibit absorption spectra of the mixture of high- and low spin states at ambient temperature. Since proto-, deutero- and mesomyoglobins have a high spin state under the same condition, the increase of the low spin iron in these formylmyoglobins may be due to the strong electron withdrawal by the formyl groups toward the periphery of the porphyrin ring. The affinities of these ferric formylmyoglobins and protomyoglobin for N3-, F-, OCN-, and SCN- increased in the order of proto-, monoformyl-monovinyl-, 2,4-diformyl-myoglobin, which corresponds to the increasing order of electron-withdrawing power of the porphyrin side chains. The pKa values of the acid-alkaline transition decreased in the same order. Although the ferric forms of the two isomeric monoformyl-monovinylmyoglobins exhibited different optical spectra, the dissociation constants of the complexes of these isomers for various ligands were similar to each other. The pKa values of the acid-alkaline transition were also similar. These results indicate that affinities of ferric myoglobin for ligands, in contrast to those of the ferrous form for oxygen and carbon monoxide (Sono, M., and Asakura, T. (1975) J. Biol. Chem. 250, 5527-5232 and Sono, M., Smith, P.D., McCray, J.A., and Asakura, T. (1976) J. Biol. Chem 251, 1418-1426), are not affected by the position of modifications at the two vinyl groups, but are determinedby the number of the formyl groups and that two vinyl groups at position 2 and 4 are equivalent in the binding of various ligands by ferric myoglobin. The electron density of the ferric iron appears to be similar for the two isomeric monoformyl-monovinylmyoglobins.

Animals↗
PubMed1977

Zinc-binding ligands in milk and intestine: a role in neonatal nutrition?

The hypothesis that a zinc-binding ligand (ZBL) recently discovered in human milk but absent from cow's milk might be related to zinc nutrition in the neonate was investigated. The zinc-binding characteristics of rat milk were examined to determine if the rat was a suitable model. By gel filtration, rat milk was found to contain a ZBL with characteristics similar to those of the ZBL found in human milk. A similar ZBL was identified in the intestinal mucosa of rats 16 days of age and older but was absent in rats from birth to 16 days. These results support the hypothesis that the ZBL of maternal milk may enhance zinc transport in the neonatal period before the development of intestinal mechanisms for zinc absorption.

Aging↗
PubMed1979

Competitive ligand - binding assay for thyroxine binding globulin. Comparison with TBG radioimmunoassay and T3 uptake test.

A simple and reproducible competitive ligand binding assay has been utilized to measure serum TBG concentration. In euthyroid subjects TBG concentration (mean +/- SD, mg/l) was 33.7 +/- 4; hyperthyroid 24 -/+ 6; T3-thyrotoxicosis 20 +/- 7; hypothyroid 37 -/+ 7; pregnant 67 -/+ 18; post-partum period 59.8 -/+ 17; oral contraceptives 45 -/+ 7. The correlation of CLBA with RIA measurement of TBG was significant (p less than 0.001). The estimations of serum TBG by CLBA correlated significantly with T3 uptake test (p less than 0.001), but at higher concentration of TBG correlation was non-linear. T4 : TBG ration according to serum T4 and TBG concentration provided a reliable index in the assessment of thyroid function.

Contraceptives, Oral↗
PubMed1979

The influence of cell surface receptor clustering on the thermodynamics of ligand binding and the kinetics of its dissociation.

We show that an equilibrium model for the clustering, by divalent ligand, of homogeneous plasma membrane-bound divalent receptors that do not change conformation predicts Scatchard plots with positive second derivatives (concave up). The result is thermodynamically indistinguishable from predictions based upon receptors that are heterogeneous for ligand, or that change conformation in a negatively cooperative way when ligand binds. A more general formulation of the theory, which allows application to dissociation kinetics, predicts that the dissociation of labeled ligand is accelerated in the presence of excess cold ligand and, moreover, that the accelerated dissociation has at least two components. The theory is briefly illustrated by fitting five different sets of data, at several temperatures for two different systems, with parameter values that are well within physically meaningful ranges. The model presented is the simplest and least ad hoc explanation thus far proposed as the basis for the kinetic phenomena, and raises the possibility that the numerous experiments in which such data are observed are primarily minifestations of cell surface clustering.

Insulin↗
PubMed1977

Inactivation and inhibition of Rous sarcoma virus by copper-binding ligands: thiosemicarbazones, 8-hydroxyquinolines, and isonicotinic acid hydrazide.

We have shown that three types of copper-binding ligands, thiosemicarbazones, 8-hydroxyquinolines, and isonicotinic acid hydrazide and their copper complexes, inactivate the transforming ability of RSV and inhibit its RNA-dependent DNA polymerases. Three other compounds, 2-pyridine thiosemicarbazone, 1-formyl isoquinoline thiosemicarbazone, and diphenyl thiocarbazone inhibit transformation by RSV intracellularly. Most but not all of these compounds bind to nucleic acids in the presence of copper, which may be important in their mode of action.

Avian Sarcoma Viruses↗
PubMed1977

New method of quantifying ligand binding based on measurement of an induced response.

A new general method is proposed for quantifying ligand-receptor interactions using the biological response induced by the ligand as an index of ligand binding. With this method the binding of human chorionic gonadotropin (hCG), several hCG derivatives, and luteinizing hormone (LH) to rat Leydig cells was measured by analysis of the ability of these materials to stimulate testosterone formation. As applied here, hormone dose-response curves were generated in the presence of increasing numbers of cells incubated in vitro in a successful attempt to alter the concentrations of bound and free hormone in the incubation mixture. Measurements of testosterone synthesis as a function of the total amounts of hormone and numbers of cells enabled us to evaluate the concentrations of both bound and free hormone at any constant fractional response (i.e. quarter-, half-, or three-quarter-maximal). We were thus able to measure hormone binding at the extremely low hormone concentrations (1 pM) within the steroidogenic dose-response range under conditions that would not have been possible using currently available radioiodinated hCG preparations. The results obrained confirmed the presence of spare functional receptors. Specific quantitative results are discussed in the text.

Animals↗
PubMed2026

Naturally Occurring CodY Variants Alter Ligand Binding, DNA Target Affinity, and Virulence in Clostridioides difficile.

Clostridioides difficile is an important nosocomial pathogen and is the major cause of antibiotic-associated diarrhea and colitis. CodY is a global transcriptional regulator that coordinates metabolism and virulence in Gram-positive pathogens by sensing branched-chain amino acids and GTP. In C. difficile, CodY represses toxin production by inhibiting transcription of tcdR and by influencing c-di-GMP turnover. Here, we characterized two naturally occurring CodY variants, CodY(Y146N) and CodY(V58A), whose substitutions lie near the GTP- and ILV-binding sites, respectively. GTP-binding by CodY(Y146N) was severely compromised, while leucine binding was enhanced; CodY(V58A) showed reduced leucine binding. Both variants exhibited reduced ligand-dependent binding to the tcdR promoter and failed to repress toxin production as effectively as CodY(WT). Expression of virulence-associated genes (tcdR, pdcB) was elevated in strains producing either variant. In a hamster infection model, both variant-producing strains were significantly more virulent than the CodY(WT) strain. These findings demonstrate that single amino acid substitutions in this global regulator can alter ligand affinity and promoter binding, potentially rewiring gene regulatory networks to enhance the pathogenic potential of C. difficile.

Clostridioides difficile↗
PubMed1975

Ligand binding and enzymic catalysis coupled through subunits in tyrosyl-tRNA synthetase.

The interaction of the tyrosyl-tRNA synthetase from Bacillus stearothermophilus with its substrates in the aminoacyl adenylation reaction has been studied by stopped-flow fluorescence. The observed changes have been assigned to their chemical and physical processes by comparison with equilibrium dialysis, pyrophosphate exchange kinetics and rapid quenching and sampling techniques to give the rate constants for ligand binding, the formation of tyrosyl adenylate, and the reverse reaction. The stoichiometry of tyrosine and ATP binding in the catalytic process has been determined directly by equilibrium dialysis and equilibrium gel filtration under pyrophosphate exchange conditions, i.e., where a steady state has been set up in which the equilibrium position favors starting materials. It is shown that the rate-determining step in the formation of tyrosyl adenylate involves 1 mole each of tyrosine and ATP. A second mole of tyrosine and ATP bind to the aminoacyl adenylate complex stabilizing the high-energy intermediate. The enzyme tyrosyl adenylate complex that is isolated by gel filtration is in a different conformational state from that in the presence of tyrosine and ATP.

Adenosine Monophosphate↗
PubMed2025

The RORγt ligand-binding domain controls the pathogenicity of IL-17A+ T cells differently in autoimmune diseases of the skin and CNS.

The transcription factor RORγt orchestrates Th17 lineage differentiation, thymic T cell development, and the pathogenesis of several autoimmune disorders. Lipid ligands are required for appropriate regulation of RORγt activity, but it is unclear to what extent lipid recognition controls RORγt function in vivo. Here, we show that the mutation of RORγt alanine-304 in the ligand-binding domain (LBD) to isoleucine (A304I) abrogates lipid-dependent Th17 differentiation and selectively ameliorates γδT17 cell-mediated psoriatic skin inflammation. In contrast, there is no improvement in experimental autoimmune encephalomyelitis in RORγtA304I mice. Consistent with this, the expression of genes characteristic of Th17 cells decreases in RORγtA304I mice, along with a compensatory increase of genes characteristic of Th1-like Th17 cells with pathogenic signatures. Thus, RORγt alanine-304 in the LBD is indispensable for generating γδT17 and conventional Th17 cells and for the suppression of the Th1-like Th17 pathogenic population, which decouples the pathogenicity of skin and CNS autoimmune diseases.

Animals↗
PubMed1978

Ligand binding studies in the mouse olfactory bulb: identification and characterization of a L-[3H]carnosine binding site.

Binding sites for the dipeptide L-carnosine (beta-alanyl-L-histidine) have been detected in membranes prepared from mouse olfactory bulbs. The binding of L-[3H]-carnosine was saturable, reversible and stereospecific and had a Kd of about 770 nM. The stereospecific binding of L-carnosine represented about 30% of the total binding at pH 6.8, and decreased markedly with increasing pH. Binding was stimulated by calcium, unaffected by zinc, magnesium or manganese and inhibited by sodium and potassium. Carnosine binding was sensitive to trypsin and phospholipases A and C, but not to neuraminidase. Nystatin and filipin, which interact with membrane lipids, also interferred with binding. Some peptide analogues of carnosine were potent inhibitors of binding, but a variety of drugs serving as potent inhibitors in other binding systems had no effect on carnosine binding. Carnosine binding to mouse olfactory bulb membranes was 15-fold higher than that seen in membranes prepared from cerebral hemispheres, 5-fold higher than that seen in membranes prepared from cerebral hemispheres, 5-fold higher than in cerebellum membranes and 3-fold higher than in membranes from spinal medulla and the olfactory tubercle-lateral olfactory tract area. Binding sites for 6 other radiolabeled receptor ligands were also detected in bulb membranes. Peripheral deafferentation of the olfactory bulbs by intranasal irrigation with ZnSO4 led to a loss greater than 90% of the L-[3H]carnosine binding in 4--5 days with much smaller losses in binding of the other 6 ligands over a 180-day observation period. This initial loss of carnosine binding after denervation was due to a loss of binding site stereo-specificity followed by a loss of binding sites. The characteristics of the carnosine binding site in olfactory bulb fulfil 6 of the 7 criteria considered relevant for a functional receptor.

Animals↗
PubMed1979

Anti-V region framework antibodies affect the ligand binding of VL dimer.

The effect of antibodies to the light chain variable region (VL) of protein MOPC-315 (alpha, lambda 2), on the binding of hapten by VL315 dimer or Fv315 (VL + VH) was studied by equilibrium dialysis. Anti-VL did not change the binding properties of Fv but affected the binding properties of VL dimer. At pH 5, the binding properties of VL in the presence or absence of anti-VL were the same, whereas at pH 8, anti-VL reduced the number of ligands bound to VL from two to one. It has previously been shown that VL dimer binds one ligand at pH 5 and two ligands at pH 8, and that VL conformation at pH 5 is tighter. Hence, our results suggest that anti-VL tightens the conformation of VL dimer at pH 8.0 such that it can bind only one ligend. Since Fv is not affected by anti-VL, the results indicate that a combining site made of two identical chains (VL dimer) can undergo a conformational change upon interaction with its antibody. Such conformational change can indirectly affect the binding properties.

Animals↗