The binding of organic anions by polyvinylpyrrolidone: Determination of intrinsic binding constant and number of binding sites by competitive binding

The binding of 4′-dibutylaminoazobenzene-4-sulfonate (butyl orange, BO) and 1-amino-4-methylaminoanthraquinone-2-sulfonate (AQ) by crosslinked polyvinylpyrrolidone and the competition between BO and AQ for binding sites of the polymer were examined. The equilibrium data showed competitive binding. Thus the intrinsic binding constants and the number of binding sites can be evaluated easily and precisely by competitive binding. The thermodynamic parameters that accompained the binding were calculated from the intrinsic binding constant and its temperature-dependence. The thermodynamic data for BO showed that the binding process is athermal and stabilized entirely by the entropy term. The binding of BO to the polymer is entropically favorable as a result of the operation of the hydrophobic effect. In contrast, with AQ a favorable free energy for a dye-polymer complex formation is associated with a large negative enthalpy and a small entropy. Therefore it is likely that the binding of AQ occurs by energetic forces and that the large aromatic ring of the dye contributes to the binding energy. On the average, BO and AQ can bind to the crosslinked polymer to the extent of 1 dye/ca 73 basemol in 0.1M tris-acetate buffer, pH 7.0.     

Iodine binding capacity and iodine binding energy of glycogen

The iodine binding capacity (IBC) of glycogen is around 0.30% (w/w) at 3°C. The amount of iodine complexed comprises about 12.5% of the mass of glycogen that takes part in the glycogen–iodine (GI) complex formation. This suggests involvement of four iodine atoms for every 25 anhydroglucose units (AGU, C₆H₁₀O₅). Since the chromophore is due to the I₄ unit within the helix of 11 AGUs, only 44% of the AGUs (11 out of 25) are involved in the complex formation. The heat of formation of the GI complex is around −40 kJ/mol of I₂ bonded. These results suggest remarkable similarities with those of the amylopectin–iodine (API) complex. © 1997 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 35: 1409–1412, 1997     

Voronoi binding site models: Calculation of binding modes and influence of drug binding data accuracy

A new and accurate method for calculating the geometrically allowed modes of binding of a ligand molecule to a Voronoi site model is reported. It is shown that the feasibility of the binding of a group of atoms to a Voronoi site reduces to a simple set of linear and quadratic inequalities and quadratic equalities which can be solved by minimization of a simple function. Newton's numerical method of solution coupled to a line search proved to be successful. Moreover, we have developed efficient molecular and site data bases to discard quickly infeasible binding modes without time-consuming numerical calculation. The method is tested with a data set consisting of the binding constants for a series of biphenyls binding to prealbumin. After determination of the conformation space of the molecules and proposal of a Voronoi site geometry, the geometrically feasible modes are calculated and the energy interaction parameters determined to fit the observed binding energies to the site within experimental error ranges. We actually allowed these ranges to vary in order to study the influence of their broadness on the site geometry and found that as they increase, one can first model the receptor as a three-region site then as a single region site, but never as a two-region site.     

Substrate binding favors enhanced NO binding to P450cam

Ferric cytochrome P450cam from Pseudomonas putida (P450cam) in buffer solution at physiological pH 7.4 reversibly binds NO to yield the nitrosyl complex P450cam(NO). The presence of 1R-camphor affects the dynamics of NO binding to P450cam and enhances the association and dissociation rate constants significantly. In the case of the substrate-free form of P450cam, subconformers are evident and the NO binding kinetics are much slower than in the presence of the substrate. The association and dissociation processes were investigated by both laser flash photolysis and stopped-flow techniques at ambient and high pressure. Large and positive values of S and V observed for NO binding to and release from the substrate-free P450cam complex are consistent with the operation of a limiting dissociative ligand substitution mechanism, where the lability of coordinated water dominates the reactivity of the iron(III)-heme center with NO. In contrast, NO binding to P450cam in the presence of camphor displays negative activation entropy and activation volume values that support a mechanism dominated by a bond formation process. Volume profiles for the binding of NO appear to be a valuable approach to explain the differences observed for P450cam in the absence and presence of the substrate and enable the clarification of the underlying reaction mechanisms at a molecular level. Changes in spin state of the iron center during the binding/release of NO contribute significantly to the observed volume effects. The results are discussed in terms of relevance for the biological function of cytochrome P450 and in context to other investigations of the related reactions between NO and imidazole- and thiolate-ligated iron(III) hemoproteins.     

Ligand binding properties of myoglobin reconstituted with iron porphycene: unusual O2 binding selectivity against CO binding

Sperm whale myoglobin, an oxygen storage hemoprotein, was successfully reconstituted with the iron porphycene having two propionates, 2,7-diethyl-3,6,12,17-tetramethyl-13,16-bis(carboxyethyl)porphycenatoiron. The physicochemical properties and ligand bindings of the reconstituted myoglobin were investigated. The ferric reconstituted myoglobin shows the remarkable stability against acid denaturation and only a low-spin characteristic in its EPR spectrum. The Fe(III)/Fe(II) redox potential (-190 mV vs NHE) determined by the spectroelectrochemical measurements was much lower than that of the wild-type. These results can be attributed to the strong coordination of His93 to the porphycene iron, which is induced by the nature of the porphycene ring symmetry. The O2 affinity of the ferrous reconstituted myoglobin is 2600-fold higher than that of the wild-type, mainly due to the decrease in the O2 dissociation rate, whereas the CO affinity is not so significantly enhanced. As a result, the O2 affinity of the reconstituted myoglobin exceeds its CO affinity (M' = K(CO)/K(O2) < 1). The ligand binding studies on H64A mutants support the fact that the slow O2 dissociation of the reconstituted myoglobin is primarily caused by the stabilization of the Fe-O2 sigma-bonding. The IR spectra for the carbon monoxide (CO) complex of the reconstituted myoglobin suggest several structural and/or electrostatic conformations of the Fe-C-O bond, but this is not directly correlated with the CO dissociation rate. The high O2 affinity and the unique characteristics of the myoglobin with the iron porphycene indicate that reconstitution with a synthesized heme is a useful method not only to understand the physiological function of myoglobin but also to create a tailor-made function on the protein.     

Lipid binding to the carotenoid binding site in photosynthetic reaction centers

Lipid binding to the carotenoid binding site near the inactive bacteriochlorophyll monomer was probed in the reaction centers of carotenoid-less mutant, R-26 from Rhodobacter sphaeroides. Recently, a marked light-induced change of the local dielectric constant in the vicinity of the inactive bacteriochlorophyll monomer was reported in wild type that was attributed to structural changes that ultimately lengthened the lifetime of the charge-separated state by 3 orders of magnitude (Deshmukh, S. S.; Williams, J. C.; Allen, J. P.; Kalman, L. Biochemistry 2011, 50, 340). Here in the R-26 reaction centers, the combination of light-induced structural changes and lipid binding resulted in a 5 orders of magnitude increase in the lifetime of the charge-separated state involving the oxidized dimer and the reduced primary quinone in proteoliposomes. Only saturated phospholipids with fatty acid chains of 12 and 14 carbon atoms long were bound successfully at 8 °C by cooling the reaction center protein slowly from room temperature. In addition to reporting a dramatic increase of the lifetime of the charge-separated state at physiologically relevant temperatures, this study reveals a novel lipid binding site in photosynthetic reaction center. These results shed light on a new potential application of the reaction center in energy storage as a light-driven biocapacitor since the charges separated by ～30 ? in a low-dielectric medium can be prevented from recombination for hours.     

Synthesis and binding properties of a macrocycle with two binding subcavities

A large, covalent macrocycle that can be served as an artificial allosteric model was prepared in a reasonable yield (36%) through the template-directed synthesis. The macrocycle contains two topologically discrete subcavities, each of which consists of four amide NHs of pyridine-2,6-dicarboxamide units. The macrocycle strongly binds two molecules of N,N,N′,N′-tetramethylterephthalamide in positive cooperative manner by hydrogen-bonding interactions. The association constants were calculated to be K₁ = 1480 ± 90 and K₂ = 5580 ± 150 M⁻¹ with the Hill coefficient (h) of 1.6 at 25 °C in CDCl₃.     

Self-assembly and binding properties of a metallomacrocycle having two interactive binding subcavities

A metallomacrocycle containing two topologically discrete binding subcavities is self-assembled and shows a positive homotropic cooperative binding behavior.     

Cation binding to biomolecules

The binding of Zn²⁺ to the purine and pyrimidine bases of the nucleic acids was studied by SCFab initio (pseudopotential) computations. The order of affinity of the bases is guanine cytosine > adenine uracil. Many geometrical features of the binding are similar to those observed previously in the interaction of the bases with Na⁺. A new feature is the possibility of chelation by Zn²⁺ between N₇ and the rotated NH₂ group of adenine.     

Voronoi binding site models

A frequently occurring problem in drug design and enzymology is that the binding constants for several compounds to the same site are known, but the geometry and energetic interactions of the site are not. This paper presents in detail a novel approach to the problem which accurately but compactly represents the allowed conformation space of each ligand, accurately depicts their three-dimensional structures, and realistically allows each ligand to adopt the conformation and positioning in the site which is most favorable energetically. The investigator supplies only the ligand structures and observed binding free energies, along with a proposed site geometry. With no further assumptions about how the ligands bind and what parts of the ligands are important in determining the binding, the algorithm fits the observed binding energies without leaving outliers, predicts exactly how each of the given ligands binds in the site, and predicts the strength and mode of binding of new compounds, regardless of chemical similarity to the original set of ligands. The method is illustrated by devising a simple site that accounts for the binding of five polychlorinated biphenyls to thyroxine binding prealbumin. This model then predicts the binding energies correctly for an additional six biphenyls, and fails on one compound.     

Cation binding to biomolecules

SCF ab initio computations are carried out on the binding of alkali and alkaline-earth cations to the phosphate monoanion. The effect of the binding on the conformational properties of the phosphodiester linkage and of the polar head of phospholipids is investigated. The results indicate that following the nature of the cation and the site of its binding, the interaction may have a profound influence on the conformation of the ligand. The consequences of this situation on the use of lanthanide probes in NMR studies are considered.     

Designed nucleotide binding motifs

Gaps in the central strand of oligonucleotide triplexes bind nucleoside phosphates tightly. Watson-Crick and Hoogsteen base pairing as design principle yield motifs with high affinity for nucleoside phosphates with A or G as nucleobase, including ATP. The second messenger 3',5'-cAMP is bound with nanomolar affinity. A designed DNA motif accommodates seven nucleotides at a time. The design was implemented for both DNA and RNA.     

Competitive mass spectrometry binding assay for characterization of three binding sites of tubulin

Tubulin is an attractive and established target for anticancer therapy. To date, the only method to determine the binding of inhibitor to tubulin has been competitive radioligand binding assays. We developed a non‐radioactive mass spectrometry (MS) binding assay to study the tubulin binding of colchicine, vinblastine and paclitaxel and to identify which of these three binding sites that a novel inhibitor binds. The method involves a very simple step of separating the unbound ligand from macromolecules using ultrafiltration. The unbound ligand in the filtrate can be accurately determined using highly sensitive and specific liquid chromatography tandem mass spectrometry (LC‐MS/MS) method using multiple reaction monitoring (MRM) mode. The assay was validated using podophyllotoxin, vincristine and docetaxel, drugs that compete to the colchicine‐, vinblastine‐ and paclitaxel‐binding sites in tubulin, respectively. This competitive binding assay allowed the reliable detection of interactions of these drugs with three binding sites on tubulin. This method was subsequently applied to determine the tubulin‐binding site of 4‐substituted methoxylbenzoyl‐aryl‐thiazoles (SMART‐H), a potent antitubulin agent developed in our laboratory. The results indicated that SMART‐H specifically and reversibly bound only to the colchicine‐binding site, but not to vinblastine‐ or paclitaxel sites. This new non‐radioligand binding method to determine the binding site on tubulin will function as a useful tool to study the binding sites of tubulin inhibitors. Copyright © 2010 John Wiley & Sons, Ltd.     

The effect of N-substitution on the metal binding properties of peptide binding sites

The influence of methyl- and ethylsubstitution at the nitrogen atom of peptide groups on their interaction with alkali and alkaline earth metal ions has been studied by means of quantum chemical calculations on the complexes of lithium, sodium and beryllium with the different substituted amides, and by means of difference energy surfaces obtained fromab initio calculations employing minimalGaussian basis sets. Characteristic ion specific differences are found to occur in the interaction according to the respective substitutions, which will influence the potential for the metal ion in the field of the peptide groups quite strongly. Binding energies and electron density distribution in the complexes are discussed with respect to recent experimental data obtained by metal nmr spectroscopy. The results of the calculations give some indications to possible ways of influencing the ion specifity and reactivity of peptide and protein metal binding sites in biological systems.

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Der Effekt der N-Substitution auf die metallbindenden Eigenschaften von Peptiden

Zusammenfassung Der Einfluß von Methyl- und Ethyl-Substitution am Stickstoff der Peptidbindung auf die Wechselwirkung mit Alkali- und Erdalkali-Metallionen wurde mittels quantenchemischer Berechnungen an Komplexen mit Lithium, Natrium und Beryllium mit verschieden substituierten Amiden, und mittels der Differenz-Energie-Flächen vonab initio Berechnungen mit minimalemGauß-Basis-Set, studiert. Es wurden charakteristische ionenspezifische Differenzen in den Wechselwirkungen-entsprechend den verschiedenen Substituenten gefunden, die das Potential der Metallionen im Feld der Peptidbindungsgruppe sehr stark beeinflussen. Es werden Bindungsenergien und Elektronendichten in den Komplexen, bezogen auf neuere experimentelle Daten der Metall-NMR-Spektroskopie, diskutiert. Die Ergebnisse der Berechnungen zeigen mögliche Wege auf, die Ionenspezifität und die Reaktivität von Peptid- und Protein-Metall-Bindungszentren in biologischen Systemen zu beeinflussen.

     

Effect of cobratoxin binding on the normal mode vibration within acetylcholine binding protein

Recent crystal structures of the acetylcholine binding protein (AChBP) have revealed surprisingly small structural alterations upon ligand binding. Here we investigate the extent to which ligand binding may affect receptor dynamics. AChBP is a homologue of the extracellular component of ligand-gated ion channels (LGICs). We have previously used an elastic network normal-mode analysis to propose a gating mechanism for the LGICs and to suggest the effects of various ligands on such motions. However, the difficulties with elastic network methods lie in their inability to account for the modest effects of a small ligand or mutation on ion channel motion. Here, we report the successful application of an elastic network normal mode technique to measure the effects of large ligand binding on receptor dynamics. The present calculations demonstrate a clear alteration in the native symmetric motions of a protein due to the presence of large protein cobratoxin ligands. In particular, normal-mode analysis revealed that cobratoxin binding to this protein significantly dampened the axially symmetric motion of the AChBP that may be associated with channel gating in the full nAChR. The results suggest that alterations in receptor dynamics could be a general feature of ligand binding.