Antigen-antibody recognition by Fourier transform IR spectroscopy/attenuated total reflection studies: biotin-avidin complex as an example

Biotin-avidin recognition is studied by Fourier transform ir spectroscopy/attenuated total reflection (FTIR/ATR) under physiological conditions. The ureido portion of biotin is confirmed to be involved in the interaction with avidin, as previously found, but when the biotin-avidin complex forms, an electrostatic interaction occurs between the carboxylate group of the biotin molecule and the protonated aminic end group of the avidin amino acid side chains. Comparison of the biotin-avidin system with the biotin-1,4-diaminobutane and biotin-tryptophan systems confirms these findings.     

A comparison of silver ion to streptavidin coated microplates

Direct comparisons are made between covalently linked streptavidin and silver ion coated microplates. Both coatings can immobilize biotinylated molecules. Silver ion coated microplate wells can immobilize 1.8 times higher amounts of biotin labeled horseradish peroxidase. The quantitation range and capacity for the capture of horseradish peroxidase using biotin labeled horseradish peroxidase are also greater for silver ion coated microplates. Approximately twice as many anti-horseradish peroxidase antibodies can be immobilized per well using silver ion coated microplates. Higher capacities are presumed to be due to the smaller footprint of silver ions as compared to streptavidin. A direct comparison between the two coatings for a beta-galactosidase ELISA showed that while the silver ion coated microplates gave higher readings, the streptavidin coated microplates exhibited smaller well-to-well variation. However, higher well to well variation for the silver microplates is attributed to the high density of anti-beta-galactosidase antibodies on the microplates and the weak binding of clone GAL-13 to beta-galactosidase, rather than the silver coating. These studies suggest silver ion coated microplates are a desirable alternative to streptavidin plates for quantitative immunoassays.     

X-ray crystallographic studies of streptavidin mutants binding to biotin

On the basis of high resolution crystallographic studies of streptavidin and its biotin complex, three principal binding motifs have been identified that contribute to the tight binding. A flexible binding loop can undergo a conformational change from an open to a closed form when biotin is bound. Additional studies described here of unbound wild-type streptavidin have provided structural views of the open conformation. Several tryptophan residues packing around the bound biotin constitute the second binding motif, one dominated by hydrophobic interactions. Mutation of these residues to alanine or phenylalanine have variable effects on the thermodynamics and kinetics of binding, but they generate only small changes in the molecular structure. Hydrogen bonding interactions also contribute significantly to the binding energetics of biotin, and the D128A mutation which breaks a hydrogen bond between the protein and a ureido NH group results in a significant structural alteration that could mimic an intermediate on the dissociation pathway. In this review, we summarize the structural aspects of biotin recognition that have been gained from crystallographic analyses of wild-type and site-directed streptavidin mutants.     

The enzymes of biotin dependent CO2 metabolism: What structures reveal about their reaction mechanisms

Biotin is the major cofactor involved in carbon dioxide metabolism. Indeed, biotin‐dependent enzymes are ubiquitous in nature and are involved in a myriad of metabolic processes including fatty acid synthesis and gluconeogenesis. The cofactor, itself, is composed of a ureido ring, a tetrahydrothiophene ring, and a valeric acid side chain. It is the ureido ring that functions as the CO₂ carrier. A complete understanding of biotin‐dependent enzymes is critically important for translational research in light of the fact that some of these enzymes serve as targets for anti‐obesity agents, antibiotics, and herbicides. Prior to 1990, however, there was a dearth of information regarding the molecular architectures of biotin‐dependent enzymes. In recent years there has been an explosion in the number of three‐dimensional structures reported for these proteins. Here we review our current understanding of the structures and functions of biotin‐dependent enzymes. In addition, we provide a critical analysis of what these structures have and have not revealed about biotin‐dependent catalysis.     

Fourier-transform infrared spectroscopic studies on avidin secondary structure and complexation with biotin and biotin-lipid assemblies.

Fourier-transform infrared studies have been carried out to investigate the secondary structure and thermal stability of hen egg white avidin and its complexes with biotin and with a biotinylated lipid derivative, N-biotinyl dimyristoyl phosphatidylethanolamine (DMBPE) in aqueous dispersion. Analysis of the amide I stretching band of avidin yielded a secondary structural content composed of approximately 66% beta-sheet and extended structures, with the remainder being attributed to disordered structure and beta-turns. Binding of biotin or specific association with the biotinylated lipid DMBPE did not result in any appreciable changes in the secondary structure content of the protein, but a change in hydrogen bond stability of the beta-sheet or extended chain regions was indicated. The latter effect was enhanced by surface interactions in the case of the biotin-lipid assemblies, as was demonstrated by electrostatic binding to a nonspecific negatively charged lipid. Difference spectra of the bound biotin implicated a direct involvement of the ureido moiety in the ligand interaction that was consistent with hydrogen bonding to amino acid residues in the avidin protein. It was found that complexation with avidin leads to a decrease in bond length of the biotin ureido carbonyl group that is consistent with a reduction of sp3 character of the C-O bond when it is hydrogen bonded to the protein. Studies of the temperature dependence of the spectra revealed that for avidin alone the secondary structure was unaltered up to approximately 75 degrees C, above which the protein undergoes a highly cooperative transition to an unfolded state with concomitant loss of ordered secondary structure. The complexes of avidin with both biotin and membrane-bound DMBPE lipid assemblies display a large increase in thermal stability compared with the native protein.     

Thermodynamic and structural consequences of flexible loop deletion by circular permutation in the streptavidin-biotin system.

A circularly permuted streptavidin (CP51/46) has been designed to remove the flexible polypeptide loop that undergoes an open to closed conformational change when biotin is bound. The original termini have been joined by a tetrapeptide linker, and four loop residues have been removed, resulting in the creation of new N- and C-termini. Isothermal titration calorimetric studies show that the association constant has been reduced approximately six orders of magnitude below that of wild-type streptavidin to 10(7) M(-1). The deltaH degrees of biotin association for CP51/46 is reduced by 11.1 kcal/mol. Crystal structures of CP51/46 and its biotin complex show no significant alterations in the binding site upon removal of the loop. A hydrogen bond between Ser45 and Ser52 found in the absence of biotin is broken in the closed conformation as the side-chain hydroxyl of Ser45 moves to hydrogen bond to a ureido nitrogen of biotin. This is true in both the wild-type and CP51/46 forms of the protein, and the hydrogen bonding interaction might thus help nucleate closure of the loop. The reduced entropic cost of binding biotin to CP51/46 is consistent with the removal of this loop and a reduction in entropic costs associated with loop closure and immobilization. The reduced enthalpic contribution to the free energy of binding is not readily explainable in terms of the molecular structure, as the binding contacts are nearly entirely conserved, and only small differences in solvent accessible surfaces are observed relative to wild-type streptavidin.     

Identification and solution structures of a single domain biotin/lipoyl attachment protein from Bacillus subtilis

Protein biotinylation and lipoylation are post-translational modifications, in which biotin or lipoic acid is covalently attached to specific proteins containing biotin/lipoyl attachment domains. All the currently reported natural proteins containing biotin/lipoyl attachment domains are multidomain proteins and can only be modified by either biotin or lipoic acid in vivo. We have identified a single domain protein with 73 amino acid residues from Bacillus subtilis strain 168, and it can be both biotinylated and lipoylated in Escherichia coli. The protein is therefore named as biotin/lipoyl attachment protein (BLAP). This is the first report that a natural single domain protein exists as both a biotin and lipoic acid receptor. The solution structure of apo-BLAP showed that it adopts a typical fold of biotin/lipoyl attachment domain. The structure of biotinylated BLAP revealed that the biotin moiety is covalently attached to the side chain of Lys(35), and the bicyclic ring of biotin is folded back and immobilized on the protein surface. The biotin moiety immobilization is mainly due to an interaction between the biotin ureido ring and the indole ring of Trp(12). NMR study also indicated that the lipoyl group of the lipoylated BLAP is also immobilized on the protein surface in a similar fashion as the biotin moiety in the biotinylated protein.     

Active Transport of Biotin in Escherichia coli K-12

The transport of [(14)C]biotin into cells of a biotin prototroph, Escherichia coli K-12 strain Y10-1, was investigated. The vitamin taken up by the cells in this strain existed primarily in the free form. Addition of glucose enhanced the rate of uptake six- to eightfold and the steady level was reached in 2 to 3 min resulting in accumulation of biotin against a concentration gradient. The uptake showed marked dependence on temperature (Q(10), 2.3; optimum, 37 C) and pH (optimum 6.6) and was inhibited by iodoacetate. Energy of activation for glucose-dependent uptake was calculated to be 16,200 cal per mol. The rate of biotin uptake with increasing biotin concentrations showed saturation kinetics with an apparent K(m) and V(max) values of 1.4 x 10(-7) M and 6.6 pmol per mg of dry cells per min respectively. The cells also accumulated biotin against a concentration gradient in the absence of added glucose, although at a much lower rate. This accumulation was much more susceptible to inhibition by azide and uncouplers of oxidative phosphorylation suggesting that the energy source was supplied through the electron-transport chain. Inhibition studies with a number of biotin analogues indicated the requirement for an intact ureido ring. The biotin uptake was inhibited in cells grown in biotin-containing medium and was shown to be the result of repression of the transport system, suggesting the control of the biotin transport.     

A pyridine bridged dicarbene ligand and its silver(I) and palladium(II) complexes: synthesis, structures, and catalytic applications

The potentially tridentate ligand 2,6-bis[(3-methylimidazolium-1-yl)methyl]pyridine dibromide reacts readily with silver(I) oxide in dichloromethane or dimethylsulfoxide to give a dinuclear silver(I)-carbene complex that was isolated as the tetrafluoroborate salt. Single crystal X-ray crystallography shows that each silver(I) ion is bridged by two ligands bonding through the carbene donors. Treatment of the silver(I) complex with suitable palladium(II) precursors gave the complexes PdCl[(CNC)]BF₄ and [PdMe(CNC)]BF₄ (CNC=2,6-bis[(3-methylimidazolin-2-yliden-1-yl)methyl]pyridine), in which the pyridyl and both carbene moieties are coordinated to a single palladium(II). The palladium(II) complexes have been fully characterised, including X-ray crystallography, and exhibit good activities in the Heck coupling reaction of 4-bromoacetophenone and n-butyl acrylate.     

Dependence of the activity of beef heart mitochondrial adenosinetriphosphatase on the properties of the catalytic metal ion

Several divalent metal ions were used as kinetic probes of the beef heart mitochondrial adenosinetriphosphatase (F1) under a variety of conditions, and the relationship between the properties of the catalytic metal ion and the catalytic activity of the enzyme was examined. Vmax for ATP hydrolysis was largest when metal ions characterized by intermediate values of acidity of coordinated water molecules (pKa) and metal-nucleotide stability constants (Kstab) were present. As temperature increased, the peak of Vmax vs. pKa (or Kstab) shifted to lower initial values of pKa or Kstab. The solvent deuterium isotope effect on Vmax (DV) was normal and largest when the metal ion present during F1-catalyzed ATP hydrolysis was most acidic and the metal nucleotide stability constant was large. When an active site tyrosine on F1 was nitrated, Vmax was most affected when the metal ion present was least acidic and the metal nucleotide stability constant was small. The isotope effect on V/K (DV/K) was normal, small, and apparently independent of the metal ion present. ADP inhibition of F1-catalyzed ATP hydrolysis is competitive, and the Ki is independent of the metal ion present. The degree of Pi inhibition of F1 is dependent on the metal ion present. The inhibition by Pi is competitive at low temperature and becomes noncompetitive as temperature increases. These and previous results support a mechanism whereby a water molecule coordinated to the metal ion of an enzyme-bound gamma-monodentate metal-ATP complex is deprotonated to begin a series of events whereby a beta,gamma-bidentate metal-ATP complex is produced. Upon hydrolysis, the bond between the metal ion and the beta-phosphate of ADP in the Pi-metal-ADP complex is broken before products (ADP and metal-Pi) are released.     

Subunit gamma of the oxaloacetate decarboxylase Na(+) pump: interaction with other subunits/domains of the complex and binding site for the Zn(2+) metal ion.

The oxaloacetate decarboxylase Na(+) pump of Klebsiella pneumoniae is an enzyme complex composed of the peripheral alpha subunit and the two integral membrane-bound subunits beta and gamma. The alpha subunit consists of the N-terminal carboxyltransferase domain and the C-terminal biotin domain, which are connected by a flexible proline/alanine-rich linker peptide. To probe interactions between the two domains of the alpha subunit and between alpha-subunit domains and the gamma subunit, the relevant polypeptides were synthesized in Escherichia coli and subjected to copurification studies. The two alpha-subunit domains had no distinct affinity toward each other and could, therefore, not be purified as a unit on avidin-sepharose. The two domains reacted together catalytically, however, performing the carboxyl transfer from oxaloacetate to protein-bound biotin. This reaction was enhanced up to 6-fold in the presence of the Zn(2+)-containing gamma subunit. On the basis of copurification with different tagged proteins, the C-terminal biotin domain but not the N-terminal carboxyltransferase domain of the alpha subunit formed a strong complex with the gamma subunit. Upon the mutation of gamma H78 to alanine, the binding affinity to subunit alpha was lost, indicating that this amino acid may be essential for formation of the oxaloacetate decarboxylase enzyme complex. The binding residues for the Zn(2+) metal ion were identified by site-directed and deletion mutagenesis. In the gamma D62A or gamma H77A mutant, the Zn(2+) content of the decarboxylase decreased to 35% or 10% of the wild-type enzyme, respectively. Less than 5% of the Zn(2+) present in the wild-type enzyme was found if the two C-terminal gamma-subunit residues H82 and P83 were deleted. Corresponding with the reduced Zn(2+) contents in these mutants, the oxaloacetate decarboxylase activities were diminished. These results indicate that aspartate 62, histidine 77, and histidine 82 of the gamma subunit are ligands for the catalytically important Zn(2+) metal ion.     

Silver(I) tetraiodoethylene complexes with twisted olefin moiety

The reactions of silver perchlorate and tetraiodoethylene in different solvents, namely, benzene and toluene, isolated two silver(I)–iodocarbon complexes, [Ag(C₂I₄)(C₆H₆)₂(ClO₄)] (1) and [Ag(C₂I₄)(ClO₄)] (2). Both compounds contain intact iodoalkenes which coordinate via σ-donation of a halogen lone pair and retain their carbon–iodine bonds. Owing to the participation of the benzene molecules in coordination, complex 1 is found to be a discrete monomer in which the five-coordinate geometry of the silver ion is comprised of two benzene molecules, one C₂I₄ group and one perchlorate ion. In contrast, the unsaturated coordination environment of the metal ion in 2 is filled by the second iodocarbon group leading to a two-dimensional framework. The coordinated tetraiodoethylene molecules involve severe twisting of the C=C double bond, causing the C=C stretching band to move to a lower frequency.     

Heavy metal resistance in clinical isolates ofPseudomonas aeruginosa

One hundred clinical isolates of Pseudomonas aeruginosa were checked for their sensitivity towards silver nitrate. Majority of the isolates were resistant at 20 mg/L and the resistance decreased with increasing concentration of silver nitrate, only 5% of the organisms showed resistance above 70 mg/L. These silver-resistant isolates were further checked for their resistance towards mercury and cadmium at 20 mg/L of concentration and the level of resistance was found to be 33 and 40%, respectively. A correlation between silver ion resistance and concurrent mercury and cadmium ion resistance was observed, suggesting a possible linkage between resistance towards various metal ions.     

Interactions between metal ions and carbohydrates. The coordination behavior of neutral erythritol to neodymium ion

A single crystal of a coordinated complex of neutral erythritol (C4H10O4,E) with a neodymium ion, NdE(II), was synthesized and studied using FT-IR and X-ray diffraction analysis. In NdE(II) (NdCl3.2.5C4H10O4.C2H5OH) the Nd3+ coordinates with one chloride ion and eight OH groups from three erythritol molecules. There are two neodymium centers linked by one erythritol molecule with same coordination structure in the molecule. Two erythritol molecules provide 1,3,4-hydroxyl groups to coordinate with a neodymium ion; another erythritol molecule coordinates to two Nd ions via its 1,2-hydroxyl groups and 3,4-hydroxyl groups, respectively. The OH groups of erythritol act as ligand to coordinate to neodymium ions, and OH groups of erythritol form hydrogen bond networks that link chain and layer together to build three-dimensional structures. The ratio of metal to ligand is 1:2.5. The structure of NdE(II) is more complicated than the previously reported NdE(I), which is NdCl3.C4H10O4.6H2O; in NdE(I), Nd3+ is coordinated to four hydroxyl groups from two erythritol molecules, four water molecules and one chloride ion. The results indicate the complexity of metal-sugar interaction.     

Studies on the biosynthesis of biotin. Production of biotin and biotin-like compounds by a pseudomonad

1. Filtrates from cultures of a strain of Pseudomonas aeruginosa, grown in a basal glucose-ammonium chloride-vitamins-salts medium, possessed biotin activity as detected by microbiological assays. Exponential-phase culture filtrates contained biotin and desthiobiotin in the approximate ratio 1:3, with smaller amounts of biotin sulphoxide and three unidentified compounds with biotin activity. 2. The addition of malonate, adipate or pimelate to the basal medium stimulated the production of compounds with biotin activity; this effect was enhanced when these compounds were included in the medium as the major carbon source. Succinate, glutarate, suberate, fumarate or oxaloacetate did not stimulate the production of compounds with biotin activity. The ratio of biotin to desthiobiotin in filtrates from cultures grown in medium containing malonate as the carbon source was about 1:1. Experiments in which mixtures of malonate and pimelate were included in the medium as the carbon sources showed that these acids probably make a similar contribution in biotin biosynthesis. 3. A number of heterocyclic compounds, including several containing the ureido group (-NH-CO-NH-), were included in the basal medium but none of them stimulated the production of compounds with biotin activity to any marked degree. 4. Several amino acids, particularly cysteine (or cystine) and lysine, when added individually as supplements to the basal medium, stimulated the production of compounds with biotin activity. Filtrates from cultures grown in medium supplemented with cysteine contained approximately equal proportions of biotin and desthiobiotin. A much greater stimulation in the production of compounds with biotin activity was obtained when certain amino acids were included in the medium as the major source of nitrogen or carbon and nitrogen; ornithine, citrulline and argininosuccinate had the most marked effect. The ratio of biotin to desthiobiotin in filtrates from these cultures was usually greater than in filtrates from cultures grown in basal medium. 5-Aminovalerate also caused some stimulation when used as the nitrogen source, but urea was inactive. The effect of binary mixtures of certain amino acids was also examined. 5. The results are discussed in relation to the possible role of the stimulatory compounds during biotin biosynthesis.     

m-[125I]iodoaniline: a useful reagent for radiolabeling biotin

Biotinyl-m-[¹²⁵I]iodoanilide (BIA) was synthesized by coupling biotin to m-[¹²⁵I]iodoaniline via a mixed anhydride reaction. m-[¹²⁵I]Iodoaniline was produced from the tin precursor, which was prepared using a palladium catalyzed reaction of hexabutylditin with m-bromoaniline. The radioiodinated BIA derivative is characterized by a stable amide and/or intact ureido group on the biotin molecule; it may thus be a useful carrier for targeting radionuclides to avidin-conjugated antibodies previously localized on tumors.     

Cyclic peptide metal salt adducts. II. crystal structure of the silver nitrate cyclosarcosylsarcosine 2:1 adduct

The crystal structure analysis of the 2:1 adduct of cyclosarcosylsarcosine with silver(I) nitrate shows that the Ag(I) ion directly interacts with the carbonyl oxygen atoms of the peptide moiety. The independent unit is composed of a half cyclosarcosylsarcosine molecule, which sits on a crystallographic center of symmetry, per each silver nitrate unit. The crystal is held together by strong coulombic interactions between the silver and the nitrate ions and by ion- dipole interactions between the silver ion and the organic molecule. The coordination at the Ag(I) ion cannot be described in terms of a regular geometry; each silver ion experiences different types of contacts with the surrounding oxygen atoms. Six Ag-O interactions are in the fange 2.35-2.68 Å; a seventh Ag-O interaction presents a distance of 2.90 Å. This latter contact is perhaps the cause of the severe distortion from the ideal octahedral geometry observed experimentally. The nitrate ion and the cyclic peptide molecule are both nearly planar.     

The intramolecular cyclization 2-Iodo-3-ureidopropionic acid.

2-Iodo-3-ureidopropionic acid resulting from the hydrolysis of 5-iodo-5,6-dihydrouracil catalyzed by either dihydrouracil amidohydrolase or hydroxide ion cyclizizes to yield 2-amino-2-oxazoline-3-carboxylic acid. This cyclization involves intramolecular attack of the ureido oxygen atom on carbon two of the ureidoacid to yield iodide ion and the oxazoline as products. The kinetics of this cyclization indicate that from pH 2 to 9 the reaction rate is pH independent. Below pH 2 the rate is diminished due to protonation of the ureido group. Above pH 12 the rate increases dramatically probably due to proton abstraction which would dramatically increase the nucleophilic character of the ureido function. In the pH independent region the reaction is not subject to catalysis by external buffers.     

Structural and biochemical studies on the regulation of biotin carboxylase by substrate inhibition and dimerization

Biotin carboxylase (BC) activity is shared among biotin-dependent carboxylases and catalyzes the Mg-ATP-dependent carboxylation of biotin using bicarbonate as the CO₂ donor. BC has been studied extensively over the years by structural, kinetic, and mutagenesis analyses. Here we report three new crystal structures of Escherichia coli BC at up to 1.9 Å resolution, complexed with different ligands. Two structures are wild-type BC in complex with two ADP molecules and two Ca²⁺ ions or two ADP molecules and one Mg²⁺ ion. One ADP molecule is in the position normally taken by the ATP substrate, whereas the other ADP molecule occupies the binding sites of bicarbonate and biotin. One Ca²⁺ ion and the Mg²⁺ ion are associated with the ADP molecule in the active site, and the other Ca²⁺ ion is coordinated by Glu-87, Glu-288, and Asn-290. Our kinetic studies confirm that ATP shows substrate inhibition and that this inhibition is competitive against bicarbonate. The third structure is on the R16E mutant in complex with bicarbonate and Mg-ADP. Arg-16 is located near the dimer interface. The R16E mutant has only a 2-fold loss in catalytic activity compared with the wild-type enzyme. Analytical ultracentrifugation experiments showed that the mutation significantly destabilized the dimer, although the presence of substrates can induce dimer formation. The binding modes of bicarbonate and Mg-ADP are essentially the same as those to the wild-type enzyme. However, the mutation greatly disrupted the dimer interface and caused a large re-organization of the dimer. The structures of these new complexes have implications for the catalysis by BC.     

A radiotracer probe to study metal interaction with human lactate dehyrogenase isoenzymes

The electrophilic Ag⁺ ion was found to destroy completely the enzymatic activity of lactate dehydrogenase isoenzyme LDH-1 while other transition metal ions reduced its activity in varying degrees. A radiotracer probe involving^110mAg-labeled silver ion was used to understand the mechanism of denaturation of LDH and also to determine the number of active sites, if any, for substrate binding with the enzyme. Purified LDH-1 was reacted with^110mAg-labeled silver ion and the mixture was passed through the sephadex G-75-120 gel to separate the^110mAg-LDH complex that might be formed during the reaction. The resulting elution curve revealed that a stable complex was formed. From the total radioactivity of^110mAg bound LDH, the specific activity of labeled Ag⁺ and the amount of LDH used the ratio of the number of moles of Ag⁺ reacted with 1 mol of LDH was computed. This was found to be approximately 4.0, indicating that there are four binding sites in LDH, probably one on each subunit. Kinetic studies of LDH catalysis of L-P reaction in the presence and absence of Ag⁺ ion suggest that silver ion is involved in competitive inhibition and that the interaction conforms to the lock-and-key model. The inhibition of catalysis by other metals is presumably of a noncompetitive type.This paper was presented at the Sixty-Sixth Annual Meeting of the Georgia Academy of Science, Valdosta State College, Valdosta, Georgia, April 28–29, 1989.