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At least 19 recordsLinked to original sources
PubMed1985

Equilibrium in the protein-immobilized-ligand-soluble-ligand system: estimation of dissociation constants of protein-soluble-ligand complexes from binding-inhibition data.

The equilibrium in the protein-immobilized-ligand-soluble-ligand system was examined theoretically and the equations found were used for determination of dissociation constants of protein-soluble-ligand complexes (K). These constants can be obtained from the s/b vs C plot [s/b = ratio of soluble and bound forms of the protein at equilibrium established in the presence of the soluble ligand (concn C)], which is linear if: (1) the concns of the complexes are much lower than the total concns of the immobilized and soluble ligands, and (2) if multiple interactions of an n-valent protein with the immobilized ligand essentially do not occur (i.e. the binding to the immobilized ligand is monovalent). The effect of violation of condition (1) is examined by computation simulation and is shown to be manifested as a non-linearity of the plot. Heterogeneity of the immobilized ligand (arising, for example, from the immobilization procedure) is predicted to have no effect on the K-values obtained. A more complex linear equation applicable principally for determination of K under more general conditions was also found. The conditions are defined under which the C50-values (i.e. concns of a series of ligands inhibiting the binding to an immobilized ligand by 50%) can be directly used for comparison of dissociation constants. The use of the s/b vs C plot was tested experimentally: transferrin, several glycoproteins or synthetic carbohydrate-containing copolymers were immobilized by adsorption in the wells of polystyrene microculture plates and thus served as immobilized ligands. Solutions of 125I-labelled ligand-binding proteins (lectins or monoclonal antibodies binding transferrin) were incubated in these ligand-coated wells in the presence of various amounts of soluble ligands (carbohydrates or transferrins): after equilibrium establishment the s/b values were determined and plotted against C and the values of K were obtained as the intercept of the plot with the abscissa. The method appears to be experimentally simple and the K-values of the lectin-sugar and monoclonal antibody-antigen complexes agree well with those determined by other methods.

Antibodies, Monoclonal↗
PubMed1990

Preferential ligand binding to multi-state acceptor systems: the unexplored paradox of acceptor self-association that is ligand-mediated but detrimental to ligand binding.

Consideration is given to the interactions of ligand with self-associating acceptor systems for which preferential ligand binding is an ambiguous term, in that the acceptor species with greater affinity for ligand possesses relatively fewer binding sites. A paradoxical situation wherein ligand-mediated self-association is seemingly detrimental to ligand binding is shown to be the predicted outcome for a transient range of ligand concentrations. This outcome reflects the existence of a critical point in the dependence of the extent of acceptor self-association upon ligand concentration that coincides with a cross-over point of ligand-binding curves for different, fixed total concentrations of acceptor. By classical differentiation methods the conditions for the existence of these critical points are established not only for two-state acceptor systems but also for three-state acceptor systems in which the ligand-binding form of monomer also undergoes reversible isomerization to an inactive state. Similar procedures are used to comment upon the forms of binding curves for the three-state acceptor systems, the Scatchard representations of which may exhibit as many as three critical points (two maxima and a minimum). This delineation of quantitative expressions for critical points and other distinctive features associated with the conflicting interplay of ligand-binding and self-association behaviour should provide a more definitive means of characterizing systems with one acceptor state the preferred binding form on affinity grounds but with the other the preferred state from the viewpoint of binding-site numbers.

Animals↗
PubMed1982

Heme ligand replacement reactions of cytochrome P-450. Characterization of the bonding atom of the axial ligand trans to thiolate as oxygen.

Evidence of several types has accumulated that cytochrome P-450 has a thiolate anion as one of the axial ligands to heme (the fifth ligand). On the other hand, there is as yet no general agreement on the nature of the axial ligand trans to thiolate (the sixth ligand), although nitrogen and oxygen have been proposed. To resolve the controversy, the ligand exchange reactions of cytochrome P-450 were investigated by the use of optical spectroscopy. Two isozymes of rabbit liver microsomal cytochrome P-450 were examined: the isozyme induced by phenobarbital (P-450LM2), which has a sixth ligand and is low spin and the isozyme induced by 5,6-benzoflavone (P-450LM4), which is without a sixth ligand and is high spin. A series of artificial ligands was chosen to model the coordination of each of the potential native ligands, including water and certain amino acid residues. When the artificial ligand coordinated through an oxygen atom, the spectrum of pentacoordinate P-450LM4 changed to one closely resembling that of native, hexacoordinate P-450LM2. The spectrum of P-450LM2 was unchanged in the presence of oxygen-coordinating ligands. However, when artificial ligands which coordinate through nitrogen or sulfur were added to either P-450LM2 or P-450LM4, the induced spectra did not resemble the native spectrum and, in fact, were distinctive and characteristic of the particular ligand type. With three of the artificial ligands, 1-butanol, 1-benzylimidazole, and diethylphenylphosphine, the binding was found to be reversible by dilution, ultrafiltration, or gel filtration. The binding of 1-pentanol and 1-benzylimidazole was competitive, as expected for heme ligands, and the number of 1-benzylimidazole binding sites per molecule of P-450LM2 was estimated as 1.1. These results provide strong evidence that the native sixth ligand in P-450LM2 is oxygen rather than nitrogen.

Animals↗
PubMed1992

Use of binding site neighbor-effect parameters to evaluate the interactions between adjacent ligands on a linear lattice. Effects on ligand-lattice association.

A method using binding site "neighbor-effect" parameters (NEPs) is introduced to evaluate the effects of interaction between adjacent ligands on their binding to an infinite linear lattice. Binding site overlap is also taken into account. This enables the conditional probability approach of McGhee & von Hippel to be extended to more complex situations. The general equation for the isotherm is v/LF = SFKF, where v is the ratio of bound ligands to lattice residues, LF is the free ligand concentration, SF is the fraction of binding sites that are free, and KF is the average association constant of a free site. Solutions are derived for three cases: symmetric ligands, and asymmetric ligands on isotropic or anisotropic lattices. For symmetric ligands there is one NEP, E, which is the ratio of the average binding affinity of a free site if the status of the lattice residue neighboring one end of the site is unspecified (left to chance) to the affinity when this residue is free (holding the other neighbor constant). Thus KF is KE2, where K is the affinity of an isolated site. If a site is n residues long, SF is f ffn-1, where f = 1 - nv is the fraction of residues that are free and ff is the conditional probability that a free residue is bordered on a given side by another free residue. The expression for ff is 1/(1 + x/E), where x is v/f, E is (1 - x + [(1 - x)2 + 4x omega]1/2)/2, and omega is the co-operativity parameter. The binding of asymmetric ligands to an isotropic lattice is described by two NEPs; the last case involves four NEPs and a bound ligand orientation parameter. For each case, the expected length distribution of clusters of bound ligands can be calculated as a function of v. When Scatchard plots with the same intercepts and initial slope are compared, it is found that ligand asymmetry lowers the isotherm (relative to the corresponding symmetric ligand isotherm), whereas lattice anisotrophy raises it.

Binding Sites↗
PubMed1991

Bivalent ligand dissociation kinetics from receptor-bound immunoglobulin E: evidence for a time-dependent increase in ligand rebinding at the cell surface.

The bivalent ligand N,N'-bis[[epsilon-[(2,4- dinitrophenyl)amino]caproyl]-L-tyrosyl]cystine [(DCT)2-Cys] binds and cross-links anti-dinitrophenyl (DNP) immunoglobulin E (IgE)-receptor complexes on the cell surface of rat basophilic leukemia cells. The rate of dissociation of this bound ligand was monitored by using a fluorescence method under two different conditions. In one case the monovalent ligand DCT was added in large excess to prevent the dissociating ligand from rebinding to unoccupied antibody combining sites. Under these conditions, dissociation of the bivalent ligand from IgE-sensitized cells proceeds to completion with kinetics that are well described by two rate constants that are independent of the time of preincubation of the bivalent ligand with the cells. In the second case, dissociation of (DCT)2-Cys from cell-bound anti-DNP IgE was monitored in the presence of a large excess of anti-DNP IgE in solution that acts as a sink to absorb the dissociated ligand. Under these conditions, the bivalent ligand becomes more resistant to dissociation as the preincubation time of the bivalent ligand with the cells is increased. An increasing fraction of the bound ligand does not dissociate on a measurable time scale in the presence of this sink. The results indicate that cell-associated IgE-receptor complexes undergo a time-dependent change that facilitates the reformation of the cross-linked state when one end of the ligand dissociates to break up the existing cross-link. The possible physical basis and functional implications of these results are discussed.

Animals↗
PubMedDate not supplied

[Cooperation effects in binding of large ligands to DNA. II. Contact interactions between adsorbed ligands].

Cooperative effects arising upon binding of biologically active ligands to DNA are considered. Equations are derived which enable one to describe the binding of two different ligands to DNA. We also consider the case when ligand can form two type of DNA complexes. The cooperative binding of the ligand in the vicinity of saturation level of binding can be described with a good accuracy by equation derived for the non-cooperative adsorption of the same ligand with some effective binding constant Keff. It is shown that cooperative effects arising upon binding of proteins and other ligands to DNA can be divided into two groups depending on the symmetry of interactions between the bound ligand molecules. In particular, if such interactions favor the formation of dimeric ligand species on the DNA, Keff approximately a1/2, where a is the ligand-ligand interaction constant. If cooperative interactions favor the formation of aggregates of unrestricted size, then Keff approximately aL+Y, where L is the size of the binding site for the ligand on DNA.

Adsorption↗
PubMed1985

Morphological analysis of ligand uptake and processing: the role of multivesicular endosomes and CURL in receptor-ligand processing.

The receptor-mediated endocytosis and intracellular processing of transferrin and mannose receptor ligands were investigated in bone marrow-derived macrophages, fibroblasts and reticulocytes. Mannosylated bovine serum albumin (BSA) conjugated to colloidal gold (Au-man-BSA) or colloidal gold-transferrin (AuTf) were used to trace ligand processing in these cells. These ligands appeared to be processed by mechanisms similar to those observed previously with other mannose receptor and galactose receptor ligand probes. After uptake via coated pits and coated vesicles, Au-man-BSA appeared in small uncoated vesicles and tubular structures and was transferred to large, sometimes multivesicular endosomes (MVEs), which sometimes had arm-like protrusions reminiscent of CURL (compartment of uncoupling of receptor and ligand) [10, 11]. Initially these structures became increasingly multivesicular, but during longer incubations the inclusion vesicles appeared to disintegrate to leave a denser, amorphous lumen. Inclusion vesicle disintegration may result from the introduction of lysosomal enzymes into these structures. These results suggest a model for differential receptor-ligand and ligand-ligand sorting. As suggested [10, 11] membrane constituents may be recycled to the plasma membrane from the arms of CURL. Receptor-bound ligands, such as transferrin, would also recycle. The luminal contents, including dissociated ligands, other soluble proteins and inclusion vesicles (containing some membrane proteins), would target to lysosomes. This would result in the lysosomal degradation of any membrane proteins that were incorporated in the inclusion vesicle membranes.

Animals↗
PubMed1979

Calculation of the concentrations of free cations and cation-ligand complexes in solutions containing multiple divalent cations and ligands.

The method described permits the computation of the concentrations of free ions and ion-ligand complexes in a solution containing arbitrary numbers of divalent cations and ligands. It is required that the pH be known, along with appropriate sets of ligand-hydrogen and ligand-divalent cation concentration binding constants. It is assumed that these sets of constants are chosen to be consistent with the ionic strength of the complete solution which contains the divalent cations and ligands. The technique is an iterative one which provides upper and lower bounds for the values of the unknowns. The method does not require initial guesses at the values of the unknowns, and it gives correct answers even when the concentrations involved are many orders of magnitude apart. The present formulation of the problem is restricted to the case where only one cation can bind to a given ligand at any one time. The method is applicable to large molecules with multiple "sub-ligands" provided these sub-ligands are independent in their function as ion-binding sites. These sub-ligands need not all have the same properties. It is also shown that a simple modification of the method permits the determination of the subset of total ion concentrations that are required in order to produce a specified subset of free ion concentrations. The modifications required to include monovalent cation binding are presented in outline form.

Adenosine Triphosphate↗
PubMed1986

Ligand and halide binding properties of chloroperoxidase: peroxidase-type active site heme environment with cytochrome P-450 type endogenous axial ligand and spectroscopic properties.

Equilibrium binding studies of exogenous ligands and halides to the active site heme iron of chloroperoxidase have been carried out from pH 2 to 7. Over twenty ligands have been studied including C, N, O, P, and S donors and the four halides. As judged from changes in the optical absorption spectra, direct binding of the ligands to the heme iron of ferric or ferrous chloroperoxidase occurs in all cases; this has been ascertained for the ferric enzyme in several cases through competition experiments with cyanide. All of the ligands except for the halides, nitrate, and acetate form exclusively low-spin complexes in analogy to results obtained with the spectroscopically related protein, cytochrome P-450-CAM [Sono, M., & Dawson, J.H. (1982) J. Biol. Chem. 257, 5496-5502]. The titration results show that, for the ferric enzyme, (i) weakly acidic ligands (pKa greater than 3) bind to the enzyme in their neutral (protonated) form, followed by deprotonation upon ligation to the heme iron. In contrast, (ii) strongly acidic ligands (pKa less than 0) including SCN-, NO3-, and the halides except for F- likely bind in their anionic (deprotonated) form to the acid form of the enzyme: a single ionizable group on the protein with a pKa less than 2 is involved in this binding. For the ferrous enzyme, (iii) a single ionizable group with the pKa value of 5.5 affects ligand binding. These results reveal that chloroperoxidase, in spite of the previously established close spectroscopic and heme iron coordination structure similarities to the P-450 enzymes, clearly belongs to the hydroperoxidases in terms of its ligand binding properties and active site heme environment. Magnetic circular dichroism studies indicate that the alkaline form (pH 9.5) of ferric chloroperoxidase has an RS-ferric heme-N donor ligand coordination structure with the N donor likely derived from histidine imidazole.

Acetates↗
PubMed1985

Uptake and transport of mannosylated ligands by alveolar macrophages. Studies on ATP-dependent receptor-ligand dissociation.

During endocytosis, mannosylated ligands enter vesicles which have a density intermediate between that of the plasma membrane and secondary lysosomes. Mannosylated ligands are transferred from these vesicles to lysosomes. A solubilization-precipitation assay was used to study the dissociation of mannosylated ligands from their receptor. In whole cells dissociation was rapid (t 1/2 (37 degrees C) = 8 min) and took place before delivery of the ligand to lysosomes. Receptor-ligand dissociation within membrane vesicles, washed free of cytosol, could be induced by addition of ATP and GTP but not ADP. Receptor-ligand dissociation caused by manipulating the pH of the vesicles suggested that the pH within endosomes was lowered to 5.5 by addition of ATP. Dissociation was blocked by proton ionophores and Zn2+, but was unaffected by inhibitors of the F1, Fo-ATPase or the Na+,K+-ATPase. Dissociation did not require Na+ or K+ and was blocked by anion transport inhibitors. Dissociation was slowed in the absence of permeant anions (Cl-). Receptor-ligand complexes within vesicles isolated as early as 2 min following ligand internalization responded to addition of ATP. The results suggest that receptor-ligand dissociation in endosomes requires ATP, possibly to power endosomal acidification via an ATP-dependent proton pump. Dissociation is enhanced in the presence of permeant anions, suggesting the involvement of an anion channel or carrier.

Adenosine Diphosphate↗
PubMed1986

A new hybridocytochemical method based on mercurated nucleic acid probes and sulfhydryl-hapten ligands. II. Effects of variations in ligand structure on the in situ detection of mercurated probes.

In the preceding paper, a method to detect specific DNA sequences with mercurated nucleic acid probes and sulfhydryl-hapten ligands has been described. Due to the instability of the bond between mercury and a negatively charged sulfhydryl-hapten ligand (trinitrophenyl-glutathione), the in situ formed hybrid could not be detected. On basis of model system experiments it was suggested that this mercury-sulfhydryl bond could be stabilized by an extra polar interaction between ligand and nucleic acid. This was achieved by reversing the net charge of the ligand. Such ligands were synthesized by reacting aliphatic diamines to the carboxyl groups of Tnp-glutathione using a water soluble carbodiimide. Gel chromatographic analysis of mercurated polynucleotide-ligand complexes showed that the stability of the mercury-sulfhydryl bond is increased by the reversal of the net charge of the ligand. In situ hybridized mercurated mouse satellite DNA to mouse liver nuclei and mercurated kinetoplast cRNA hybridized to Crithidia fasciculata were immunocytochemically detected after the introduction of these positively charged ligands. The described method is applicable for RNA and DNA probes. It has a sensitivity comparable to other non-autoradiographic methods, is relatively simple to perform and can be carried out with ordinary laboratory chemicals.

Animals↗
PubMed1990

Nuclear magnetic resonance studies of the solution chemistry of metal complexes. 26. Mixed ligand complexes of cadmium, nitrilotriacetic acid, glutathione, and related ligands.

The complexation of glutathione and related ligands by the nitrilotriacetic acid complex of Cd2+ (Cd(NTA)-) has been investigated by 1H NMR as a model for the coordination chemistry of Cd2+ and GSH in biological systems. Related ligands included glycine, glutamic acid, cysteine, N-acetylcysteine, penicillamine, N-acetylpenicillamine, mercaptosuccinic acid, and the S-methyl derivative of glutathione. The nature of the complexes formed was deduced from 1H NMR spectra of Cd(NTA)- and the ligands. Mixed ligand complexes (Cd(NTA)L) and single ligand complexes (CdLx) are formed with the thiol ligands, whereas only mixed ligand complexes form with glycine, glutamic acid and S-methylglutathione. Formation constants of the mixed and the single ligand complexes were determined from NMR data. The results indicate that formation constants for binding of a thiolate donor group by Cd2+, either as the free ion or in a coordinately unsaturated complex, are in the range 10(5)-10(6).

Acetates↗
PubMed1987

A general method of analysis of ligand-macromolecule equilibria using a spectroscopic signal from the ligand to monitor binding. Application to Escherichia coli single-strand binding protein-nucleic acid interactions.

We describe a general method for the analysis of ligand-macromolecule binding equilibria for cases in which the interaction is monitored by a change in a signal originating from the ligand. This method allows the absolute determination of the average degree of ligand binding per macromolecule without any assumptions concerning the number of modes or states for ligand binding or the relationship between the fractional signal change and the fraction of bound ligand. Although this method is generally applicable to any type of signal, we discuss the details of the method as it applies to the analysis of binding data monitored by a change in fluorescence of a ligand upon binding to a nucleic acid. We apply the analysis to the equilibrium binding of Escherichia coli single-strand binding (SSB) protein to single-stranded nucleic acids, which is monitored by the quenching of the intrinsic tryptophan fluorescence of the SSB protein. With this method, one can quantitatively determine the relationship between the fractional signal change of the ligand and the fraction of bound ligand, LB/LT, and rigorously test whether the signal change is directly proportional to LB/LT. For E. coli SSB protein binding to single-stranded nucleic acids in its (SSB)65 binding mode [Lohman, T. M., & Overman, L. B. (1985) J. Biol. Chem. 260, 3594; Chrysogelos, S., & Griffith, J. (1982) Proc. Natl. Acad. Sci. U.S.A. 79, 5803], we show that the fractional quenching of the SSB fluorescence is equal to the fraction of bound SSB.

Bacterial Proteins↗
PubMed1984

Biochemical characteristics of iodothyronine monodeiodination by rat liver microsomes: the interaction between iodothyronine substrate analogs and the ligand binding site of the iodothyronine deiodinase resembles that of the TBPA-iodothyronine ligand binding.

T4-analogs modified at the aliphatic side chain R are substrates for rat liver microsomal iodothyronine-5'(3')-deiodinase (ITH-D). The variation of the substrate constitution allows a mapping of the ITH-D substrate ligand-binding site. Highest affinity for the ITH-5'(3')-D was presented by Tetrac among a homologous series of carboxylic acid side chain analogs. A net negative charge of the side chain and/or the blockage of the amino function increase the affinity of the enzyme-ligand interaction. However, not only charge (electrostatic interactions), but also steric (constitution) and configurational (D-, L-alanine) contributions affect the ligand-binding site interaction. These studies present further evidence that the route of deiodination is dependent on properties of the ligand-binding site and/or catalytically-active site of the enzyme, and not on the pKa-value of the 4'-OH-group of the ITH-analogue ligands. Alterations of incubation-pH change the dissociation state of the thiolate-imidazolium ion-pair of the enzyme ligand-binding site. This can provoke changes in the enzymic route of the T4-monodeiodination cascade from 5'(3')- to the 5(3)-deiodination pathway and vice versa. The same shift can be obtained by the choice of the configuration of the alanine side chain. ITH-D exhibits substrate (ligand) binding characteristics similar to both TBPA and the nuclear T3-receptor with respect to the ITH-analogue side chain constitution: All three prefer acetic acid derivatives as ligands. In contrast to the nuclear T3-receptor both ITH-D and TBPA prefer ITH-(analogues) with a 3',5'-disubstitution which yields a dissociated 4'-phenoxi group of the molecule. These similarities may suggest that ITH-binding proteins, ITH-receptors and ITH-metabolizing enzymes may represent a closely related family of proteins. They may possibly be derived from a common ancestral ITH-binding protein. The limited substrate specificity of rat liver ITH-D, which fulfills a major contribution in ITH-metabolism in vivo, may be of physiological relevance for the poorly characterized metabolism of naturally occurring (Tetrac) and pharmacologically important (D-T4) ITH-analogs.

Animals↗
PubMed1994

Electrostatic complementarity between proteins and ligands. 2. Ligand moieties.

Drug design strategies consider factors governing intermolecular interactions to build up putative ligands. In many strategies, the ligand is constructed using fragments which are placed in the site sequentially. The optimization is then performed with each fragment. We would like to examine if this optimization strategy could generate ligands with optimal electrostatic interactions. The electrostatic complementarities between constituent moieties and the receptor site have been calculated. The whole-ligand complementarity does not appear to be the mathematical mean of the individual complementarities, nor have we found a simple relationship between the moiety and whole-ligand complementarities. The results demonstrate clearly that, using a simple model, it is very difficult to predict the electrostatic potential complementarity of the whole ligand from the complementarities of its constituent chemical moieties. This means that ligand design strategies must optimize the electrostatic complementarity globally, and not moiety by moiety.

4-Hydroxybenzoate-3-Monooxygenase↗
PubMed1989

Influence of ligand valency on ligand-influenced monomer-dimer equilibrium systems and biological control mechanisms.

Two specific ligand-influenced monomer-dimer equilibrium systems are discussed. Each has a ligand-to-dimer subunit ratio of 0.5. Equilibrium characteristics of the system are described in terms of the effect of a bivalent ligand on both experimental and theoretical analysis. It is shown that Hill expressions need to be modified for multivalent ligand systems, and care is needed in equilibrium parameter determination. Some unique properties of these systems are retained, yet others are altered in the presence of a multivalent ligand. A suggestion as to the minimum amount of information needed to describe completely a ligand-influenced monomer-dimer system is given. The estrogen-receptor system is presented as an attractive biological model for both theoretical and experimental study of ligand-influenced polymerizing systems and their role in cellular control requirements.

Kinetics↗
PubMed1995

The P-selectin glycoprotein ligand functions as a common human leukocyte ligand for P- and E-selectins.

P- and E-selectins belong to a family of Ca(2+)-dependent lectins and function as receptors for myeloid leukocytes. We have described a panel of monoclonal antibodies which recognize a sialoglycoprotein from human neutrophils and HL-60 promyelocytic cells and inhibit adhesion of these cells to P-selectin. In this study, we show that the E-selectin receptor-globulin (E-selectin Rg) affinity chromatography can isolate specifically only one glycoprotein from [3H]glucosamine-labeled HL-60 cells in a Ca(2+)-dependent manner. This protein has a molecular mass of approximately 120 kDa under reducing conditions, which appears to be identical with the previously characterized glycoprotein ligand for P-selectin. The molecule can be cross-depleted by and cross-bound to the E- and P-selectin columns. The chromatographic profile of desialylated O-linked carbohydrates from molecules purified by P- and E-selectin affinity chromatography are identical. Both have five structures at 12.8, 9.8, 6.3, 3.5, and 2.5 glucose units. PL5 monoclonal antibody to the P-selectin sialoglycoprotein ligand, E-selectin Rg, and antiserum to P-selectin glycoprotein ligand-1 (PSGL-1) all recognize the purified P-selectin ligand on ligand blots and immunoblots. Furthermore, PL5 monoclonal antibody blocks adhesion of HL-60 cells and human neutrophils to E-selectin Rg. Taken together, our results demonstrate that the P- and E-selectin ligand defined in this study is PSGL-1 and suggest that this molecule is an important leukocyte ligand for both P- and E-selectins.

Amino Acid Sequence↗