Showing papers on "Cooperative binding published in 2004"

Understanding noncovalent interactions: ligand binding energy and catalytic efficiency from ligand-induced reductions in motion within receptors and enzymes.

Abstract: Noncovalent interactions are sometimes treated as additive and this enables useful average binding energies for common interactions in aqueous solution to be derived. However, the additive approach is often not applicable, since noncovalent interactions are often either mutually reinforcing (positively cooperative) or mutually weakening (negatively cooperative). Ligand binding energy is derived (positively cooperative binding) when a ligand reduces motion within a receptor. Similarly, transition-state binding energy is derived in enzyme-catalyzed reactions when the substrate transition state reduces the motions within an enzyme. Ligands and substrates can in this way improve their affinities for these proteins. The further organization occurs with a benefit in bonding (enthalpy) and a limitation in dynamics (cost in entropy), but does not demand the making of new noncovalent interactions, simply the strengthening of existing ones. Negative cooperativity induces converse effects: less efficient packing, a cost in enthalpy, and a benefit in entropy.

Thermodynamic Analysis of Receptors Based on Guanidinium/Boronic Acid Groups for the Complexation of Carboxylates, α-Hydroxycarboxylates, and Diols: Driving Force for Binding and Cooperativity

Abstract: The thermodynamics of guanidinium and boronic acid interactions with carboxylates, alpha-hydroxycarboxylates, and diols were studied by determination of the binding constants of a variety of different guests to four different hosts (7-10). Each host contains a different combination of guanidinium groups and boronic acids. The guests included molecules with carboxylate and/or diol moieties, such as citrate, tartrate, and fructose, among others. The Gibbs free energies of binding were determined by UV/Vis absorption spectroscopy, by use of indicator displacement assays. The receptor based on three guanidinium groups (7) was selective for the tricarboxylate guest. The receptors that incorporated boronic acids (8-10) had higher affinities for guests that included alpha-hydroxycarboxylate and catechol moieties over guests containing only carboxylates or alkanediols. Isothermal titration calorimetry revealed the enthalpic and entropic contributions to the Gibbs free energies of binding. The binding of citrate and tartrate was investigated with hosts 7-10, for which all the binding events were exothermic, with positive entropy. Because of the selectivity of hosts 8-10, a simple boronic acid (14) was also investigated and determined to be selective for alpha-hydroxycarboxylates and catechols over amino acids and alkanediols. Further, the cooperativity of 8 and 9 in binding tartrate was also investigated, revealing little or no cooperativity with 8, but negative cooperativity with 9. A linear entropy/enthalpy compensation relationship for all the hosts 7-10, 14, and the carboxylate-/diol-containing guests was also obtained. This relationship indicates that increasing enthalpy of binding is offset by similar losses in entropy for molecular recognition involving guanidinium and boronic acid groups.

CD20 binding molecules

Abstract: The present invention relates to CD20 binding molecules and nucleic acid sequences encoding CD20 binding molecules. In particular, the present invention relates to CD20 binding molecules with a high binding affinity, and a low dissociation rate, with regard to human CD20. Preferably, the CD20 binding molecules of the present invention comprise light and/or heavy chain variable regions with fully human frameworks (e.g. human germline frameworks).

Structural mechanism of the simultaneous binding of two drugs to a multidrug-binding protein

Abstract: The structural basis of simultaneous binding of two or more different drugs by any multidrug-binding protein is unknown and also how this can lead to a noncompetitive, uncompetitive or cooperative binding mechanism. Here, we describe the crystal structure of the Staphylococcus aureus multidrug-binding transcription repressor, QacR, bound simultaneously to ethidium (Et) and proflavin (Pf). The structure underscores the plasticity of the multidrug-binding pocket and reveals an alternative, Pf-induced binding mode for Et. To monitor the simultaneous binding of Pf and Et to QacR, as well as to determine the effects on the binding affinity of one drug when the other drug is prebound, a novel application of near-ultraviolet circular dichroism (UVCD) was developed. The UVCD equilibrium-binding studies revealed identical affinities of Pf for QacR in the presence or absence of Et, but significantly diminished affinity of Et for QacR when Pf is prebound, findings that are readily explicable by their structures. The principles for simultaneous binding of two different drugs discerned here are likely employed by the multidrug efflux transporters.

Binding specificity of multiprotein signaling complexes is determined by both cooperative interactions and affinity preferences.

Abstract: The generation of multiprotein complexes at receptors and adapter proteins is crucial for the activation of intracellular signaling pathways. In this study, we used multiple biochemical and biophysical methods to examine the binding properties of several SH2 and SH3 domain-containing signaling proteins as they interact with the adapter protein linker for activation of T-cells (LAT) to form multiprotein complexes. We observed that the binding specificity of these proteins for various LAT tyrosines appears to be constrained both by the affinity of binding and by cooperative protein-protein interactions. These studies provide quantitative information on how different binding parameters can determine in vivo binding site specificity observed for multiprotein signaling complexes.

High-affinity binding of tumor-suppressor protein p53 and HMGB1 to hemicatenated DNA loops.

Abstract: We have recently observed that chromatin architectural protein HMGB1 (previously reported to be involved in numerous biological processes such as DNA replication, recombination, repair, tumor growth, and metastasis) could bind with extremely high affinity (K(d) 40-fold higher (K(d) approximately 0.5 nM) than that for its natural specific binding sites within its target genes (Mdm2 promoter). Binding of p53 to hcDNA remains detectable in the presence of up to approximately 4 orders of magnitude of mass excess of competitor linear DNA, suggesting a high specificity of the interaction. p53 displays a higher affinity for hcDNA than for DNA minicircles (lacking functional p53-specific binding sequence) with a size similar to that of the loop within the hcDNA, indicating that the extreme affinity of p53 for hcDNA is likely due to the binding of the protein to the hemicatenane. Although binding of p53 to hcDNA occurs in the absence of the nonspecific DNA-binding extreme carboxy-terminal regulatory domain (30-C, residues 363-393), the isolated 30-C domain (but not the sequence-specific p53 "core domain", residues 94-312) can also bind hcDNA. Only the full-length p53 can form stable ternary complexes with hcDNA and HMGB1. The possible biological relevance of p53 and HMGB1 binding to hemicatenanes is discussed.

Zinc ions trigger conformational change and oligomerization of hepatitis B virus capsid protein.

Abstract: Assembly of virus particles in infected cells is likely to be a tightly regulated process. Previously, we found that in vitro assembly of hepatitis B virus (HBV) capsid protein is highly dependent on protein and NaCl concentration. Here we show that micromolar concentrations of Zn2+ are sufficient to initiate assembly of capsid protein, whereas other mono- and divalent cations elicited assembly only at millimolar concentrations, similar to those required for NaCl-induced assembly. Altered intrinsic protein fluorescence and highly cooperative binding of at least four Zn2+ ions (KD approximately 7 microM) indicated that binding induced a conformational change in capsid protein. At 37 degrees C, Zn2+ enhanced the initial rate of assembly and produced normal capsids, but it did not alter the extent of assembly at equilibrium. Assembly mediated by high zinc concentrations (> or =300 microM) yielded few capsids but produced a population of oligomers recognized by capsid-specific antibodies, suggesting a kinetically trapped assembly reaction. Comparison of kinetic simulations to in vitro assembly reactions leads us to suggest that kinetic trapping was due to the enhancement of the nucleation rate relative to the elongation rate. Zinc-induced HBV assembly has hallmarks of an allosterically regulated process: ligand binding at one site influences binding at other sites (cooperativity) indicating that binding is associated with conformational change, and binding of ligand alters the biological activity of assembly. We conclude that zinc binding enhances the kinetics of assembly by promoting formation of an intermediate that is readily consumed in the reaction. Free zinc ions may not be the true in vivo activator of assembly, but they provide a model for regulation of assembly.

Mode of Action for Linear Peptide Inhibitors of HIV-1 gp120 Interactions

Abstract: The linear peptide 12p1 (RINNIPWSEAMM) was previously isolated from a phage display library and was found to inhibit interaction of HIV-1 gp120 with both CD4 and a CCR5 surrogate, mAb 17b [Ferrer, M., and Harrison, S. (1999) J. Virol. 73, 5795-5802]. In this work, we investigated the mechanism that leads to this dual inhibition of gp120 binding. We found that there is a direct interaction of 12p1 with gp120, which occurs with a binding stoichiometry of 1:1. The peptide inhibits binding of monomeric YU2 gp120 to both sCD4 and 17b at IC(50) values of 1.1 and 1.6 microM, respectively. The 12p1 peptide also inhibited the binding of these ligands to trimeric envelope glycoproteins, blocked the binding of gp120 to the native coreceptor CCR5, and specifically inhibited HIV-1 infection of target cells in vitro. Analyses of sCD4 saturation of monomeric gp120 in the presence or absence of a fixed concentration of peptide suggest that 12p1 suppression of CD4 binding to gp120 is due to allosteric inhibitory effects rather than competitive inhibition of CD4 binding. Using a panel of gp120 mutants that exhibit weakened inhibition by 12p1, the putative binding site of the peptide was mapped to a region immediately adjacent to, but distinguishable from, the CD4 binding footprint. In the case of the peptide, the effects of single-12p1 residue substitutions and various peptide truncations indicate that the side chain of Trp7 and other structural elements of 12p1 are critical for gp120 binding or efficient inhibition of binding of a ligand to gp120. Finally, 12p1 was unable to inhibit binding of sCD4 to a gp120 mutant that is believed to resemble the CD4-induced conformation of gp120. These results suggest that 12p1 preferentially binds gp120 prior to engagement of CD4; binding of the peptide to gp120 limits the interaction with ligands (CD4 and CCR5) that are generally crucial for viral entry. More importantly, these results indicate that 12p1 binds to a unique site that may prove to be a prototypic target for novel CD4-gp120 inhibitors.

Investigation of the interaction of a putative allosteric modulator, N-(2,3-diphenyl-1,2,4-thiadiazole-5-(2H)-ylidene) methanamine hydrobromide (SCH-202676), with M1 muscarinic acetylcholine receptors.

Abstract: The interaction between a novel G protein-coupled receptor modulator, N-(2,3-diphenyl-1,2,4-thiadiazole-5-(2H)-ylidene) methanamine hydrobromide (SCH-202676), and the M(1) muscarinic acetylcholine receptor (mAChR) was investigated. In contrast to the prototypical mAChR allosteric modulator, heptane 1,7-bis-(dimethyl-3'-phthalimidopropyl)-ammonium bromide (C(7)/3-phth), SCH-202676 had no effect on the dissociation kinetics of [(3)H]N-methylscopolamine ([(3)H]NMS) at M(1) mAChRs stably expressed in Chinese hamster ovary (CHO) cell membranes. However, SCH-202676 completely inhibited the binding of [(3)H]NMS in membrane preparations, with a Hill slope significantly greater than unity, indicative of positive cooperativity in the binding of the inhibitor. Moreover, SCH-202676 caused dextral shifts of the [(3)H]NMS saturation binding curve that were greater than expected for a competitive interaction. The addition of C(7)/3-phth (100 microM) had no significant effect on the inhibitory potency of SCH-202676. In contrast to the findings in cell membranes, the interaction between SCH-202676 and [(3)H]NMS in intact M(1) CHO cells yielded saturation and inhibition isotherms that were compatible with the predictions for a competitive interaction. Intact cell assays of acetylcholine-mediated phosphoinositide hydrolysis in the absence or presence of SCH-202676 revealed a mixed competitive/noncompetitive mode of interaction that was dependent on the concentration of SCH-202676. These data reveal that the nature of the interaction between SCH-202676 and the M(1) mAChR is dependent on whether it is studied using intact versus broken cell preparations. It is proposed that SCH-202676 uses a dual mode of ligand-receptor interaction involving both extra- and intracellular attachment points on the M(1) mAChR that are distinct from the allosteric binding site recognized by prototypical mAChR modulators such as C(7)/3-phth.

No need to be HAMLET or BAMLET to interact with histones: Binding of monomeric α-lactalbumin to histones and basic poly-amino acids

Abstract: The ability of a specific complex of human α-lactalbumin with oleic acid (HAMLET) to induce cell death with selectivity for tumor and undifferentiated cells was shown recently to be mediated by interaction of HAMLET with histone proteins irreversibly disrupting chromatin structure [Duringer, C., et al. (2003) J. Biol. Chem. 278, 42131−42135]. Here we show that monomeric α-lactalbumin (α-LA) in the absence of fatty acids is also able to bind efficiently to the primary target of HAMLET, histone HIII, regardless of Ca2+ content. Thus, the modification of α-LA by oleic acid is not required for binding to histones. We suggest that interaction of negatively charged α-LA with the basic histone stabilizes apo-α-LA and destabilizes the Ca2+-bound protein due to compensation for excess negative charge of α-LA's Ca2+-binding loop by positively charged residues of the histone. Spectrofluorimetric curves of titration of α-LA by histone H3 were well approximated by a scheme of cooperative binding of four α-LA molecules...

Multivalent Protein-Carbohydrate Interactions: Isothermal Titration Microcalorimetry Studies

Abstract: Publisher Summary A wide variety of cellular and pathological processes are mediated by carbohydrate–protein interactions. These interactions generally require high-affinity binding. However, carbohydrate-binding proteins (lectins) typically show low affinities for simple mono- and oligosaccharides. Higher affinity interactions occur when lectins that are oligomeric proteins, bind to the carbohydrate chains of cell surface glycolipids and glycoproteins, which possess multiple binding epitopes. As a consequence, considerable attention is given toward understanding the underlying mechanisms responsible for the enhanced affinity of multivalent carbohydrates for lectins. Insight into the thermodynamic basis for the enhanced affinities of multivalent (clustered) glycosides binding to the lectins concanavalin A (ConA) and Dioclea grandiflora (DGL) is obtained by isothermal titration microcalorimetry (ITC). ITC measurements provide direct determinations of binding enthalpy, ΔH, the association constant, K a , and the number of binding sites of the protein, n. From measurements of K a , the free energy of binding, ΔG, can be calculated. The entropy of binding, ΔS, is obtained from ΔH and ΔG. Thus, ITC measurements can determine the complete thermodynamics of binding of a carbohydrate to a lectin. ConA and DGL are mannose/glucose-specific lectins with similar binding specificities. They possess relatively high affinities for the monovalent trisaccharide 3, 6-di-O-(α-D-mannopyranosyl)-α-D-mannopyranoside as compared with mannose. Synthetic multivalent clustered glycosides bearing multiple terminal mannose or mannotriose residues show increased affinities for ConA and DGL up to nearly 100-fold as assessed by enzyme-linked lectin assay and hemagglutination inhibition. To gain insight into the thermodynamic basis for the enhanced affinities of these multivalent saccharides, binding of synthetic dimeric analogs of α-D-mannopyranoside and di-, tri-, and tetrameric analogs of 3,6-di-O-(α- D -mannopyranosyl)-α- D -mannopyranoside to ConA and DGL was studied by ITC. The results show that ITC yields important thermodynamic insight into the mechanism(s) of enhanced affinities of these multivalent carbohydrates for these two lectins. The results also show that the negative cooperativity that occurs during binding is associated with the multivalent carbohydrates and not the proteins, and that entropy effects play a dominant role in the enhanced affinities of these ligands.

CD23 Trimers Are Preassociated on the Cell Surface Even in the Absence of Its Ligand, IgE

Abstract: Allergic disease is mediated by high levels of allergen-specific IgE. IgE binding to CD23, the low affinity receptor for IgE, results in a negative feedback signal leading to a decrease in IgE production. Previous studies have shown that CD23 associates as an oligomer and that cooperative binding of at least two lectin domains is required for high affinity IgE binding to CD23. We have previously shown that cooperative binding is required for regulation of IgE production. This study describes the production of several mAbs that bind the stalk region of murine CD23. One of the Abs, 19G5, inhibited the IgE/CD23 interaction at 37 degrees C, but not at 4 degrees C. Analysis of the binding properties of these Abs revealed that CD23 dissociates at high temperatures, such as 37 degrees C; however, the N terminus is constitutively associated, indicating partial, rather than complete, dissociation. A novel finding was that the stalk region, previously thought to mediate trimer association, was not required for oligomerization. These data reveal important information about the structure of CD23 that may be useful in modulating IgE production.

Binding isotherm determination by isothermal titration calorimetry

Abstract: A simple method for determination of binding isotherm in the protein-ligand interaction was introduced using isothermal titration calorimetric data. This general method was applied to the study of the interaction of myelin basic protein (MBP) from bovine central nervous system with divalent copper ion at 27°C in Tris buffer solution at pH=7.2. The binding isotherm for copper-MBP interaction is easily obtained by carrying out titration calorimetric experiment in two different concentrations of MBP. MBP has two binding sites for copper ion, which show positive cooperativity in its sites. The intrinsic association equilibrium constants are 0.083 and 1.740 ?M-1 in the first and second binding sites, respectively. Hence, occupation of the first site has produced an appreciable enhancement 21 of the binding affinity of the second site. The molar enthalpies of binding are -13.5 and -14.8 kJ mol-1 in the first and second binding sites, respectively.

“Induced-Fit” Mechanism for Catecholamine Binding to the β2-Adrenergic Receptor

Abstract: We engineered single and multiple mutations of serines 203, 204, and 207 in the fifth transmembrane domain of the beta(2)-adrenergic receptor, a region known to interact with hydroxyl groups of the catechol ring. Using such mutants, we measured the binding affinities of a panel of six catecholamine agonists differing only in the presence of substituents in the ethanolamine tail of the molecule. Although all ligands shared an intact catechol ring, they exhibited different losses of binding energy in response to the mutations. For all mutations, we found a clear relationship between the loss of binding caused by receptor mutation and that caused by the ligand modification. This indicates that the catechol ring and the ethanolamine tail synergistically influence their respective interactions when binding to the receptor. To verify this idea by a formal thermodynamic test, we used a double-mutant cycle analysis. We compared the effects of each receptor mutation with those induced by the modifications of the ligand's tail. Because such changes disrupt interactions occurring at different receptor domains, they should produce cumulative losses. In contrast, we found positive cooperativity between such effects. This means that the binding of each side of the catecholamine can enhance the binding of the other, through an effect that is probably propagated via a conformational change. We suggest that the agonist-binding pocket is not rigid but is dynamically formed as the ligand builds an increasing number of contacts with the receptor.