Prosthetic group content and ligand-binding properties of spinach nitrite reductase

Chemical analysis of the ferredoxin-dependent native form (Mr = 85,000) of spinach nitrite reductase has demonstrated a siroheme content that approaches 2 mol of siroheme/mol of enzyme. A widely studied modified (Mr = 61,000) form of nitrite reductase, that has lost much of the native enzyme's ability to use ferredoxin as an electron donor, contains approximately 1 mol of siroheme/mol of enzyme. Quantitation of the high spin ferri-siroheme EPR signals and of nitrite-binding sites of the two preparations confirmed that the native enzyme's siroheme content is approximately twice that of the modified enzyme. Plots of nitrite and cyanide binding to the native enzyme versus ligand concentration are sigmoidal, with Hill coefficients of 1.6-1.8 and 2.3-2.8, respectively. Plots of enzyme activity versus nitrite concentration for the native enzyme are sigmoidal with a Hill coefficient of 2.4. Cyanide inhibition of enzymatic activity was shown to be not competitive. Addition of cyanide to the native enzyme resulted in a diminution of the high spin ferri-siroheme EPR signal and produced EPR signals with g values of 2.71, 2.33, and 1.49 due to low spin ferri-siroheme.     

Spectroscopic properties of spinach catalase

Spinach catalase (hydrogen-peroxide: hydrogen-peroxide oxidoreductase, EC 1.11.1.6) has been purified to homogeneity. The purified enzyme has a specific activity of 25 000 units per mg protein. The presence of 2-mercaptoethanol and phenylmethylsulfonyl fluoride (PMSF) were required for high yields of the enzyme. The molecular weight of the enzyme was estimated to be 125 000 by gel filtration. Subunit analysis by polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate revealed a single peptide with M_r 55 000. The enzyme, which exhibits optical absorbance maxima at 279, 403, 542, 592 and 723 nm and shoulders at 290, 500 and 630 nm, contains 2 mol iron per mol protein. One of the two irons can be attributed to protoheme, while the other iron appears to be present in a novel heme. The oxidized catalase exhibited two sets of high-spin, ferriheme EPR signals.     

Active and inhibited human catalase structures: ligand and NADPH binding and catalytic mechanism

Human catalase is an heme-containing peroxisomal enzyme that breaks down hydrogen peroxide to water and oxygen; it is implicated in ethanol metabolism, inflammation, apoptosis, aging and cancer. The 1. 5 A resolution human enzyme structure, both with and without bound NADPH, establishes the conserved features of mammalian catalase fold and assembly, implicates Tyr370 as the tyrosine radical, suggests the structural basis for redox-sensitive binding of cognate mRNA via the catalase NADPH binding site, and identifies an unexpectedly substantial number of water-mediated domain contacts. A molecular ruler mechanism based on observed water positions in the 25 A-long channel resolves problems for selecting hydrogen peroxide. Control of water-mediated hydrogen bonds by this ruler selects for the longer hydrogen peroxide and explains the paradoxical effects of mutations that increase active site access but lower catalytic rate. The heme active site is tuned without compromising peroxide binding through a Tyr-Arg-His-Asp charge relay, arginine residue to heme carboxylate group hydrogen bonding, and aromatic stacking. Structures of the non-specific cyanide and specific 3-amino-1,2, 4-triazole inhibitor complexes of human catalase identify their modes of inhibition and help reveal the catalytic mechanism of catalase. Taken together, these resting state and inhibited human catalase structures support specific, structure-based mechanisms for the catalase substrate recognition, reaction and inhibition and provide a molecular basis for understanding ethanol intoxication and the likely effects of human polymorphisms.     

Frictional resistance to motions of bimane-labelled spinach calmodulin in response to ligand binding

The single cysteinyl residue 26 of spinach calmodulin was labelled with the thiol-specific bimane fluorescence probe. Following application of stoichiometric quantities of Ca2+ or aluminum ions to the protein, temperature-dependent fluorescence changes (anisotropy, lifetime) could be monitored via the label. From these data the Y function could be constructed which, as a function of temperature, seems to consist of two linear regions which intersect at the critical temperature, Tc. From the Y function the thermal coefficient, b(T), of the frictional resistance to fluorophore rotation could be determined. b(T) was dependent on the type and stoichiometry of the ligand(s) bound to calmodulin. Changes of the thermal coefficient apparently resulted in part from ligand-triggered structural pertubations transmitted over a considerable distance to calmodulin region I, the site of the fluorophore.     

Methyl group reorientation under ligand binding probed by pseudocontact shifts

Liquid-state NMR spectroscopy is a powerful technique to elucidate binding properties of ligands on proteins. Ligands binding in hydrophobic pockets are often in close proximity to methyl groups and binding can lead to subtle displacements of methyl containing side chains to accommodate the ligand. To establish whether pseudocontact shifts can be used to characterize ligand binding and the effects on methyl groups, the N-terminal domain of HSP90 was tagged with caged lanthanoid NMR probe 5 at three positions and titrated with a ligand. Binding was monitored using the resonances of leucine and valine methyl groups. The pseudocontact shifts (PCS) caused by ytterbium result in enhanced dispersion of the methyl spectrum, allowing more resonances to be observed. The effects of tag attachment on the spectrum and ligand binding are small. Significant changes in PCS were observed upon ligand binding, indicating displacements of several methyl groups. By determining the cross-section of PCS iso-surfaces generated by two or three paramagnetic centers, the new position of a methyl group can be estimated, showing displacements in the range of 1–3 Å for methyl groups in the binding site. The information about such subtle but significant changes may be used to improve docking studies and can find application in fragment-based drug discovery.     

Echinococcus granulosus antigen B hydrophobic ligand binding properties

Antigen B (AgB), an immunodominant component of the cestode parasite Echinococcus granulosus, presents homology to and shares apparent structural similarities with helix-rich hydrophobic ligand binding proteins (HLBPs) from other cestodes. In order to investigate the fatty acid binding properties of AgB, two of its subunit components (rAgB8/1 and rAgB8/2) were expressed in Escherichia coli and purified, and the native antigen was purified from the hydatid cyst fluid by affinity chromatography using a monoclonal antibody raised against rAgB8/1. The interaction of the purified native and recombinant proteins with the fluorescent ligands DAUDA, ANS, DACA and 16-AP was investigated. The palmitic acid derived fluorescent ligand, 16-AP, showed the greatest enhancement in fluorescence when bound to native AgB or to its recombinant subunits, and the dissociation constants for 16-AP binding were determined. Surprisingly, in contrast to HLBPs from other cestodes, interactions with other fatty acids, including palmitic acid, caused an increase in fluorescence instead of competing with 16-AP. Our results suggest that AgB might have evolved different functions in the binding of hydrophobic compounds, dependent on cestode environment.     

Trifluoromethyl group as a pharmacophore: effect of replacing a CF3 group on binding and agonist activity of a glucocorticoid receptor ligand

Compound 1, a potent glucocorticoid receptor ligand, contains a quaternary carbon bearing trifluoromethyl and hydroxyl groups. This paper describes the effect of replacing the trifluoromethyl group on binding and agonist activity of the GR ligand 1. The results illustrate that replacing the CF3 group with a cyclohexylmethyl or benzyl group maintains the GR binding potency. These substitutions alter the functional behavior of the GR ligands from agonists to antagonists. Docking studies suggest that the benzyl analog 19 binds in a similar fashion as the GR antagonist, RU486. The central benzyl group of 19 and the C-11 dimethylaniline moiety of RU486 overlay. Binding of compound 19 is believed to force helix 12 to adopt an open conformation and this leads to the antagonist properties of the non-CF3 ligands carrying a large group at the center of the molecule.     

Calculation of thermodynamic properties of species from binding of a ligand by a macromolecule

In the absence of experimental methods for determining concentrations of species in protein-ligand binding, it is not possible to determine the thermodynamic properties of species directly. However, this article on a simple reaction system shows that measurements of the average number of oxygen molecules bound at various T, pH and concentrations of molecular oxygen can be used to calculate thermodynamic properties of species. The simple system considered has some of the characteristics of the binding of oxygen by hemoglobin, but it has been simplified so that the method for obtaining thermodynamic information can be clarified. A table of standard thermodynamic properties of species is the most efficient way to store thermodynamic information on a reaction system. All the standard further transformed thermodynamic properties at specified T, pH and concentrations of molecular oxygen, all the standard transformed thermodynamic properties at specified T and pH, and all the standard thermodynamic properties of species at a specified temperature can be calculated. These calculations are based on the fact that the mathematical function for the standard further transformed Gibbs energy of the system contains all the thermodynamic information on the system. These properties are all interrelated by Maxwell equations.     

The extraordinary ligand binding properties of human serum albumin

Human serum albumin (HSA), the most prominent protein in plasma, binds different classes of ligands at multiple sites. HSA provides a depot for many compounds, affects pharmacokinetics of many drugs, holds some ligands in a strained orientation providing their metabolic modification, renders potential toxins harmless transporting them to disposal sites, accounts for most of the antioxidant capacity of human serum, and acts as a NO-carrier. The globular domain structural organization of monomeric HSA is at the root of its allosteric properties which are reminiscent of those of multimeric proteins. Here, structural, functional, biotechnological, and biomedical aspects of ligand binding to HSA are summarized.     

Thermodynamic properties of ligand binding by monoclonal anti-fluorescyl antibodies

The effects of temperature on the binding of fluorescein by three monoclonal anti-fluorescyl antibodies (4-4-20, 20-19-1, and 20-20-3) were assessed by measurements of affinity constants (Ka) over a temperature range of 2-70 degrees C. Values for Ka were determined from the degree of ligand association by using fluorescence methodology. Curvilinear van't Hoff plots (ln Ka vs. T-1) were observed for all three antibodies, indicating that their standard enthalpy changes (delta Ho) were temperature dependent. This phenomenon was further investigated by plotting the changes in unitary free energy (delta Gu), standard enthalpy (delta Ho), and unitary entropy (delta Su) vs. temperature. Strong temperature dependencies were observed for enthalpy and entropy values, while free energy plots were only weakly dependent on temperature. At low temperatures (4 degrees C), entropy played a major role in the binding of fluorescein by all three antibodies, while enthalpy dominated at higher temperatures. This was a consequence of the negative heat capacity changes (delta Cpo approximately equal to -320 cal K-1 mol-1) observed for these antibodies, which produced a negative trend in both enthalpy and entropy values with increasing temperature. The negative heat capacity values also indicated that the hydrophobic effect was instrumental in the binding of fluorescein. Entropy changes were lower than expected for hydrophobic binding alone, suggesting that other forces were acting to mitigate the hydrophobic effect. One possibility was that the binding of fluorescein acted to restrain vibrational fluctuations in the active-site region, producing negative changes in both heat capacity and entropy.(ABSTRACT TRUNCATED AT 250 WORDS)     

alpha-Neo-endorphin: receptor binding properties of the tritiated ligand

Tritiated porcine alpha-neo-endorphin has been prepared from its corresponding iodinated analog. The iodinated analog (diiodotyrosine at position 1) was synthesized, along with its non-iodinated counterpart, by the solid-phase method. Catalytic exchange of this iodinated analog in the presence of tritium yielded tritiated porcine alpha-neo-endorphin having a specific activity of 45.5 Ci/mmole. Both the native, iodinated and tritiated alpha-neo-endorphin analogs were shown to be homogenous by chromatography on carboxymethylcellulose, paper chromatography, paper electrophoresis, high performance liquid chromatography and amino acid analysis. For the first time binding of alpha-neo-endorphin to rat membrane preparations is described using [3H2-Tyr1]alpha-neo-endorphin as the ligand. The binding is time-dependent and saturable with respect to alpha-neo-endorphin. Scatchard analysis was bi-phasic with KDs of 0.20 and 3.75 nM. Displacement binding studies indicate that the receptor for alpha-neo-endorphin has "kappa" and possibly "epsilon" binding characteristics.     

Synthesis and receptor binding properties of chimeric peptides containing a mu-opioid receptor ligand and nociceptin/orphanin FQ receptor ligand Ac-RYYRIK-amide

Four chimera peptides composed of ORL1 receptor ligand Ac-RYYRIK-NH2 and a mu-opioid receptor agonist dermorphin YAFGYPS-NH2 or YRFB-NH2, with a spacer linking the two pharmacophores, were synthesized and tested for their receptor binding properties. Chimera peptides with long spacers (a Lys and five or eight Gly residues) showed synergistically improved affinity for both the mu-opioid receptor and ORL1 receptor, while the chimera peptides with short spacers (Lys residue only) showed decreased or similar affinity compared to the monomeric receptor ligands. Chimera peptides containing long spacers may prove to be useful tools for studying ORL1 receptor/mu-opioid receptor heterodimers.     

Hydrophobic ligand binding properties of the human lipocalin apolipoprotein M

Apolipoprotein M (apoM) is a plasma protein associated mainly with HDL. ApoM is suggested to be important for the formation of prebeta-HDL, but its mechanism of action is unknown. Homology modeling has suggested apoM to be a lipocalin. Lipocalins share a structurally conserved beta-barrel, which in many lipocalins bind hydrophobic ligands. The aim of this study was to test the ability of apoM to bind different hydrophobic substances. ApoM was produced both in Escherichia coli and in HEK 293 cells. Characterization of both variants with electrophoretic and immunological methods suggested apoM from E. coli to be correctly folded. Intrinsic tryptophan fluorescence of both apoM variants revealed that retinol, all-trans-retinoic acid, and 9-cis-retinoic acid bound (dissociation constant = 2-3 microM), whereas other tested substances (e.g., cholesterol, vitamin K, and arachidonic acid) did not. The intrinsic fluorescence of two apoM mutants carrying single tryptophans was quenched by retinol and retinoic acid to the same extent as wild-type apoM, indicating that the environment of both tryptophans was affected by the binding. In conclusion, the binding of retinol and retinoic acid supports the hypothesis that apoM is a lipocalin. The physiological relevance of this binding has yet to be elucidated.     

A cyanobacterial hemoglobin with unusual ligand binding kinetics and stability properties

The glbN gene of the cyanobacterium Nostoc commune UTEX 584 encodes a hemoprotein, named cyanoglobin, that has high oxygen affinity. The basis for the high oxygen affinity of cyanoglobin was investigated through kinetic studies that utilized stopped-flow spectrophotometry and flash photolysis. Association and dissociation rate constants were measured at 20 degrees C for oxygen, carbon monoxide, nitric oxide, and methyl and ethyl isocyanides. The association rate constants for the binding of these five ligands to cyanoglobin are the highest reported for any naturally occurring hemoglobin, suggesting an unhindered and apolar ligand binding pocket. Cyanoglobin also shows high rates of autoxidation and hemin loss, indicating that the prosthetic group is readily accessible to solvent. The ligand binding behavior of cyanoglobin was more similar to that of leghemoglobin a than to that of sperm whale myoglobin. Collectively, the data support the model of cyanoglobin function described by Hill et al. [(1996) J. Bacteriol. 178, 6587-6598], in which cyanoglobin sequesters oxygen, and presents it to, or is a part of, a terminal cytochrome oxidase complex in Nostoc commune UTEX 584 under microaerobic conditions, when nitrogen fixation, and thus ATP demand, is maximal.     

Fluorescence and NMR investigations on the ligand binding properties of adenylate kinases

A new system for measurement of affinities of adenylate kinases (AK) for substrates and inhibitors is presented. This system is based on the use of the fluorescent ligand alpha,omega-di[(3' or 2')-O-(N-methylanthraniloyl)adenosine-5'] pentaphosphate (mAP5Am), which is an analogue of the bisubstrate inhibitor diadenosine pentaphosphate (AP5A). It allows the determination of dissociation constants for any ligand in the range of 1 x 10(-9) to 5 x 10(-2) M. Affinities for different bisubstrate inhibitors (AP4A, AP5A, AP6A) and substrates (AMP, ADP, ATP, GTP) were determined in the presence and absence of magnesium. An analysis of the binding of bisubstrate inhibitors is proposed and applied to these data. The techniques are used to describe the properties of a mutant enzyme with Gln-28----His (Q28H) prepared by site-directed mutagenesis in comparison to those of wild-type AK from Escherichia coli. This newly introduced histidine is already present in most other adenylate kinases and was regarded to be important or even essential for the catalytic reaction of AK. Temperature denaturation experiments indicate that the mutant enzyme has the same thermal stability as the wild-type enzyme and, as NMR studies indicate, also a very similar structure. However, steady-state catalytic studies and binding experiments showed that the affinities for substrates and inhibitors are elevated from 3-fold (AMP) to 5-fold (ATP) to 15-fold (AP5A) compared to those of the wild-type enzyme. Together with the results obtained by Tian et al. [Tian, G., Sanders, C. R., Kishi, F., Nakazawa, A., & Tsai, M.-D. (1988) Biochemistry 27, 5544-5552] on the effect of replacement of the conserved His-36 in the cytosolic AK (AK1) from chicken by glutamine and asparagine, this shows that residues 28 of AK from E. coli (AKec) and 36 of AK1 are situated in a comparable environment and are not essential for catalytic activity.     

Coordination polymers derived from a bis-pyridyl-bis-amide ligand: Supramolecular structural diversities and anion binding properties

Six new coordination polymers namely [{Cu(μ-L1)(CH₃COO)₂}]_∝1a, [{Cu(μ-L1)₂(CH₃COO)₂]_∝1b, [{Cu(μ-L1)₂(H₂O)₂}(NO₃)₂]_∝2, [{Cu(μ-L1)₂(H₂O)₂}(ClO₄)₂]_∝3, [{Cu(μ-L1)(H₂O)₂(μ-SO₄)}·3H₂O]_∝4a and [{Cu(μ-L1)₂SO₄}·X]_∝4b (L1 = N,N′-bis-(3-pyridyl)terephthalamide) have been synthesized. Single crystal structures of five coordination polymers namely 1a, 2-4b and the free ligand L1 are discussed in the context of the effect of conformation dependent ligating topology of the ligands, hydrogen bonding backbone, counter anions on the resultant supramolecular structures observed in these coordination polymers. It was revealed from the single crystal X-ray structure analysis that conformation dependent ligating topology of the bis-amide ligand L1, counter anion’s ligating strength dependent metal: ligand ratio, hydrogen bonding ability of the ligand as well as counter anions are responsible for the formation of 1D zigzag, 1D looped chain, 2D corrugated sheet in 1a, 2-3, 4a−4b, respectively. By following in situ coordination polymer crystallization technique, anion binding and separation studies have also been performed; nitrate anion has been separated as neat coordination polymer crystals from a complex mixture of anions.     

Biochemical characterization and ligand binding properties of neuroglobin, a novel member of the globin family

Neuroglobin is a recently discovered member of the globin superfamily that is suggested to enhance the O(2) supply of the vertebrate brain. Spectral measurements with human and mouse recombinant neuroglobin provide evidence for a hexacoordinated deoxy ferrous (Fe(2+)) form, indicating a His-Fe(2+)-His binding scheme. O(2) or CO can displace the endogenous protein ligand, which is identified as the distal histidine by mutagenesis. The ferric (Fe(3+)) form of neuroglobin is also hexacoordinated with the protein ligand E7-His and does not exhibit pH dependence. Flash photolysis studies show a high recombination rate (k(on)) and a slow dissociation rate (k(off)) for both O(2) and CO, indicating a high intrinsic affinity for these ligands. However, because the rate-limiting step in ligand combination with the deoxy hexacoordinated form involves the dissociation of the protein ligand, O(2) and CO binding is suggested to be slow in vivo. Because of this competition, the observed O(2) affinity of recombinant human neuroglobin is average (1 torr at 37 degrees C). Neuroglobin has a high autoxidation rate, resulting in an oxidation at 37 degrees C by air within a few minutes. The oxidation/reduction potential of mouse neuroglobin (E'(o) = -129 mV) lies within the physiological range. Under natural conditions, recombinant mouse neuroglobin occurs as a monomer with disulfide-dependent formation of dimers. The biochemical and kinetic characteristics are discussed in view of the possible functions of neuroglobin in the vertebrate brain.