Polyamine-based anion receptors: Extraction and structural studies

In the discussion that follows some of the more recent progress in the area of anion binding by synthetic polyamine receptors is presented, with emphasis given to work undertaken by the authors’ groups. A continuing theme in these studies has been the relationship between receptor structure and its anion extraction properties.Systematic solvent extraction and structural studies for halide and perrhenate complexes with polyamines of tripodal, macrocyclic and macrobicyclic architecture that contain both aromatic moieties and four to eight amine functions have been performed in order to derive relevant structure-binding/extractability relationships. The results demonstrate that the binding and extraction behaviour of the polyamines towards halides and perrhenate is a complex function of their structural features, degree of protonation and lipophilic properties. The extraction is characterized by the preferred formation of mono- and diprotonated amine species in the organic phase. X-ray structure studies of iodide and perrhenate complexes with open-chain tetraamino derivatives and octaamino cryptands in different protonation states lead to the conclusion that in the first case only limited chelation of the anion occurs and in the second only highly protonated species are able to encapsulate the anion. The structural patterns observed are strongly influenced by the presence of water molecules in the crystals.     

Epitope affinity chromatography and biophysical studies of monoclonal antibodies and recombinant antibody fragments

Peptide epitope affinity chromatography is a powerful technique for the purification of antibodies. This study aims to demonstrate the versatility of the technique and to show how biophysical techniques such as circular dichroism (CD) and fluorescence quenching (FQ) can aid the rational design of affinity ligands and characterization of antibody-based reagents. The performance of a number of peptide ligands for the purification of a range of different antibodies and recombinant fragments is investigated by automated fast-protein liquid chromatography. Purified products are analyzed for purity by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. They are then radiolabelled and the immunoreactivity is determined. Ligands are analyzed for secondary structural characteristics by CD and for binding affinity by FQ. Finally, a study is performed to investigate the thermal stability of a recombinant antibody fragment by CD analysis. It is found that simple ligand modifications such as the introduction of a C-terminal cysteine residue can improve purification performance. The FQ studies show that the modified peptide has a higher affinity for antibody. The CD analysis shows that it has a tendency to dimerize because of the formation of disulfide bonds. The versatility of epitope affinity is demonstrated through the purification of a recombinant diabody (dbFv) and by the use of a separate peptide matrix for the purification of an unrelated antibody. All studies result in antibody preparations of high purity and immunoreactivity. The CD analysis of the dbFv shows that it is denatured at 37 degrees C and is therefore unsuitable as a targeting reagent for use in humans in its present form. It is concluded that epitope affinity chromatography coupled with biophysical analyses plays an important role in the production and characterization of antibody-based reagents for targeted diagnosis and therapy of human diseases.     

Atomistic Modeling of Silica Based Sol-Gel Processes

Density Functional Theory is used to study water, methanol, ethanol, TMOS, and TEOS molecules and the most important silica clusters participating in sol-gel processes. Calculated bond lengths, bond angles and electric dipole moments compare well with experimental data. The energy of these molecules is reported and used to discuss the energetics of the hydrolysis and condensation reactions. Molecular Dynamics is employed to simulate liquid water, methanol, ethanol, TMOS, TEOS and experimental sol-gel solutions. Calculated densities and enthalpies of vaporisation compare well with experimental data. Preliminary results are presented for MD simulations of sol-gel solutions.     

Sonoluminescence quenching of organic compounds in aqueous solution: frequency effects and implications for sonochemistry

Solute-induced quenching of sonoluminescence (SL) is reported for aqueous solutions of two homologous series of methyl esters and ketones using low (20 kHz) and high (515 kHz) ultrasound frequencies. SL data at 20 kHz from aqueous solutions containing alcohols and carboxylic acids are also presented to compare with previously published results at 515 kHz. In addition to supporting the previous findings on the existence of stable and transient bubbles at 515 and 20 kHz, respectively, the results suggest that the hydrogen-bonding characteristics of the solutes also play a major role in the extent of SL quenching. An increase in the SL intensity at low concentrations for most of the solutes suggests that these solutes increase the number of "active" bubbles by hindering the coalescence of bubbles. It is concluded that the effect of the solutes on the SL signal from aqueous solutions at both frequencies is primarily due to the balance of two factors, namely, the incorporation of solute within the bubble, leading to SL quenching, and the prevention of coalescence of the bubbles, leading to SL enhancement. At the higher frequency, SL quenching by the solutes is the main influence on the emission yield. However, at the lower frequency, hindrance to coalescence by the solutes dominates at lower concentrations and leads to SL enhancement. The implications of these results for optimizing conditions for aqueous sonochemical reactions are discussed.     

On the representation of electrostatic fields around ab initio charge distributions

Summary We compare two methods (Mulliken charges and a distributed multipole analysis, DMA) of representing an ab initio charge distribution for calculating the electrostatic field and potential outside the molecule, using pyrimidine and the RNA base uracil as examples. This is done using a 3-D graphical display of the electrostatic fields, which, when used with real-time rotation, zooming and clipping, has many advantages for qualitatively assessing the electrostatic interactions of a molecule. The errors involved in using Mulliken point charges may be of similar magnitude to the total electrostatic field in regions which are important in recognition processes. The DMA representation automatically includes the anisotropic electrostatic effects of non-spherical features in the charge distribution of each atom, and yet the displayed electrostatic fields around the atoms which have lone-pair density do not show marked anisotropy.     

HPLC of 9-fluorenylmethylchloroformate-polyamine derivatives with fluorescence detection

Summary There are a number of reagents available for fluorescent labelling of primary amines. These include dansyl chloride, o-phthalaldehyde, fluorescamine, and a new reagent, 9-fluorenylmethylchloroformate (FMOC), reported recently. This paper describes a reversed-phase HPLC procedure for the separation and fluorescence detection of polyamines following pre-column derivatization with FMOC. The polyamines studied by this method include putrescine, cadaverine, spermidine, and spermine. Experiments were carried out to determine maximum fluorescence excitation and emission wavelengths, optimum reaction pH, linear ranges, and minimum detection limits for each of the polyamines. The HPLC method includes a gradient program which provides complete separation from serum hydrolysate components and specificity for the four polyamines with detection limits ranging from 2 to 9 pg. This procedure was applied to hydrolyzed serum samples.     

Sampling unfolding intermediates in calmodulin by single-molecule spectroscopy

We used single-pair fluorescence resonance energy transfer (spFRET) measurements to characterize denatured and partially denatured states of the multidomain calcium signaling protein calmodulin (CaM) in both its apo and Ca(2+)-bound forms. The results demonstrate the existence of an unfolding intermediate. A CaM mutant (CaM-T34C-T110C) was doubly labeled with fluorescent probes AlexaFlour 488 and Texas Red at opposing globular domains. Single-molecule distributions of the distance between fluorophores were obtained by spFRET at varying levels of the denaturant urea. Multiple conformational states of CaM were observed, and the amplitude of each conformation was dependent on urea concentration, with the amplitude of an extended conformation increasing upon denaturation. The distributions at intermediate urea concentrations could not be adequately described as a combination of native and denatured conformations, showing that CaM does not denature via a two-state process and demonstrating that at least one intermediate is present. The intermediate conformations formed upon addition of urea were different for Ca(2+)-CaM and apoCaM. An increase in the amplitude of a compact conformation in CaM was observed for apoCaM but not for Ca(2+)-CAM upon the addition of urea. The changes in the single-molecule distributions of CaM upon denaturation can be described by either a range of intermediate structures or by the presence of a single unfolding intermediate that grows in amplitude upon denaturation. A model for stepwise unfolding of CaM is suggested in which the domains of CaM unfold sequentially.     

Quantitation of SR 27417 in human plasma using electrospray liquid chromatography-tandem mass spectrometry: A study of ion suppression

The effect of coeluting matrix compounds on the quantitation of SR 27417 in human plasma using electrospray liquid chromatography-tandem mass spectrometry has been examined. During the method development stage of this assay, plasma samples spiked with the analyte at 100 pg/mL were extracted using three different procedures: a hexane liquid-liquid extraction, an ethyl acetate back-extraction, and a solid phase extraction. Ion intensity of the analyte was found to be related inversely to the percent ionization of coeluting matrix components as evidenced by full scan spectra. The ethyl acetate back-extraction, which contained the fewest coeluting components, resulted in the highest ion intensity for the analyte. An assay comparison was done by using the liquid-liquid hexane and the ethyl acetate back-extractions for sample preparation. Replicate 1-mL samples (n=5) at 11 concentrations from 5 to 2000 pg/mL were extracted and analyzed. The results for the ethyl acetate back-extracted samples were acceptable from 2000 to 5 pg/mL with accuracy ranging from ?11.6 to 2.61% of the nominal concentrations. In contrast, the hexane liquid-liquid method had poor accuracy and precision below 20 pg/mL. The difference is explained by suppression of analyte ion intensity. These results are consistent with the current theory of electrospray ionization.     

Design and Construction of a Pulsed Field-Gradient NMR Probe for a High-Field Superconducting Magnet

We describe the design and construction of a high-resolution pulsed field-gradient NMR probe for use in a high-field superconducting magnet. Overview and details of the design and construction of the probe case, rf circuitry, temperature control and shielded gradient coils for a heteronuclear probe suitable for a spectrometer (Bruker MSL-300) equipped with a wide bore (i.e., 89 mm) magnet (Oxford) are given. The interior of the probe is designed so mat it may be easily moved to variable height so as to accept easily various gradient coils. A design for a novel jig for the winding of saddle-geometry rf coils is given.