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.     

Development of the continuously variable volume reactor for flow injection analysis: Part 1. Design, capabilities and testing

A new apparatus for mixing sample and reagent in flow injection analysis (FIA) is described. The continuously variable volume reactor (CVVR) replaces the conventional mixing coil in a flow injection (FI) manifold to provide mixing and dilution. A linear actuator motor allows control of the chamber volume via LabVIEW software. The chamber volume can be incremented in steps of 1 μl over the range 68-1704 μl. In addition, the chamber has an integral variable-speed stirring unit that is also under computer control. Experiments were performed to evaluate the dispersion characteristics of this new device, evaluate the volume reproducibility, and understand the mixing characteristics. Use of the chamber is shown in the determination of iron(II) in pond water, and in NIST SRM 1643d with excellent results and a detection limit of 3.7 μg/l iron(II). Advantages of the CVVR and future research activities using the device are discussed.     

Receptor-bound conformation of an alpha(5)beta(1) integrin antagonist by (15)N-edited 2D transferred nuclear overhauser effects

We report the results of (15)N-edited 2D transferred NOE experiments of the partially (15)N-labeled alpha(5)beta(1) antagonist c[Mpa(15)N-Arg-(15)N-Gly-(15)N-Asp-(15)N-Asp-(15)N-Val-Cys]-NH(2) (Mpa denotes mercaptopropionic acid) in the presence of the native alpha(5)beta(1) receptor. The alpha(5)beta(1) integrin receptor is believed to be involved in tumor metastasis and the rational design of alpha(5)beta(1) integrin antagonist is therefore of considerable interest. Our experiments provide insight into the alpha(5)beta(1) receptor-bound conformation of the antagonist c[MpaRGDDVC]-NH2 and will be important for the design of novel antagonists.     

Versatile solid-phase synthesis of secondary amines from alcohols. Development of an N-Boc-(o-nitrobenzene)sulfonamide linker

The development of a versatile amine releasing linker based on the modified o-nitrobenzene sulfonamide protective group is described. This new N-Boc-o-nitrobenzenesulfonamide (Boc-ONBS) linker enables the elaboration on resin of primary and secondary amines by sequential substitution of the sulfonamide moiety using the Mitsunobu reaction. A 16-member array of secondary and Boc protected primary amines was then prepared using this linker.     

X-ray photoelectron spectroscopy and magnetic studies on the effect of pore size, wall thickness, and wall composition on superparamagnetic cobaltocene mesoporous Nb, Ta, and Ti composites

Recent results in our group demonstrated that mixed oxidation state mesoporous niobium oxide cobaltocene composites display superparamagnetism at certain composition ratios. This was the first report of superparamagnetism in nanoscale molecular ensembles. A series of mesoporous niobium oxide materials were synthesized in order to understand the role of pore size and thickness of the walls in the mesostructure on the magnetic properties. Mesoporous Ti oxide and Ta oxide composites were also synthesized in order to investigate the effect of changing the wall composition on the magnetic properties of this new series of materials. All samples were characterized by X-ray diffraction, nitrogen adsorption, ultraviolet spectroscopy, X-ray photoelectron spectroscopy, scanning electron microscopy, and superconducting quantum interference device magnetometry. The results of this study showed that variation of wall thickness or pore size in the Nb system had little effect on the properties and that superparamagnetism most likely arises from mixed oxidation state cobaltocene grains residing in the individual pores and not from the free electrons in the mesostructure or much larger domains. The Langevin function was applied to the isothermal magnetic data from the Nb composites and gave mean superparamagnetic particle sizes of ca. 14 nm in each system. The Co(II) to Co(III) ratios in these materials were approximately 1:1. The Ti and Ta materials showed no sign of superparamagnetism and only very low levels of neutral cobaltocene in the pores. This suggests that a critical amount of cobaltocene is required to bring about superparamagnetic behavior.     

Some diels—alder reactions of η1-bonded cyclopentadienylmetal compounds

Bis(cyclopentadienyl)mercury readily undergoes Diels—Alder reactions with RCCR (R = CO₂Me or CF₃), CF₃CFCFCF₃, CF₃CFCF₂, (CF₃)₂CC(CN)₂, C₂(CN)₄ and Ph$\text{NCONNC}$O to give stable adducts characterised by¹H, ¹⁹F and ¹³C NMR, spectroscopy. Similar reactions of CF₃CCCF₃ and CF₃CFCFCF₃ with the cyclopentadiene derivatives Me₃MC₅H₅ and (Me₃M)₂C₅H₄ (M = Si, Sn) are also described.     

New approach to molecular docking and its application to virtual screening of chemical databases

This paper describes the validation of a molecular docking method and its application to virtual database screening. The code flexibly docks ligand molecules into rigid receptor structures using a tabu search methodology driven by an empirically derived function for estimating the binding affinity of a protein-ligand complex. The docking method has been tested on 70 ligand-receptor complexes for which the experimental binding affinity and binding geometry are known. The lowest energy geometry produced by the docking protocol is within 2.0 A root mean square of the experimental binding mode for 79% of the complexes. The method has been applied to the problem of virtual database screening to identify known ligands for thrombin, factor Xa, and the estrogen receptor. A database of 10,000 randomly chosen "druglike" molecules has been docked into the three receptor structures. In each case known receptor ligands were included in the study. The results showed good separation between the predicted binding affinities of the known ligand set and the database subset.     

Ion atmosphere relaxation and percolative electron transfer in Co bipyridine DNA molten salts

Polypyridyl complexes of Co decorated with 350-Da polyether chains (Co(350)(2+)) form molten phases of nucleic acids when paired with DNA counterions (Co(350)DNA) or 25-mer oligonucleotides. Analysis of voltammetry and chronoamperometry of mixtures of these phases with complexes having ClO(4)(-) counterions (Co(350)(ClO(4))(2)) and no other diluent provides charge transport rates from the oxidation and reduction currents for the complexes. As the mole fraction of the Co(350)(ClO(4))(2) complex in the mixture is varied from ca. 0.25 to 1, the physical diffusion constants derived from the Co(III/II) wave increase from 1 x 10(-11) cm(2)/s to 5 x 10(-10) cm(2)/s, and apparent diffusion constants dominated by the Co(II/I) electron self-exchange increase from 1 x 10(-10) cm(2)/s to 2 x 10(-8) cm(2)/s. Pure Co(350)DNA melts, containing no Co(350)(ClO(4))(2) complex, do not exhibit recognizable voltammetric waves; DNA suppresses the Co(II/I) electron transfer reactions of Co complexes for which it is the counterion. There are therefore two microscopically distinct kinds of Co(350) complexes, those with DNA and those with ClO(4)(-) counterions, with respect to their Co(II/I) electron-transfer dynamics, leading to percolative behavior in their mixtures. The electron-transfer rates of the Co(II/I) couple are controlled by the diffusive relaxation of the ionic atmosphere around the reaction pair, and the inactivity of the bound Co complexes can be attributed to the very low mobility of the anionic phosphate groups in the DNA counterion. Substitution of sulfonated polystyrene for DNA produced similar results, suggesting that this phenomenon is general to other polymer counterions of low mobility. We conclude that the measured Co(II/I) charge transport and electron-transfer rate constants reflect more the diffusive mobility of the perchlorate counterion than the intrinsic Co(II/I) electron hopping rate.     

Imaging the quantum-state specific differential cross sections of HCl formed from reactions of chlorine atoms with methanol and dimethyl ether

Center-of-mass frame scattering angle distributions obtained directly from crossed molecular beam velocity map images are reported for HCl formed in different rotational levels of its vibrational ground state by reaction of Cl atoms with CH3OH and CH3OCH3. Products are observed to scatter over all angles, with peaks in the distribution in the forward and backward directions (theta = 0 and 180 degrees with respect to the relative velocity vectors of the Cl atoms). Products of both reactions exhibit differential cross sections that vary with the rotational quantum number of the HCl, with a greater propensity for forward scatter for J = 2, shifting to more pronounced backward scatter for J = 5. This trend is, however, more evident for reaction of dimethyl ether than for methanol. The mean fractions of the available energy channeled into product kinetic energy vary with scattering angle, but the angle-averaged fractions are, respectively, 0.37 and 0.42 for the methanol and dimethyl ether reactions. On average, 46% or more of the available energy of the reactions becomes internal energy of the radical co-product. Results are interpreted with the aid of computed energies of transition states and molecular complexes along the reaction pathways, and comparisons are drawn with recent measurements of the scattering distributions and energy release for reactions of Cl atoms with small alkanes.     

The magnetic moment of103Ru

The nuclear magnetic moment of¹⁰³Ru has been determined using the technique of low-temperature nuclear orientation on¹⁰³Ru as a dilute impurity in Fe. The Fe lattice was cooled to 1.7 mK using a PrNi₅ enhanced nuclear demagnetisation stage precooled with a³He–⁴He dilution refrigerator. The¹⁰³RuFe system was observed to have a long nuclear spin-lattice relaxation time, but analysis of the relaxation indicates that the¹⁰³Ru nuclei are close to thermal equilibrium with the Fe lattice at times>200 min after demagnetising. From the near thermal equilibrium anisotropy of the 497 keV -ray in¹⁰³Rh we have deduced the nuclear magnetic moment as |(¹⁰³Ru)|=0.18(2)_N. This value is almost independent of the choice of spinI=3/2 or 5/2 for the nucleus, but is only consistent with systematics ifI(¹⁰³Ru)=3/2 and <0. UsingI=3/2 we obtain the E2/M1 mixing ratio of the 497 keV -ray as =–0.42(4). The sign of the anisotropy of the 610 keV -ray from the 650 keV level in¹⁰³Rh is only consistent with an allowed -decay to the state ifI(650 keV,¹⁰³Rh)=5/2. The E2/M1 mixing ratio of the 610 keV -ray is then =+0.15(3) or +60( _–40 ⁺ ), <–80. From the initial rise in -ray anisotropy following demagnetisation we determine the Korringa constant for¹⁰³RuFe to beC=5.7(5) K·s.