A new tool for the rational design of methylbiotin hosts

To study the binding mode of biotin related compounds with artificial hosts, we have developed a new tool to be used as a guide to test their behaviour prior to their synthesis. In that way, we have considered a set of 23 complexes comprising biotin and urea derivatives with synthetic hosts to develop a Partial Least Squares Cross-Validated (PLS-CV) model. The data, for such a model, are the binding constants (K_b) of each complex and the interaction energies (−E_min) calculated by molecular mechanics with AMBER and OPLS force fields. The predictive power of the model has been verified.     

A benzthiazole-based simple receptor in fluorescence sensing of biotin ester and urea

A benzthiazole-based receptor 1 has been designed and synthesized for recognition of biotin ester and urea in CHCl₃ containing 1% CH₃CN. The receptor binds biotin methyl ester and urea with moderate binding constant values and shows significant increase in emission of benzthiazole motif. The emission characteristics of 1 upon complexation clearly distinguishes biotin methyl ester and urea from thiourea and N,N′-dimethylurea. Characterization and sensing properties of the receptor 1 were evaluated by ¹H NMR, UV-vis, and fluorescence spectroscopic methods.     

The origins of femtomolar protein-ligand binding: hydrogen-bond cooperativity and desolvation energetics in the biotin-(strept)avidin binding site

The unusually strong reversible binding of biotin by avidin and streptavidin has been investigated by density functional and MP2 ab initio quantum mechanical methods. The solvation of biotin by water has also been studied through QM/MM/MC calculations. The ureido moiety of biotin in the bound state hydrogen bonds to five residues, three to the carbonyl oxygen and one for each--NH group. These five hydrogen bonds act cooperatively, leading to stabilization that is larger than the sum of individual hydrogen-bonding energies. The charged aspartate is the key residue that provides the driving force for cooperativity in the hydrogen-bonding network for both avidin and streptavidin by greatly polarizing the urea of biotin. If the residue is removed, the network is disrupted, and the attenuation of the energetic contributions from the neighboring residues results in significant reduction of cooperative interactions. Aspartate is directly hydrogen-bonded with biotin in streptavidin and is one residue removed in avidin. The hydrogen-bonding groups in streptavidin are computed to give larger cooperative hydrogen-bonding effects than avidin. However, the net gain in electrostatic binding energy is predicted to favor the avidin-bicyclic urea complex due to the relatively large penalty for desolvation of the streptavidin binding site (specifically expulsion of bound water molecules). QM/MM/MC calculations involving biotin and the ureido moiety in aqueous solution, featuring PDDG/PM3, show that water interactions with the bicyclic urea are much weaker than (strept)avidin interactions due to relatively low polarization of the urea group in water.     

Naphthyridine-based receptors for flurometric detection of urea and biotin

Naphthyridine-based receptors 1–4 have been designed and synthesized for the recognition of urea in CHCl₃ containing 1% CH₃CN. Receptor 1 also binds biotin and its methyl ester with moderate binding constant values. In comparison, receptor 2 is less efficient in recognising biotin and its methyl ester analogue. Receptor 1 binds urea and biotin with binding constant values of 1.02 × 10⁴ and 1.08 × 10⁴ M^?1, respectively, in CHCl₃ containing 1% CH₃CN and shows significant change in emission of naphthyridine upon complexation. Characterization and sensing properties of the receptors were evaluated by ¹H NMR, UV–vis and fluorescence spectroscopic methods.     

The biotin enzyme family: conserved structural motifs and domain rearrangements

The biotin carboxylase family is comprised of a group of enzymes that utilize a covalently bound prosthetic group, biotin, as a cofactor. These enzymes, which include acetyl-CoA carboxylase, pyruvate carboxylase, propionyl-CoA carboxylase, methylcrotonyl-CoA carboxylase, geranoyl-CoA carboxylase, oxaloacetate decarboxylase, methylmalonyl-CoA decarboxylase, transcarboxylase and urea amidolyase, are found in diverse biosynthetic pathways in both pro-karyotes and eukaryotes. The reactions catalyzed by most members of this group of enzymes share two common features: (1) carboxylation of biotin, apparently via the formation of a carboxyphosphate intermediate, followed by (2) transcarboxylation of CO(2) from biotin to specific acceptor molecules to yield different products. Structural determinations by NMR and X-ray crystallography, complemented by mutagenesis studies, have identified some motifs that are structurally or catalytically important. Analysis of the amino acid sequences of a number of biotin carboxylases not only shows remarkable similarities within certain domains but also that there appears to have been domain rearrangements between groups of carboxylases. Acyl-coenzyme A derivatives, which bind either as substrates or as allosteric regulators of the biotin carboxylases, do not appear to share any of the CoA binding motifs that have been identified in other CoA-SH/acyl-CoA binding proteins. Further comparisons of biotin-dependent carboxylases with other groups of enzymes in the protein data bank reveal that this family of biotin enzymes has strong similarities in specific domains to a number of ATP-utilizing enzymes and to the lipoyl-containing enzymes. These structural homologies are so extensive as to be highly suggestive of evolutionary relationships between biotin carboxylases and these other enzymes.     

Voltammetric detection of avidin and biotin by biotin labeled with cysteine

An avidin-biotin assay was developed from a voltammetric procedure using biotin labeled with cysteine. Mercury(II) as a marker was used to detect avidin and biotin, because the oxidation wave of mercury decreases when the cysteine part of labeled biotin(LB) complexes with mercury(II).The formation of the mercury(II)-cysteine complex is suppressed when the LB binds to the biotin site of avidin. Accordingly, the concentration of avidin can be estimated from the increasing mercury peak current. Detection of biotin is also carried out by a competitive reaction of biotin and the LB to the binding site on avidin, where the addition of biotin decreases the peak current of mercury. Limits of detection for avidin and biotin were in the 10^–9 mol/L range. The length of the spacer between the cysteine and biotin was investigated. It was observed that the strength of binding increased with increasing length of spacer. Size considerations rules out steric influences, so it is suggested that the binding constant depends on hydrophobic interactions in the binding site.     

Biotin-specific synthetic receptors prepared using molecular imprinting

The composition of new molecularly imprinted polymers (MIPs) specific for biotin was optimised using molecular modelling software. Three functional monomers: methacrylic acid (MAA), 2-(trifluoromethyl)acrylic acid (TFAA) and 2-acrylamido-2-methylpropanesulfonic acid (AMPSA), which demonstrated the highest binding scores with biotin, were tested on their ability to generate specific binding sites. The imprinted polymers were photografted to the surface of polystyrene microspheres in water. The affinity of the synthetic “receptor” sites was evaluated in binding experiments using horseradish peroxidase-labelled biotin. Good correlation was found between the modelling results and the performance of the materials in the template re-binding study. The dissociation constants for all MIPs were 1.4-16.8 nM, which is sufficient for most analytical applications where biotin is used as a label.     

Ultrathin coatings from isocyanate terminated star PEG prepolymers: patterning of proteins on the layers

This study presents the easy and fast patterning of low molecular weight molecules that act as binding partners for proteins on Star PEG coatings. These coatings are prepared from isocyanate terminated star shaped prepolymers and form a highly cross-linked network on the substrate in which the stars are connected via urea groups and free amino groups are present. Streptavidin has been patterned on these layers by microcontact printing (muCP) of an amino reactive biotin derivative and consecutive binding of streptavidin to the biotin. Patterns of Ni(2+)-nitriltriacetic acid (NTA) receptors have been prepared by printing amino functional NTA molecules in freshly prepared Star PEG layers that still contain amino reactive isocyanate groups. Complexation of the NTA groups with Ni(II) ions enabled the binding of His-tag enhanced green fluorescent protein (EGFP) in the desired pattern on the substrates. Since the unmodified Star PEG layers prevent unspecific protein adsorption, His-EGFP could selectively be bound to the sample by immersion into crude, nonpurified His-tag EGFP containing cell lysate.     

Specific interaction of desthiobiotin lipids and water-soluble biotin compounds with streptavidin

As shown for biotin lipids (Ref. 1), the formation of perfect 2-D crystalline streptavidin domains can also be observed in the plane of desthiobiotin lipid monolayers. The binding constant of streptavidin with desthiobiotin (K_a = 5·10¹³ mol⁻¹) is lower than that with biotin (K_a = 10¹⁵ mol⁻¹) (Ref. 2). By adding free biotin into the subphase a competitive replacement and a detaching of the streptavidin domains from the desthiobiotin lipid monolayer takes place. Streptavidin domains built at receptor lipid monolayers are still functional. As could be shown, there are two biotin binding sites at each protein molecule that are fully accessible to biotin (Ref. 1). This can be proven by the interaction with biotinylated ferritin and fluoresceinated biotin. Further coupling of an anti-FITC-antibody can proceed and a second protein layer can be formed. Using a bifunctional biotin linker a second crystalline streptavidin layer underneath the first one can be obtained.     

Voltammetric homogeneous binding assay of biotin without a separation step using iminobiotin labeled with an electroactive compound.

Avidin, which is one type of glycoprotein, has a strong affinity with biotin (Ka = 10(15) M(-1)). Iminobiotin also forms a complex with avidin (Ka = 10(8) M(-1) at pH 9.5). The avidin-iminobiotin complex changes to the avidin-biotin complex in the presence of biotin because of the difference of the binding constant to avidin. In this study, the interaction between avidin and iminobiotin labeled with an electroactive compound was investigated by voltammetry. After avidin and the labeled iminobiotin (LI) were incubated in 0.1 M phosphate buffer (pH 7.0), the peak currents of LI were measured in various concentrations of biotin. The peak currents increased with increasing the concentration of biotin. Thus, this observation indicates the formation of avidin-biotin complex. On the other hand, the formation of avidin-iminobiotin complex depended on the pH of the solution. LI combines with the avidin at pH 5.6-8.9 and dissociates at pH 4.6.     

Biotin-functional oligo(p-phenylene vinylene)s synthesized using click chemistry

Using Cu(1)-catalyzed [3+2] Huisgen ‘click’ cycloaddition, a rigid rod - like oligo(p-phenylene vinylene) (OPV) was functionalized at both ends with biotin ligands, combining the valuable electro-optical properties of conjugated organic molecules with the biological recognition capability of biotin. Biotin can be placed at variable distances from the oligomer via appropriate length of a hydrophilic spacer, which also serves to regulate the binding capabilities of the two terminal biotin units. To demonstrate this binding potential, networks were formed with streptavidin-coated quantum dots. The synthetic conditions are presented, together with representative optimizations of the key reactions. The organic compounds were analyzed by means of ATR/FTIR, ¹H NMR (200 or 600 MHz), ¹³C NMR, 2D NMR (HMBC, HMQC experiments), MS (ESI or MALDI-TOF), and optical spectroscopy. Networks were imaged with TEM.     

Development of an enzyme-linked immunosorbent assay (ELISA)-like fluorescence assay to investigate the interactions of glycosaminoglycans to cells

Sulfated glycosaminoglycans were labeled with biotin to study their interaction with cells in culture. Thus, heparin, heparan sulfate, chondroitin 4-sulfate, chondroitin 6-sulfate and dermatan sulfate were labeled using biotin-hydrazide, under different conditions. The structural characteristics of the biotinylated products were determined by chemical (molar ratios of hexosamine, uronic acid, sulfate and biotin) and enzymatic methods (susceptibility to degradation by chondroitinases and heparitinases). The binding of biotinylated glycosaminoglycans was investigated both in endothelial and smooth muscle cells in culture, using a novel time resolved fluorometric method based on interaction of europium-labeled streptavidin with the biotin covalently linked to the compounds. The interactions of glycosaminoglycans were saturable and number of binding sites could be obtained for each individual compound. The apparent dissociation constant varied among the different glycosaminoglycans and between the two cell lines. The interactions of the biotinylated glycosaminoglycans with the cells were also evaluated using confocal microscopy. We propose a convenient and reliable method for the preparation of biotinylated glycosaminoglycans, as well as a sensitive non-competitive fluorescence-based assay for studies of the interactions and binding of these compounds to cells in culture.     

A polyphenylene dendrimer-detergent complex as a highly fluorescent probe for bioassays

The synthesis of a polyphenylene dendrimer carrying three perylenemonoimide dyes as well as one biotin group is presented. Due to the hydrophobic polyphenylene scaffold, this dendrimer is insoluble in water thus preventing investigations in aqueous media. However, the use of an appropriate detergent results in the formation of well-defined supramolecular dendrimer-detergent complexes being soluble in aqueous media. The dendrimer-detergent complexes have a constant hydrodynamic radius of 7.1 nm measured by light scattering and fluorescence correlation spectroscopy and exhibit a high stability in the presence of blood serum proteins. The specific binding of the dendrimer-detergent complexes carrying a single biotin group to the protein streptavidin is demonstrated using a magnetic bead assay.     

Triton X-100 enhances ion-pair-driven molecular recognition in aqueous media. Further work on a chemosensor for inositol trisphosphate

Molecular recognition in water based on ion-pairing is hampered by competition from the solvent. We have reported that synthetic receptor 1 recognizes inositol trisphosphate (IP3) with a binding constant of 10(8) M(-1) in methanol. In this paper, instead of working in methanol, we report that the surfactant Triton-X 100 also yields a large absorbance or fluorescence change and a binding constant on the order of 10(6) M(-1).     

Steric crowding effects on target detection in an affinity biosensor

This work quantifies the impact of steric crowding on whole antibody (Ab) receptor immobilization and target Ab detection and also demonstrates how the versatile biotin/streptavidin receptor immobilization system must be tuned to optimize target detection in designing biosensors. Results are demonstrated on a label-free optical biosensor fabricated from n-type macroporous porous silicon (PSi) with approximately 88-107 nm diameter pores. We employ a sandwich assay scheme comprising a linking chemistry (biotin/streptavidin) to attach biotinylated anti-rabbit IgG (receptor) to detect rabbit IgG (target). A "bottom-up" approach was taken to investigate each layer of the sandwich assay to optimize target binding. Steric crowding was observed to hinder subsequent layer binding for each layer in the sandwich (biotin, streptavidin, and receptor). Our results give definitive evidence that the onset of steric crowding within the biotin layer occurs at a surface coverage of 57%, which is much higher compared to that from published work on well-ordered self-assembled biotin monolayers on planar gold surfaces. This difference is attributed to the topographical heterogeneity of the PSi substrate. Streptavidin (SA) binding to surface-linked biotin was altered by preblocking the streptavidin binding sites with biotin. Through consistent trends in data, preblocking SA was shown to reduce steric crowding within the SA layer, which translated into increased receptor immobilization. The final detection range of rabbit IgG was 0.07-3 mg mL(-1) (0.4-17 ng mm(-2)), and binding specificity was demonstrated by employing an anti-chicken IgG control receptor. This study underlines the importance of considering binding avidity and surface topography in optimizing chip-based biosensors.     

Determination of the binding specificity of the 12S subunit of the transcarboxylase by saturation transfer difference NMR

In this study we present the characterization of the interaction of biotin and methylmalonyl-CoA (MMCoA) with the carboxyltransferase subunit (12S) from the transcarboxylase (TC) from Propionibacterium shermanii. This biotin dependent multienzyme complex catalyses the transfer of carbon dioxide from methylmalonyl-CoA (MMCoA) to pyruvate. The Saturation Transfer Difference NMR (STD) technique was performed to determine the binding epitope from biotin and MMCoA to the 12S subunit. We could show by titrations during STD experiments that biotin and MMCoA bind cooperatively in one binding pocket.     

Interaction of biotin with Mg-O bonds: bifunctional binding and recognition of biotin and related ligands by the Mg(15-crown-5)2+ unit

The interaction between biotin and the macrocyclic magnesium complex Mg(15-crown-5)(Otf)2 (15-crown-5 is 1,4,7,10,13-pentaoxacyclopentadecane, Otf(-) is trifluoromethanesulfonate anion) in solution was studied as a model for metal-biotin interactions that may be important in its speciation and function. Shifts in the solution IR spectrum establish that the interaction is dominated by ligation between the carbonyl oxygen of the ureido ring of biotin and the Mg2+ cation. However, comparative binding studies using NMR spectroscopy and conductivity reveal a substantial enthalpic contribution to binding that arises from interactions between the ureido -NH moiety and the macrocyclic ring. This is interpreted in terms of a weak-to-moderate hydrogen bond formed between the -NH group and an oxygen from the crown, which is simultaneously coordinated to Mg2+. This hypothesis is reinforced by quantitative examination of the binding of N-methylated derivatives of 2-imidazolidone, which shows that N,N'-dimethylation decreases the affinity of Mg(15-crown-5)(Otf)2 for the ligand by 2 orders of magnitude. This can be understood in terms of the structure of Mg(15-crown-5)(Otf)2. It shows a pentagonal bipyramidal coordination geometry where the five equatorial positions are occupied by the macrocyclic oxygen donors. The axial positions are occupied by weakly coordinating Otf(-) anions, which are readily displaced by biotin and related derivatives. The M-O(crown) bond distance ranges from 2.1 to 2.3 A, providing structural complementarity for the 2.2 A C=O...HN- bite distance in the ureido group, which leads to strong interaction. The contribution from hydrogen bonding illustrates the importance of second-shell interactions in the biocoordination chemistry of Mg2+. These can serve to organize cofactor interactions with biomolecules, as was recently demonstrated for a biotin-selective RNA aptamer that depends on a direct biotin-magnesium interaction for recognition of biotin (Nix, J.; Sussman, D.; Wilson, C. J. Mol. Biol. 2000, 296, 1235-1244). These results are significant in the context of the observed magnesium requirement in biotin-dependent carboxylase enzymes, where noncovalent interactions with biotin may be important in its activation toward carboxylation in the first step of biotin-dependent CO2 transfer. The synthetic system presented here also suggests that the Mg-O bond may be considered a constituent design element in the rational preparation of complexes to bind and recognize biotin.     

Electrostatic polarization is critical for the strong binding in streptavidin‐biotin system

The origin of strong affinity of biotin and its analogs binding to (strept)avidin is still the subject of an ongoing controversy. In this work, thermodynamic integration is carried out to study of the difference of binding free energies between biotin and iminobiotin to streptavidin. Three atomic charge schemes are implemented and compared. One is the traditional AMBER charge, and the other two, termed the polarized protein‐specific charge, are based on a linear scaling quantum mechanical method and a continuous solvation model and have polarization effect partially or fully included. The result indicates that when nonpolarized AMBER force field is applied, the result is much underestimated. When electronic polarization is gradually included, the difference of binding affinity increases along with it. Using the linear‐response approximation to eliminate the error in self‐charging process, the corrected binding affinity agrees well with the experimental observation. This study is direct evidence indicating that polarization effect is critical for the strong binding in streptavidin‐biotin system. © 2012 Wiley Periodicals, Inc.     

300 Mhz 1H NMR spectra and conformations of biotin and related hexahydrothienoimidazolone derivatives

¹H NMR spectra of biotin and four related hexahydrothienoimidazolones in which the endo pentanoate side chain of biotin is replaced by another endo or exo substituent, and the urea nitrogen atoms are substituted with benzyl groups, have been obtained at 300 MHz. Vicinal coupling constants differentiate cis and trans proton pairs. The generalized Karplus equation was utilized to calculate dihedral angles from vicinal proton-proton coupling constants. The conformation of biotin in solution, calculated from coupling constants, is in good agreement with solid state X-ray crystallographic data.