Spatial confinement of avidin domains in microwell arrays

Microwell arrays were chemically etched across the distal faces of coherent fiber-optic bundles. A typical 1.6 mm diameter array comprised approximately 3000 individual microwells that were approximately 1-14 microm deep and approximately 22 microm wide. A methodology involving organosilane functionalized microwell surfaces and site-selective photobiotin chemistry was developed to partially fill microwells with a thin avidin layer. Avidin microwell arrays were characterized using charge coupled device optical microscopy and scanning electron microscopy. The avidin microwell arrays had individual well volumes that were six orders of magnitude smaller and up to 30-fold more numerous than commercially available avidin-coated microtiter plates. Preliminary results indicated that individual avidin microwells were ideally suited to house single biological cells. Using standard epifluorescence microscope optics and a mercury-arc lamp, an individual 22 microm wide microwell could be optically addressed and selectively filled with avidin without the use of a photolithographic mask. The ability to control both the size and position of avidin domains on the microwell array surface demonstrates the utility of this methodology towards fabricating a single microwell array with multianalyte sensing capabilities.     

Synthetic metal-binding protein surface domains for metal ion-dependent interaction chromatography. II. Immobilization of synthetic metal-binding peptides from metal ion transport proteins as model bioactive protein surface domains.

This preliminary investigation tests the premise that biologically relevant (1) peptide-metal ion interactions, and (2) metal ion-dependent macromolecular recognition events (e.g., peptide-peptide interactions) may be modeled by biomimetic affinity chromatography. Divinylsulfone-activated agarose (6%) was used to immobilize three different synthetic peptides representing metal-binding protein surface domains from the human plasma metal transport protein histidine-rich glycoprotein (HRG). The synthetic peptides represented 1-3 multiple repeat units of the 5-residue sequence (Gly-His-His-Pro-His) found in the C-terminal of HRG. By frontal analyses, immobilized HRG peptides of the type (GHHPH)nG, where n = 1-3, were each found to have a similar binding capacity for both Cu(II) ions and Zn(II) ions (31-38 mumol/ml gel). The metal ion-dependent interaction of a variety of model peptides with each of the immobilized HRG peptide affinity columns demonstrated differences in selectivity despite the similar internal sequence homology and metal ion binding capacity. The immobilized 11-residue HRG peptide was loaded with Cu(II) ions and used to demonstrate selective adsorption and isolation of proteins from human plasma. These results suggest that immobilized metal-binding peptides selected from known solvent-exposed protein surface metal-binding domains may be useful model systems to evaluate the specificity of biologically relevant metal ion-dependent interaction and transfer events in vitro.     

Mapping of possible prion protein self-interaction domains using peptide arrays

Background  

The common event in transmissible spongiform encephalopathies (TSEs) or prion diseases is the conversion of host-encoded protease sensitive cellular prion protein (PrP^C) into strain dependent isoforms of scrapie associated protease resistant isoform (PrP^Sc) of prion protein (PrP). These processes are determined by similarities as well as strain dependent variations in the PrP structure. Selective self-interaction between PrP molecules is the most probable basis for initiation of these processes, potentially influenced by chaperone molecules, however the mechanisms behind these processes are far from understood. We previously determined that polymorphisms do not affect initial PrP^C to PrP^Sc binding but rather modulate a subsequent step in the conversion process. Determining possible sites of self-interaction could elucidate which amino acid(s) or amino acid sequences contribute to binding and further conversion into other isoforms. To this end, ovine – and bovine PrP peptide-arrays consisting of 15-mer overlapping peptides were probed with recombinant sheep PrP^C fused to maltose binding protein (MBP-PrP).     

Catalytic asymmetric synthesis of acyclic arrays by tandem 1,4-addition-aldol reactions

Herein, we report efficient acyclic stereocontrol in tandem 1,4-addition-aldol reactions triggered by catalytic asymmetric organometallic addition. Grignard reagents add to alpha,beta-unsaturated thioesters in a 1,4-fashion and the resulting magnesium enolates are trapped with aromatic or aliphatic aldehydes. The process provides a range of tandem products bearing three contiguous stereocenters with excellent control of relative and absolute stereochemistry. The various diastereomeric products have been fully characterized using single-crystal X-ray analysis and the origins of stereocontrol in this tandem protocol are discussed. The versatility and efficiency of this methodology are demonstrated in the first catalytic asymmetric synthesis of (-)-phaseolinic acid with 54% overall yield via a short and concise route.     

Diffusion in heterogeneous media containing impermeable domains arranged in parallel arrays of variable orientation

Effective diffusivity through heterogeneous media containing impermeable and geometrically anisotropic domains depends on the domain orientation relative to the diffusion direction. A particular class of heterogeneous membranes in which domain orientation can be controlled in situ, side-chain liquid-crystalline polymers (SCLCPs), are being investigated as responsive, or variable permeability membranes for use in a variety of applications including controlled release drug delivery. This paper describes a geometric model for predicting the effective diffusivity through this type of membranes as a function of domain orientation, volume fraction, and aspect ratio. Estimates of effective diffusivity were also generated using random walk simulations. Results from the two methods agree well with each other. Predicted effective diffusivities in systems with domains aligned either orthogonal or parallel to the diffusion direction are compared to results from available literature models. Model predictions are compared to experimentally obtained transport properties through SCLCPs in which liquid-crystalline domain orientation is modulated by externally applied electric field.     

The role of tandem acyl carrier protein domains in polyunsaturated fatty acid biosynthesis

Acyl carrier protein (ACP) plays an essential role in fatty acid and polyketide biosynthesis, and most of the fatty acid synthases (FASs) and polyketide synthases (PKSs) known to date are characterized with a single ACP for each cycle of chain elongation. Polyunsaturated fatty acid (PUFA) biosynthesis is catalyzed by the PUFA synthase, and all PUFA synthases known to date contain tandem ACPs (ranging from 5 to 9). Using the Pfa PUFA synthase from Shewanella japonica as a model system, we report here that these tandem ACPs are functionally equivalent regardless of their physical location within the PUFA synthase subunit, but the total number of ACPs controls the overall PUFA titer. These findings set the stage to interrogate other domains and subunits of PUFA synthase for their roles in controlling the final PUFA products and could potentially be exploited to improve PUFA production.     

Site selection spectroscopy luminescence of solutions with laser excitation

The narrow line emission observed by Personov et al. at low temperature in a glassy matrix from perylene has been shown to be observable from many other molecules. Spectra of 1-chloronaphthalene and tetracene are presented. Narrow line phosphorescence was not observed. Narrow line fluorescence was also absent when the excitation energy was 1500 cm^?1 greater than the 0–0 fluorescence level and in these two cases it is suggested that heating of the matrix by radiationless processes causes the spectral broadening.     

Trends in metal-binding and metalloprotein analysis

This review describes recent tendencies for metal-binding and metalloprotein analysis, emphasizing metal quantification in proteins through X-ray, atomic absorption, mass spectrometric techniques, and others. Hyphenated techniques such as capillary electrophoresis-synchrotron radiation X-ray fluorescence (CE-SRXRF), laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS), matrix-assisted laser desorption/ionisation-time-of-flight mass spectrometry (MALDI-TOF-MS), etc. are also presented. As protein separation techniques electrophoresis (mainly sodium dodecyl sulphate-polyacrylamide gel electrophoresis, SDS-PAGE), capillary electrophoresis (CE) and high-performance liquid chromatography (HPLC) are indicated, due to their inherent sensitivity, resolution and/or easy implementation. Latest challenges in metallomics are also commented.     

Formation of a [1 + 1] metallomacrocycle from a heterotritopic ligand containing two terpy and one bipy metal-binding domains

Reaction of the heterotritopic ligand L, which contains one bipy and two terpy metal-binding domains linked by a flexible spacer with iron(II) chloride results in the formation of a [1 + 1] metallomacrocycle.     

Site selection spectroscopy of SiO2:Eu3+ gels

Silica gels doped with Eu³⁺ ions were studied at temperatures between 10 K and 300 K by site selection spectroscopy in samples heated up to 200°C. The ⁵D₀ ⁷F₀ transition shows internal structures due to the different environments of the europium ions. Lifetimes, energy levels and homogeneous linewidths are site dependent. In the wet gel the Eu³⁺ ions prefer a liquid-like environment and only when the liquid is removed by heat treatment, the ion is linked more strongly to the silica network.     

Supramolecular tandem enzyme assays for multiparameter sensor arrays and enantiomeric excess determination of amino acids

The coupling of an enzymatic transformation with dynamic host-guest exchange allows the unselective binding of macrocycles to be used for highly selective analyte sensing. The resulting supramolecular tandem enzyme assays require the enzymatic substrate and its corresponding product to differ significantly in their affinity for macrocycles, for example, cation receptors, and to show a differential propensity to displace a fluorescent dye from its host-guest complex. The enzymatic transformation results in a concomitant dye displacement that can be accurately followed by optical spectroscopy, specifically fluorescence. By exploiting this label-free continuous enzyme assay principle with the fluorescent dye Dapoxyl and the macrocyclic host cucurbit[7]uril, a multiparameter sensor array has been designed, which is capable of detecting the presence of amino acids (e.g. histidine, arginine, lysine, and tyrosine) and their decarboxylases. Only in the presence of both, the particular amino acid and the corresponding decarboxylase, is the amine or diamine product formed. These products are more highly positively charged than the substrate, have a higher affinity for the macrocycle and, therefore, displace the dye from the complex. The extension of the high selectivity and muM sensitivity of the tandem assay principle has also allowed for the accurate measurement of D-lysine enantiomeric excesses of up to 99.98 %, as only the L-enantiomer is accepted by the enzyme as a substrate and is converted to the product that is responsible for the observed fluorescence signal.     

Crystallization-induced secondary selection from a tandem driven dynamic combinatorial resolution process

Crystallization-induced secondary selection from a tandem driven dynamic combinatorial library is presented. In a one-pot experiment, an initial nitroaldol equilibrium was kinetically driven by a tandem reaction resulting in a subsequent dynamic library of diastereoisomers. This library was then further driven by a phase change, resulting in amplification and isolation of a highly diastereomerically enriched and synthetically interesting isoindolinone.     

Site of alkylation of N-methyl- and N-ethylaniline in the gas phase: a tandem mass spectrometric study

N-Methylaniline (NMA) was ethylated and N-ethylaniline (NEA) was methylated under chemical ionization conditions using C₂H₅I and CH₃I, respectively, as reagent gases. The structures of the resulting m/z 136 adduct ions have been probed using metastable ion and collision-induced dissociation (CID) methods. From the similarity of the spectra obtained and from the presence of structure-diagnostic ions at m/z 59 (CH₃NHC₂H₅^+•) and m/z 44 (CH₃NHCH₂⁺), it is concluded that predominantly N-alkylation occurs in both systems. This interpretation was aided by the use of C₂D₅I and CD₃I as reagents. Adduct ions of m/z 136 were also formed by ethylation of the isomeric toluidines and by methylation of the ring-ethylanilines. The resulting CID mass spectra were distinctly different from those obtained for the m/z 136 ions obtained by alkylation of NMA and NEA. Protonation of N-ethyl-N-methylaniline using CH₃C(O)CH₃ as Brønsted acid reagent produced an m/z 136 species whose CID mass spectrum also featured intense ion signals at m/z 59 and 44. This observation led to the conclusion that protonation with acetone as reagent results, in this case, in dominant N-protonation. However, the CID mass spectrum of the m/z 136 ion formed when CH₃OH was the protonating agent featured a weak signal at m/z 44 and no signal at m/z 59. Hence it was concluded that the latter m/z 136 ion contains a larger contribution from the ring-protonated adduct. Copyright © 2004 John Wiley & Sons, Ltd.     

Patterning pallet arrays for cell selection based on high-resolution measurements of fluorescent biosensors

Pallet arrays enable cells to be separated while they remain adherent to a surface and provide a much greater range of cell selection criteria relative to that of current technologies. However there remains a need to further broaden cell selection criteria to include dynamic intracellular signaling events. To demonstrate the feasibility of measuring cellular protein behavior on the arrays using high resolution microscopy, the surfaces of individual pallets were modified to minimize the impact of scattered light at the pallet edges. The surfaces of the three-dimensional pallets on an array were patterned with a coating such as fibronectin using a customized stamping tool. Micropatterns of varying shape and size were printed in designated regions on the pallets in single or multiple steps to demonstrate the reliability and precision of patterning molecules on the pallet surface. Use of a fibronectin matrix stamped at the center of each pallet permitted the localization of H1299 and mouse embryonic fibroblast (MEF) cells to the pallet centers and away from the edges. Compared to pallet arrays with fibronectin coating the entire top surface, arrays with a central fibronectin pattern increased the percentage of cells localized to the pallet center by 3-4-fold. Localization of cells to the pallet center also enabled the physical separation of cells from optical artifacts created by the rough pallet side walls. To demonstrate the measurement of dynamic intracellular signaling on the arrays, fluorescence measurements of high spatial resolution were performed using a RhoA GTPase biosensor. This biosensor utilized fluorescence resonance energy transfer (FRET) between cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) to measure localized RhoA activity in cellular ruffles at the cell periphery. These results demonstrated the ability to perform spatially resolved measurements of fluorescence-based sensors on the pallet arrays. Thus, the patterned pallet arrays should enable novel cell separations in which cell selection is based on complex cellular signaling properties.     

Site selection spectroscopy of polyatomic molecules: principles, applications and possibilities

Brief review of a new branch in the spectroscopy of complex organic molecules in solutions - Site Selection Spectroscopy - is given. Principles and methods to reveal a line structure in the inhomogeneously broadened absorption and luminescence spectra by means of selective laser excitation are described. Some examples are shown to demonstrate new possibilities of selective methods for precise investigations of: energy levels of organic molecules; electron-phonon interactions; the Zeeman and Stark effects, spectrochemical analysis of complex organic materials, etc.     

Synthesis and metal-binding properties of chelating fluorescein derivatives

[reaction: see text] Two routes to highly functionalized metal-chelating fluorescein derivatives have been pursued. Compound 3 is partially quenched by a variety of first-row transition metal ions in aqueous solution, with EC(50) values ranging from 0.4 to 60 microM. Compounds of this type may find application in biological sensing.     

Mapping noncovalent ligand binding to stemloop domains of the HIV-1 packaging signal by tandem mass spectrometry

The binding modes and structural determinants of the noncovalent complexes formed by aminoglycoside antibiotics with conserved domains of the HIV-1 packaging signal (Psi-RNA) were investigated using electrospray ionization (ESI) Fourier transform mass spectrometry (FTMS). The location of the aminoglycoside binding sites on the different stemloop structures was revealed by characteristic coverage gaps in the ion series obtained by sustained off-resonance irradiation collision induced dissociation (SORI-CID) of the antibiotic-RNA assemblies. The site positions were confirmed using mutants that eliminated salient structural features of the Psi-RNA domains. The effects of the mutations on the binding properties of the different substrates served to validate the position of the aminoglycoside site on the wild-type structures. Additional information was provided by docking experiments performed on the different aminoglycoside-stemloop complexes. The results have shown that, in the absence of features disrupting the regular A-helix of the double-stranded stem, aminoglycosides tend to bind in an area situated between the upper stem and the loop regions, as demonstrated for stemloop SL3. The presence of a tandem wobbles motif in SL4 modifies the regular geometry of the upper stem, which does not affect the general site location, but greatly increases its solution binding affinity compared with SL3. The platform motif in SL2 locates the binding site in the stem midsection and confers upon this stemloop an intermediate affinity toward aminoglycosides. In SL3 and SL4, the extensive overlap of the antibiotic site with the region used to bind the nucleocapsid (NC) protein provides the basis for a competition mechanism that could explain the aminoglycoside inhibition of the NC.SL3 and NC.SL4 assemblies. In contrast, the minimal overlap between the aminoglycoside and the NC sites in SL2 accounts for the absence of inhibition of the NC.SL2 complex.     

Synthesis and metal-binding studies of a novel pyrene discotic

The synthesis of a novel bis-crown quinoxalino[2′,3′:9,10]phenanthro[4,5-abc]phenazine discotic and its binding properties to a series of alkali and alkaline-earth metals is reported. A schematic representation of the binding equilibrium of the sensor to the metal is proposed. The binding constant of the sensor to barium(II) was estimated to be 1.4 × 10⁴ M⁻¹ based on ¹H NMR studies.