Selectivity over coverage in de novo sequencing of IgGs

Although incredibly diverse in specificity, millions of unique Immunoglobulin G (IgG) molecules in the human antibody repertoire share most of their amino acid sequence. These constant parts of IgG do not yield any useful information in attempts to sequence antibodies de novo. Therefore, methods focusing solely on the variable regions and providing unambiguous sequence reads are strongly advantageous. We report a mass spectrometry-based method that uses electron capture dissociation (ECD) to provide straightforward-to-read sequence ladders for the variable parts of both the light and heavy chains, with a preference for the functionally important CDR3. We optimized this method on the therapeutic antibody Trastuzumab and demonstrate its applicability on two monoclonal quartets of the four IgG subclasses, IgG1, IgG2, IgG3 and IgG4. The method is based on proteolytically separating the variable F(ab′)₂ part from the conserved Fc part, whereafter the F(ab′)₂ portions are mass-analyzed and fragmented by ECD. Pure ECD, without additional collisional activation, leads to straightforward-to-read sequence tags covering the CDR3 of both the light and heavy chains. Using molecular modelling and structural analysis, we discuss and explain this selective fragmentation behavior and describe how structural features of the different IgG subclasses lead to distinct fragmentation patterns. Overall, we foresee that pure ECD on F(ab′)₂ or Fab molecules can become a valuable tool for the de novo sequencing of serum antibodies.     

Llama-derived single-domain antibodies for the detection of botulinum A neurotoxin

Single-domain antibodies (sdAb) specific for botulinum neurotoxin serotype A (BoNT A) were selected from an immune llama phage display library derived from a llama that was immunized with BoNT A toxoid. The constructed phage library was panned using two methods: panning on plates coated with BoNT A toxoid (BoNT A Td) and BoNT A complex toxoid (BoNT Ac Td) and panning on microspheres coupled to BoNT A Td and BoNT A toxin (BoNT A Tx). Both panning methods selected for binders that had identical sequences, suggesting that panning on toxoided material may be as effective as panning on bead-immobilized toxin for isolating specific binders. All of the isolated binders tested were observed to recognize bead-immobilized BoNT A Tx in direct binding assays, and showed very little cross-reactivity towards other BoNT serotypes and unrelated protein. Sandwich assays that incorporated selected sdAb as capture and tracer elements demonstrated that all of the sdAb were able to recognize soluble (“live”) BoNT A Tx and BoNT Ac Tx with virtually no cross-reactivity with other BoNT serotypes. The isolated sdAb did not exhibit the high degree of thermal stability often associated with these reagents; after the first heating cycle most of the binding activity was lost, but the portion of the protein that did refold and recover antigen-binding activity showed only minimal loss on subsequent heating and cooling cycles. The binding kinetics of selected binders, assessed by both an equilibrium fluid array assay as well as surface plasmon resonance (SPR) using toxoided material, gave dissociation constants (K _D ) in the range 2.2 × 10⁻¹¹ to 1.6 × 10⁻¹⁰ M. These high-affinity binders may prove beneficial to the development of recombinant reagents for the rapid detection of BoNT A, particularly in field screening and monitoring applications.     

Tight Molecular Recognition of Benzo[a]pyrene by a High‐Affinity Antibody

Benzo[a ]pyrene, which is produced during the incomplete combustion of organic material, is an abundant noxious pollutant because of its carcinogenic metabolic degradation products. The high‐affinity (K _D≈3 nm ) monoclonal antibody 22F12 allows facile bioanalytical quantification of benzo[a ]pyrene even in complex matrices. We report the functional and X‐ray crystallographic analysis of 22F12 in complex with 3‐hydroxybenzo[a ]pyrene after cloning of the V‐genes and production as a recombinant Fab fragment. The polycyclic aromatic hydrocarbon is bound in a deep pocket between the light and heavy chains, surrounded mainly by aromatic and aliphatic amino acid side chains. Interestingly, the hapten–antibody interface is less densely packed than expected and reveals polar, H‐bond‐like interactions with the polycyclic aromatic π‐electron system, which may allow the antibody to maintain a large, predominantly hydrophobic binding site in an aqueous environment while providing sufficient complementarity to its ligand.     

Production of a humanized Fab fragment of a neutralizing antibody against rabies virus

This paper describes the production of a functional humanized Fab fragment of a neutralizing antibody against the rabies virus. It is a prototype of a therapeutic agent that could be an alternative to equine anti-rabies immunoglobulins and anti-rabies serum immunoglobulins obtained from the blood of vaccinated human donors. Variable fragments of the high-affinity light and heavy chains neutralizing an antibody against the rabies virus were cloned and sequenced. Mouse constant regions were replaced by human constant regions followed by expression of the humanized Fab fragments in a yeast expression system. The immunochemical properties of the Fab fragments were evaluated using ELISA, polyacrylamide gel electrophoresis, and the Western blot assay. The binding capability of the produced humanized Fab fragments surpasses that of the parental antibody. A high degree of humanization was confirmed using sera against human immunoglobulins. The yield of the humanized Fab fragments was 21 mg per liter of culture medium. The purified Fab fragment preparation did not contain traces of the isolated light and heavy chains of the humanized Fab fragments.     

Modeling the interactions of a peptide-major histocompatibility class I ligand with its receptors. II. Cross-reaction between a monoclonal antibody and two αβ T cell receptors

The recombinant antibody, pSAN13.4.1, has a unique T cell like specificity; it binds an Influenza Hemagglutinin octapeptide (Ha_255–262) in an MHC (H-2K^k)-restricted manner, and a detailed comparison of the fine specificity of pSAN13.4.1 with the fine specificity of two Ha_255–262-specific, H-2K^k-restricted T cell hybridomas has supported this contention. A three-dimensional model of pSAN13.4.1 has been derived by homology modeling techniques. Subsequently, the structure of the pSAN13.4.1 antibody in complex with the antigenic Ha-K^k ligand was derived after a flexible and automated docking of the MHC-peptide pair into the Fab combining site. Interestingly, the most energetically favored binding mode shows numerous analogies to the recently determined recognition of class I MHC-peptide complexes by T cell receptors (TCRs). The pSAN13.4.1 also binds diagonally across the MHC binding groove but is more deeply anchored to the peptide-MHC (pep/MHC) ligand than TCRs, notably through numerous interactions of its heavy chain. The present model accounts well for the experimentally determined binding affinity of a set of 144 single amino acid substituted Ha analogues and the observed shared specificity between the pSAN antibody and two different T cell receptors for the Ha-K^k antigenic ligand. Analogies and differences between Fab and TCR recognition are explained by dissecting the binding role of each chain of the immune receptors as well as the contribution of all peptide amino acids.     

Chromatographic behaviour of monoclonal antibodies against wild-type amidase from Pseudomonas aeruginosa on immobilized metal chelates

The aim of this work was to devise a one‐step purification procedure for monoclonal antibodies (MAbs) of IgG class by immobilized metal affinity chromatography (IMAC). Therefore, several stationary phases were prepared containing immobilized metal chelates in order to study the chromatographic behaviour of MAbs against wild‐type amidase from Pseudomonas aeruginosa. Such MAbs adsorbed to Cu(II), Ni(II), Zn(II) and Co(II)–IDA agarose columns. The increase in ligand concentration and the use of longer spacer arms and higher pH values resulted in higher adsorption of MAbs into immobilized metal chelates. The dynamic binding capacity and the maximum binding capacity were 1.33 ± 0.015 and 3.214 ± 0.021 mg IgG/mL of sedimented commercial matrix, respectively. A K_D of 4.53 × 10⁻⁷ m was obtained from batch isotherm measurements. The combination of tailor‐made stationary phases of IMAC and the correct selection of adsorption conditions permitted a one‐step purification procedure to be devised for MAbs of IgG class. Culture supernatants containing MAbs were purified by IMAC on commercial‐Zn(II) and EPI‐30–IDA–Zn(II) Sepharose 6B columns and by affinity chromatography on Protein A‐Sepharose CL‐4B. This MAb preparation revealed on SDS–PAGE two protein bands with M_r of 50 and 22 kDa corresponding to the heavy and light chains, respectively. Copyright © 2011 John Wiley & Sons, Ltd.     

A Highly K+‐Selective Two‐Photon Fluorescent Probe

A highly K⁺‐selective two‐photon fluorescent probe for the in vitro monitoring of physiological K⁺ levels in the range of 1–100 mM is reported. The two‐photon excited fluorescence (TPEF) probe shows a fluorescence enhancement (FE) by a factor of about three in the presence of 160 mM K⁺, independently of one‐photon (OP, 430 nm) or two‐photon (TP, 860 nm) excitation and comparable K⁺‐induced FEs in the presence of competitive Na⁺ ions. The estimated dissociation constant (K_d) values in Na⁺‐free solutions (K_d^OP=(28±5) mM and K_d^TP=(36±6) mM ) and in combined K⁺/Na⁺ solutions (K_d^OP=(38±8) mM and K_d^TP=(46±25) mM ) reflecting the high K⁺/Na⁺ selectivity of the fluorescent probe. The TP absorption cross‐section (σ_2PA) of the TPEF probe+160 mM K⁺ is 26 GM at 860 nm. Therefore, the TPEF probe is a suitable tool for the in vitro determination of K⁺.     

Construction of Human Nonimmune Library and Selection of scFvs Against IL-33

Interleukin (IL) 33 plays very important roles in inflammatory and allergic diseases. To select human single-chain Fv fragments (scFvs) against IL-33, a nonimmune phage library system was constructed. The full-length cDNA library was synthesized for amplification of the variable heavy chain (V_H) and variable light chain (V_L). By overlapping extension PCR for splicing V_H and V_L, the full-length scFv library DNA were amplified and then transformed into Escherichia coli TG1. The scFv library was constructed successfully which contained 2.5?×?10⁸ independent clones with full-length scFv inserts. The results of fingerprint maps of the scFvs by BstN I and DNA sequencing from the library at random proved that the library was diverse. The human IL-33 was amplified, expressed, and purified. The purified IL-33 with bioactivity was biotinylated and used as antigen for selection of scFv library by phage display. After three rounds of affinity selection, about 30?% of clones have specific binding activity with IL-33. Five of those with good binding activity were transformed into E. coli strain HB2151 for soluble expression. The selected scFvs were further identified by western blot and sequencing. Those selected scFvs could be used for further research of their effect on inflammatory and allergic diseases such as asthma by blockade of IL-33.     

Fluorescence-labelled antigen-binding fragments (Fab) from monoclonal antibody 5F12 detect human erythropoietin in immunoaffinity capillary electrophoresis

A faster and more convenient method is required for the detection of recombinant erythropoietin (Epo) in human body fluids. In the present study we wanted to elucidate the principal suitability of immunoaffinity capillary electrophoresis (CE) in this respect. CE offers itself as a high-speed, high-throughput technique provided a suitable affinity reagent is available. We chose monoclonal antibody 5F12 from Amgen which binds to a conformation-independent epitope in the N-terminal region of the human Epo protein. For CE with laser-induced fluorescence detection it was necessary to produce fluorescently labelled antibody with one single antigen binding site. Monomeric antigen-binding fragments (Fab) were obtained by site-selective cleavage of the pure antibody and labelled with the fluorescent dye, Alexa Fluor 488. The mixture of labelled isomers was partially resolved by ion exchange HPLC and isoelectric focusing. The fluorescent Fab could be used to detect erythropoietin by immunoaffinity capillary isoelectric focusing and zone capillary electrophoresis via its antigen complex.Abbreviations BGE background electrolyte - CE capillary electrophoresis - Epo Erythropoietin - Fab antigen-binding fragment - FITC fluorescein isothiocyanate - IEF isoelectric focusing - mAb monoclonal antibody - PBS phosphate-buffered saline - rHuEpo recombinant human erythropoietin - scFv (recombinant) single chain variable fragment - SDS-PAGE denaturing polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate - ECL enzyme-coupled chemoluminescence - v_H variable domain - c_H1–3 constant domains of an antibody's heavy chain     

Novel and Ultrasensitive Sandwich Enzyme Immunoassay (Sandwich Transfer Enzyme Immunoassay) for Antigens

Abstract

A novel and ultrasensitive sandwich enzyme immunoassay (sandwich transfer enzyme immunoassay) for antigens is described. Antigens were reacted with dinitrophenyl monoclonal mouse antibody IgG₁ and rabbit antibody Fab′-ß-D-galactosidase conjugates. The complex formed of antigens with dinitrophenyl monoclonal mouse antibody IgG₁ and rabbit antibody Fab′-ß-D-galactosidase conjugates was trapped onto affinity-purified rabbit (antidinitrophenyl bovine serum a1bumin) IgG-coated polystyrene balls. After eliminating excess of the conjugates, the complex was eluted from the polystyrene balls with dinitrophenyl-L-lysine and transfered to clean polystyrene balls coated with affinity-purified rabbit (anti-mouse IgG) IgG. ß-D-Galactosidase activity bound to the (anti-mouse IgG) IgG-coated polystyrene balls was assayed by fluorimetry. Nonspecifically bound ß-D-galactosidase activity considerably decreased with less decrease in specifically bound ß-D-galactosidase activity. As a result, the detection limits of human thyroid-stimulating hormone (0.01 nu, 0.02 amol) and human growth hormone (10 fg, 0.5 amol) by the present enzyme immunoassay were 30-fold lower than those by the conventional enzyme immunoassay, in which antigens were incubated with monoclonal mouse antibody IgG₁-coated polystyrene balls and rabbit antibody Fab′-ß-D-galactosidase conjugates.     

Development of highly sensitive chemiluminescence enzyme immunoassay based on the anti-recombinant HC subunit of botulinum neurotoxin type A monoclonal antibodies

Botulinum neurotoxins (BoNTs) are the most poisonous substances ever known. The early detection of these toxins could bear more time for appropriate medical intervention. The standard method for detecting BoNTs is the mouse bioassay, which is time consuming (up to 4 days) and requires a large number of laboratory animals. The immunologic detection methods could detect the toxins within a day, but most of these methods are less sensitive compared with the mouse bioassay due to the lack of high-affinity antibodies. Recently, the recombinant H_C subunit of botulinum neurotoxin type A (rAH_C) was expressed as an effective vaccine against botulism, indicating that the rAH_C could be an effective immunogen that raises the monoclonal antibody (mAb) for detecting BoNT/A. After immunized BALB/c mice with rAH_C, 56 mAbs were generated. Two of these mAbs were selected to establish a highly sensitive sandwich chemiluminescence enzyme immunoassay (CLEIA), in which FMMU-BTA-49 and FMMU-BTA-22 were used as capture antibody and detection antibody, respectively. The calculated limit of detection (LOD) based on molecular weight of rAH_C and BoNT/A reached 0.45 pg mL⁻¹. This CLEIA can be used in the detection of BoNT/A in matrices such as milk and beef extract. This method has 20–40 fold lower LOD than that of the mouse bioassay and takes only 3 h to complete the detection, indicating that it can be used as a valuable method to detect and quantify BoNT/A.     

Vertical random variability of the distribution coefficient in the soil and its effect on the migration of fallout radionuclides

In the field, the distribution coefficient, K _d, for the sorption of a radionuclide by the soil cannot be expected to be constant. Even in a well defined soil horizon, K _d will vary stochastically in horizontal as well as in vertical direction around a mean value. The horizontal random variability of K _d produce a pronounced tailing effect in the concentration depth profile of a fallout radionuclide, much less is known on the corresponding effect of the vertical random variability. To analyze this effect theoretically, the classical convection-dispersion model in combination with the random-walk particle method was applied. The concentration depth profile of a radionuclide was calculated one year after deposition assuming (1) constant values of the pore water velocity, the diffusion/dispersion coefficient, and the distribution coefficient (K _d = 100 cm^3.g^-1), and (2) exhibiting a vertical variability for K _d according to a log-normal distribution with a geometric mean of 100 cm^3.g^-1 and a coefficient of variation of CV = 0.53. The results show that these two concentration depth profiles are only slightly different, the location of the peak is shifted somewhat upwards, and the dispersion of the concentration depth profile is slightly larger. A substantial tailing effect of the concentration depth profile is not perceivable. Especially with respect to the location of the peak, a very good approximation of the concentration depth profile is obtained if the arithmetic mean of the K _d-values (K _d = 113 cm^3.g^-1) and a slightly increased dispersion coefficient are used in the analytical solution of the classical convection-dispersion equation with constant K _d. The evaluation of the observed concentration depth profile with the analytical solution of the classical convection-dispersion equation with constant parameters will, within the usual experimental limits, hardly reveal the presence of a log-normal random distribution of K _d in the vertical direction in contrast to the horizontal direction.     

Micro-Scale Frontal Affinity Chromatography with Mass Spectrometric Detection: A New Method for the Screening of Compound Libraries

In one run the binding constants K_d for all the active components of a ligand library at sub-microgram quantities can be determined. A mixture of ligands is continuously infused through a column of immobilized receptor, and the eluent analyzed by electrospray mass spectrometry. From the affinity chromatogram produced (see picture) the breakthrough volume of a single compound and hence its K_d value can be determined.     

The distribution coefficient of60Co in sediments from the Solway Firth, UK

The behaviour of⁶⁰Co in sea water and sediments typical of the Solway Firth has been investigated. The distribution coefficient,K _d, of⁶⁰Co²⁺ in sediments was determined using the batch sorption method and theK _d variation with aqueous phase composition, sediment type and pH has been studied. Adsorption of⁶⁰Co by sediments was found to be highest in de-ionised water and lower in NaCl solution (31 salinity). Adsorption was lowest in natural sea water, where theK _d range was 2,270 to 2,750. Variation ofK _d with sediment grain size was observed. It was shown that⁶⁰Co adsorption was strongly dependent on pH in de-ionised water, with less variation in NaCl solution. Variance of⁶⁰CoK _d values were lowest in sea water in the range pH 5–8 indicating a more conservative behaviour of⁶⁰Co than previously recognised. Hence⁶⁰Co dispersion will be predominantly govemed by tidal behaviour.     

A Highly K+‐Selective Fluorescent Probe – Tuning the K+‐Complex Stability and the K+/Na+ Selectivity by Varying the Lariat‐Alkoxy Unit of a Phenylaza[18]crown‐6 Ionophore

A desirable goal is to synthesize easily accessible and highly K⁺/Na⁺‐selective fluoroionophores to monitor physiological K⁺ levels in vitro and in vivo. Therefore, highly K⁺/Na⁺‐selective ionophores have to be developed. Herein, we obtained in a sequence of only four synthetic steps a set of K⁺‐responsive fluorescent probes 4 , 5 and 6 . In a systematic study, we investigated the influence of the alkoxy substitution in ortho position of the aniline moiety in π‐conjugated aniline‐1,2,3‐triazole‐coumarin‐fluoroionophores 4 , 5 and 6 [R=MeO ( 4 ), EtO ( 5 ) and iPrO ( 6 )] towards the K⁺‐complex stability and K⁺/Na⁺ selectivity. The highest K⁺‐complex stability showed fluoroionophore 4 with a dissociation constant K_d of 19 mm , but the K_d value increases to 31 mm in combined K⁺/Na⁺ solutions, indicating a poor K⁺/Na⁺ selectivity. By contrast, 6 showed even in the presence of competitive Na⁺ ions equal K_d values (K_d^K+=45 mm and K_d^K+/Na+=45 mm ) and equal K⁺‐induced fluorescence enhancement factors (FEFs=2.3). Thus, the fluorescent probe 6 showed an outstanding K⁺/Na⁺ selectivity and is a suitable fluorescent tool to measure physiological K⁺ levels in the range of 10–80 mm in vitro. Further, the isopropoxy‐substituted N‐phenylaza[18]crown‐6 ionophore in 6 is a highly K⁺‐selective building block with a feasible synthetic route.     

Anionic polymerization with alkaline-earth counterion. II. Polymerization of styrene initiated by dicarbanionic oligostyrylbarium in THF

The propagation kinetics of anionic polymerization of styrene initiated by dicarbanionic oligostyrylbarium (PS⁼Ba⁺⁺) in THF are described. The apparent propagation rate constant k_p increases drastically with the degree of polymerization (DP) of living chains and tends at 20°C, for the highest molecular weight (DP ? 5000), to the value determined for monocarbanionic polystyrylbarium(PS^?)₂Ba⁺⁺. At given DP, the propagation step follows usual first-order kinetics with respect to monomer, and k_p is inversely proportional to carbanion concentration; as observed for (PS^?)₂Ba⁺⁺. Similar behavior is observed in the temperature range from ?60 to +20°C. The activation energy of the propagation is 4–5 kcal/mole (16.7–21 kJ/mole). It is shown that k_p may be considered as directly proportional to the dissociation constant K_d of ion pairs (～S^?Ba^++?S～ is considered as an ion pair ～(SBa)⁺S^?～). The striking variation of k_p with the DP living chains is interpreted in terms of cyclic living chains, in which both carbanionic ends are bound to the same cation. Values of the intramolecular dissociation constant K_d of ion pairs included in such a model are computed as a function of DP, and their variation is found to fit rather well with experimental data.     

Determination of human IgG by solid-substrate room-temperature phosphorescence immunoassay based on an antibody labeled with nanoparticles containing rhodamine 6G luminescent molecules

Luminescent 50-nm silicon dioxide nanoparticles containing both types of rhodamine 6G (R; particles denoted R-SiO₂) were synthesized by the sol–gel method. In the presence of Pb(Ac)₂ as a heavy atom perturber the particle can emit the intense and stable room-temperature phosphorescence (RTP) signal of R on a polyamide membrane, with _ex^max/_em^max=470/635 nm for R. Our research indicates that the specific immune reaction between goat-anti-human IgG antibody labeled with R-SiO₂ and human IgG can be carried out quantitatively on a polyamide membrane, and the phosphorescence intensity was enhanced after the immunoreaction. Thus a new method for solid-substrate room-temperature phosphorescence immunoassay (SS-RTP-IA) for determination of human IgG was established on the basis of antibody labeled with the nanoparticles containing binary luminescent molecules. The linear range of this method is 0.0624–20.0 pg spot^–1 of human IgG (corresponding to a concentration range of 0.156–50.0 ng mL^–1, sample volume 0.40 L spot^–1). The regression equations of the working curves are I_p=71.27+7.208m_IgG (pg spot^–1) (r=0.9996). Detection limits calculated as 3S_b/k are 0.022 pg spot^–1. Compared with the same IA using fluorescein isothiocyanate (FITC) as the marker the new method was more sensitive and had a wider linear range. After elevenfold replicate measurement RSD are 4.5 and 3.6% for samples containing 0.156 and 50.0 ng mL^–1 IgG, respectively. This method is sensitive, accurate, and of high precision.     

A new langbeinite‐type phosphate K2GdHf(PO4)3: synthesis,crystal structure,band structure and luminescence properties

Langbeinite‐type compounds are a large family that include phosphates, sulfates and arsenates, and which are accompanied by interesting physical properties. This work reports a new disordered langbeinite‐type compound, K₂GdHf(PO₄)₃ [dipotassium gadolinium hafnium tris(phosphate)], and its structure as determined by single‐crystal X‐ray diffraction. Theoretical studies reveal that K₂GdHf(PO₄)₃ is an insulator with a direct band gap of 4.600 eV and that the optical transition originates from the O‐2p→Hf‐5d transition. A Ce³⁺‐doped phosphor, K₂Gd_0.99Ce_0.01Hf(PO₄)₃, was prepared and its luminescence properties studied. With 324 nm light excitation, a blue emission band was observed due to the 5d¹→4f¹ transition of Ce³⁺. The average luminescence lifetime was calculated to be 5.437 µs and the CIE chromaticity coordinates were (0.162, 0.035). One may expect that K₂Gd_0.99Ce_0.01Hf(PO₄)₃ can be used as a good blue phosphor for three‐colour white‐light‐emitting diodes (WLEDs).     

A review on distribution coefficient (Kd) of some selected radionuclides in soil/sediment over the last three decades

This review paper presents the different methods to estimate K_d and subsequent compiles of the K_d data on U, Ra, Th, ¹³⁷Cs and ⁶⁰Co in soil/sediment under various aquatic medium based on the extensive literature survey over the last 3-decades (1990–2019). The estimated K_d values show a very wide range and make more difficult to derive generic value. The finding suggests that K_d values are to be estimated for site-specific conditions while assessing the radionuclide transport modeling and risk analysis around the nuclear facilities. Review includes research papers, reports, reviewed papers, dissertations, published compilations and other technical documents.