Michael J Taussig's research while affiliated with Babraham Institute and other places
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Publications (76)
The 2015 Alpbach Workshop on Affinity Proteomics, organised by the EU AFFINOMICS consortium, was the 7(th) workshop in this series. As in previous years, the focus of the event was the current state of affinity methods for proteome analysis, including complementarity with mass spectrometry, progress in recombinant binder production methods, alterna...
We report the development of a new database of technology services and products for analysis of biobank samples in biomedical
research. BARCdb, the Biobanking Analysis Resource Catalogue (http://www.barcdb.org), is a freely available web resource, listing expertise and molecular resource capabilities of research centres and biotechnology
companies....
Alongside mass spectrometry, antibodies and other specific protein binding molecules have a special place in proteomics as affinity reagents in a toolbox of applications for determining protein location, quantitative distribution and function (affinity proteomics). The realisation that the range of research antibodies available, while apparently va...
Foreword to the special issue of New Biotechnology comprising review articles by former steering committee members to mark the end of the European Science Foundation Research Networking Programme in Functional Genomics.
Unlabelled:
We have previously described a protein arraying process based on cell free expression from DNA template arrays (DNA Array to Protein Array, DAPA). Here, we have investigated the influence of different array support coatings (Ni-NTA, Epoxy, 3D-Epoxy and Polyethylene glycol methacrylate (PEGMA)). Their optimal combination yields an incre...
Affinity proteomics is the field of proteome analysis based on the use of antibodies and other binding reagents as protein-specific detection probes. In this review, the particular strengths of affinity methods for determination of protein localization, functional characterization, biomarker discovery and intracellular applications, and their resul...
In affinity proteomics, specific protein-binding molecules (a.k.a. binders), principally antibodies, are applied as reagents in proteome analysis. In recent years, advances in binder technologies have created the potential for an unprecedented view on protein expression and distribution patterns in plasma, cells and tissues and increasingly on prot...
Management of data to produce scientific knowledge is a key challenge for biological research in the 21st century. Emerging high-throughput technologies allow life science researchers to produce big data at speeds and in amounts that were unthinkable just a few years ago. This places high demands on all aspects of the workflow: from data capture (i...
Ribosome display is a cell-free display technology for in vitro selection and optimisation of proteins from large diversified libraries. It operates through the formation of stable protein-ribosome-mRNA (PRM) complexes and selection of ligand-binding proteins, followed by DNA recovery from the selected genetic information. Both prokaryotic and euka...
Protein arrays are miniaturised and highly parallelised formats of interaction-based functional protein assays. Major bottlenecks in protein microarraying are the limited availability and high cost of purified, functional proteins for immobilisation and the limited stability of immobilised proteins in their functional state. In contrast, protein-co...
The development of protein microarrays makes possible interaction-based protein assays in miniaturised, multiplexed formats. A major requirement determining their uptake and use is the availability and stability of purified, functional proteins for immobilisation. With conventional methods, involving individual expression and purification of recomb...
We have previously described the 'DNA array to protein array' (DAPA) method for microarraying of proteins expressed by cell-free systems in situ on the array surface. In this technique, a DNA array on one slide acts as the template for generating a protein array on a second slide, mediated by a cell free lysate between the two juxtaposed slides. He...
The "4D Biology Workshop for Health and Disease", held on 16-17th of March 2010 in Brussels, aimed at finding the best organising principles for large-scale proteomics, interactomics and structural genomics/biology initiatives, and setting the vision for future high-throughput research and large-scale data gathering in biological and medical scienc...
In vitro antibody generation technologies have now been available for two decades. Research reagents prepared via phage display are becoming available and several recent studies have demonstrated that these technologies are now sufficiently advanced to facilitate generation of a comprehensive renewable resource of antibodies for any protein encoded...
We wish to alert your readers to MIAPAR, the minimum information about a protein affinity reagent. This is a proposal developed within the community as an important first step in formalizing standards in reporting the production and properties of protein binding reagents, such as antibodies, developed and sold for the identification and detection o...
Protein affinity reagents (PARs), most commonly antibodies, are essential reagents for protein characterization in basic research, biotechnology, and diagnostics as well as the fastest growing class of therapeutics. Large numbers of PARs are available commercially; however, their quality is often uncertain. In addition, currently available PARs cov...
We describe a method for identification of protein-protein interactions by combining two cell-free protein technologies, namely ribosome display and protein in situ immobilisation. The method requires only PCR fragments as the starting material, the target proteins being made through cell-free protein synthesis, either associated with their encodin...
Protein affinity reagents (PARs), most commonly antibodies, are essential reagents for protein characterization in basic research, biotechnology, and diagnostics as well as the fastest growing class of therapeutics. Large numbers of PARs are available commercially; however, their quality is often uncertain. In addition, currently available PARs cov...
Protein microarrays are versatile tools for parallel, miniaturized screening of binding events involving large numbers of immobilized proteins in a time- and cost-effective manner. They are increasingly applied for high-throughput protein analyses in many research areas, such as protein interactions, expression profiling and target discovery. While...
It has been shown previously that certain bacteria rapidly (3 h) up-regulated in vivo microfold cell (M cell)-mediated transport of Ag across the follicle-associated epithelium of intestinal Peyer's patch. Our aim was to determine whether soluble mediators secreted following host-bacteria interaction were involved in this event. A combination of pr...
We describe a method, DNA array to protein array (DAPA), which allows the 'printing' of replicate protein arrays directly from a DNA array template using cell-free protein synthesis. At least 20 copies of a protein array can be obtained from a single DNA array. DAPA eliminates the need for separate protein expression, purification and spotting, and...
In situ or on-chip protein array methods use cell free expression systems to produce proteins directly onto an immobilising surface from co-distributed or pre-arrayed DNA or RNA, enabling protein arrays to be created on demand. These methods address three issues in protein array technology: (i) efficient protein expression and availability, (ii) fu...
Ribosome display is a powerful method for selection of single-chain antibodies in vitro. It operates through the formation of libraries of antibody-ribosome-mRNA complexes that are selected on immobilized antigen, followed by recovery of the genetic information from the mRNA by RT-PCR. Both prokaryotic and eukaryotic versions are used. We describe...
Protein arrays make possible the functional screening of large numbers of immobilized proteins in parallel. To facilitate the supply of proteins and to avoid their deterioration on storage, we describe our protein in situ array (PISA) method for production of protein arrays in a single step directly from PCR DNA, using cell-free transcription and t...
Recombinant antibodies are now well established alternatives to monoclonal and polyclonal antibodies. In this article, the selection of antibody combining sites by in vitro display methods, namely phage, yeast, ribosome and mRNA display is reviewed, with a particular focus on the cell free technique of ribosome display. Its advantages discussed and...
In healthy mammals, maturation of B cells expressing heavy (H) chain immunoglobulin (Ig) without light (L) chain is prevented by chaperone association of the H chain in the endoplasmic reticulum. Camelids are an exception, expressing homodimeric IgGs, an antibody type that to date has not been found in mice or humans. In camelids, immunization with...
Cell-free transcription and translation provides an open, controllable environment for production of correctly folded, soluble proteins and allows the rapid generation of proteins from DNA without the need for cloning. Thus it is becoming an increasingly attractive alternative to conventional in vivo expression systems, especially when parallel exp...
Essential to the ambition of characterising fully the human proteome are systematic and comprehensive collections of specific affinity reagents directed against all human proteins, including splice variants and modifications. Although a large number of affinity reagents are available commercially, their quality is often questionable and only a frac...
Ribosome display is a cell-free system permitting gene selection through the physical association of genetic material (mRNA) and its phenotypic (protein) product. While often used to select single-chain antibodies from large libraries by panning against immobilized antigens, we have adapted ribosome display for use in the 'reverse' format in order...
Rheumatoid factors (RF) are autoantibodies that recognize epitopes in the Fc region of immunoglobulin (Ig) G and that correlate with the clinical severity of rheumatoid arthritis (RA). Here we report the X-ray crystallographic structure, at 3 A resolution, of a complex between the Fc region of human IgG1 and the Fab fragment of a monoclonal IgM RF...
Ribosome display is a cell-free technology for the in vitro selection and evolution of proteins encoded by DNA libraries, in which individual nascent proteins (phenotypes) are linked physically to their corresponding mRNA (genotypes) in stable protein-ribosome-mRNA (PRM) complexes. Formation of the complexes can be achieved through deletion of the...
ProteomeBinders is a new European consortium aiming to establish a comprehensive resource of well-characterized affinity reagents, including but not limited to antibodies, for analysis of the human proteome. Given the huge diversity of the proteome, the scale of the project is potentially immense but nevertheless feasible in the context of a pan-Eu...
While cell-free systems are increasingly used for protein expression in structural and functional studies, several proteins are difficult to express or expressed only at low levels in cell-free lysates. Here, we report that fusion of the human immunoglobulin kappa light chain constant domain (Ckappa) at the C terminus of four representative protein...
The crystal structures of the Fab' fragment of the anti-progesterone monoclonal antibody DB3 and its complexes with steroid haptens have shown that the D-JH junctional residue TrpH100 is a key contributor to binding site interactions with ligands. The indole group of TrpH100 also undergoes a significant conformational change between the bound and u...
Antibody-based microarray is a novel technology with great promise in biomedicine that will provide unique means to perform global proteome analysis. In the process of designing the high-density antibody microarrays required, several critical key issues have been identified that remain to be resolved. In particular, there is a great need for specif...
There is a particular need in protein analysis and purification for specific, functional, and generic methods of protein immobilization on solid supports. Here we describe a double-hexahistidine (His6) tag sequence, comprising two hexahistidines separated by an 11-amino acid spacer, which shows at least 1 order of magnitude stronger binding to Ni-N...
In ribosome display, proteins are linked to their encoding genetic material as protein-ribosome-mRNA complexes. The technology has been applied to the isolation of antibodies and other proteins from large PCR-derived libraries. Here we demonstrate the specificity of eukaryotic ribosome complexes and investigate recovery and display procedures using...
Arrays of antibodies and of other types of ligand-binding molecule (e.g. protein scaffolds or aptamers) provide a means for rapid detection of proteins and other analytes in multiple samples and ultimately for screening the human proteome in health and disease. The chief reasons for using an array-based approach to diagnostics and proteomics relate...
Antibodies are becoming increasingly important for both basic research and clinical applications. With the completion of genome sequencing, antibodies are required for the global analysis and detection of every encoded protein. In therapeutics, a number of antibodies have been used for disease treatment (1).
Protein array technology offers a powerful tool to bridge genomics and proteomics. Currently, the bottleneck in the generation of protein arrays is the comprehensive production of functional proteins. We have developed a rapid cell-free method, DiscernArray, which creates functional protein arrays directly from PCR DNA by in vitro synthesis of indi...
Highly specific and sensitive procedures will be required to evaluate proteomes. Proximity ligation is a recently introduced mechanism for protein analysis. In this technique, the convergence of sets of protein-binding reagents on individual target molecules juxtaposes attached nucleic acid sequences. Through a ligation reaction a DNA reporter sequ...
The multidomain bacterial surface protein L (PpL) is a virulence factor expressed by only 10% of Peptostreptococcus magnus strains, and its expression is correlated with bacterial vaginosis. The molecular basis for its ability to recognize 60% of mammalian immunoglobulin light chain variable regions (V(L)) has been described recently by x-ray cryst...
In the absence of a method to ensure that crystals can be obtained for any given protein, the possibility of developing scaffolds for protein crystallisation becomes attractive. Among several approaches that could yield scaffolds, two are particularly promising: the first is based on immunoglobulin Fab fragments and immunoglobulin binding proteins...
Ribosome display is a cell-free system for the in vitro selection of proteins and peptides from large libraries. It uses the principle of coupling individual nascent proteins (phenotypes)
to their corresponding mRNA (genotypes), through the formation of stable protein-ribosome-mRNA (PRM) complexes. This permits
the simultaneous isolation of a funct...
Theoretically a crystal may contain both complexed and uncomplexed molecules simultaneously in the same lattice. Since we seldom screen for such possibilities, such occurrences are only rarely reported. Here we propose that stoichiometry should be one of the parameters to be screened in the crystallization of macromolecular complexes. By allowing f...
Protein arrays are fast becoming established as a means to monitor protein expression
levels and investigate protein interactions and function. They present particular technical
demands that will need to be solved in order to achieve the maximum capability of efficient
and sensitive protein analysis in the high throughput setting of functional geno...
We describe a format for production of protein arrays termed ‘protein in situ array’ (PISA). A PISA is rapidly generated in one step directly from PCR-generated DNA fragments by cell-free protein expression
and in situ immobilisation at a surface. The template for expression is DNA encoding individual proteins or domains, which is produced
by PCR u...
Peptostreptococcus magnus protein L (PpL) is a multidomain, bacterial surface protein whose presence correlates with virulence. It consists of up to five homologous immunoglobulin binding domains that interact with the variable (VL) regions of kappa light chains found on two thirds of mammalian antibodies.
We refined the crystal structure of the co...
Linear interaction energy/molecular dynamics calculations have been used to compute steroid/antibody binding energies. The absolute binding affinities of 10 steroids to antibody DB3 and of a hapten to catalytic antibody 1E9 are computed and compared to experiment. A detailed analysis of the molecular origins of the observed binding patterns is prov...
Human placental alkaline phosphatase (PLAP) is one of three tissue-specific human APs extensively studied because of its ectopic expression in tumors. The crystal structure, determined at 1.8-A resolution, reveals that during evolution, only the overall features of the enzyme have been conserved with respect to Escherichia coli. The surface is deep...
Staphylococcus aureus produces a virulence factor, protein A (SpA), that contains five homologous Ig-binding domains. The interactions of SpA with the Fab region of membrane-anchored Igs can stimulate a large fraction of B cells, contributing to lymphocyte clonal selection. To understand the molecular basis for this activity, we have solved the cry...
The recently determined X-ray crystal structure of a human rheumatoid factor Fab bound to IgG Fc provides the basis of a new hypothesis for the origin of these autoantibodies in rheumatoid arthritis. The observation that Fc is bound outside the conventional antigen combining site suggests a novel form of crossreactivity with simultaneous binding of...
In antibody-ribosome-mRNA complex (ARM) ribosome display, stable complexes of nascent protein, mRNA and ribosomes are produced in a eukaryotic in vitro expression system, through coupled transcription and translation of DNA lacking a 3' stop codon. Selection of the protein simultaneously captures the relevant mRNA, which is recovered as DNA by coup...
We have produced mice that carry the human Ig heavy (IgH) and both kappa and lambda light chain transloci in a background in which the endogenous IgH and kappa loci have been inactivated. The B lymphocyte population in these translocus mice is restored to about one-third of normal levels, with preferential (3:1) expression of human lambda over huma...
By a combination of seeding and changing the growth medium new crystal forms may be obtained. The procedure is called an epitaxial jump. The seeds used in the seeding are from crystals of the same or related protein. For example, seeding followed by an increase in precipitant concentration has given higher diffracting crystals of the complex betwee...
We describe a rapid, eukaryotic, in vitro method for selection and evolution of antibody combining sites using antibody-ribosome-mRNA (ARM) complexes as selection
particles. ARMs carrying single-chain (VH/K) binding fragments specific for progesterone were selected using antigen-coupled magnetic beads; selection simultaneously
captured the genetic...
Rheumatoid factors (RF) are autoantibodies with reactivity towards the Fc regions of IgG molecules (1). They are found in the sera and synovia of most patients with rheumatoid arthritis (RA), and high levels of RF are associated with severe disease and poor prognosis (2,3) suggesting that they have a causative role in the pathology of this disease....
Transgenic mice have been created that carry human immunoglobulin heavy and light chain genes in germline configuration and that have the corresponding endogenous genes silenced. The transgenes are either minigene constructs or large, almost authentic, transloci on yeast artificial chromosomes and undergo B-cell-specific DNA rearrangement and hyper...
Rheumatoid factors are the characteristic autoantibodies of rheumatoid arthritis, which bind to the Fc regions of IgG molecules. Here we report the crystal structure of the Fab fragment of a patient-derived IgM rheumatoid factor (RF-AN) complexed with human IgG4 Fc, at 3.2 A resolution. This is the first structure of an autoantibody-autoantigen com...
Antibody 1E9 catalyzes the bimolecular Diels–Alder reaction between tetrachlorothiophene dioxide and N‐ethylmaleimide with high catalytic efficiency. The genes encoding the heavy and light chains were cloned, sequenced, and expressed as a mouse/human chimera in a murine hybridoma. Comparison with the closely related and structurally characterized a...
Two major unanswered questions concerning the specificity of antibodies are: how do structurally different antigens bind with high affinity to the same antibody, and what are the limits of the antibody combining site complementarity and flexibility that contribute to such crossreactivity? We report here a comparative analysis of the X-ray structure...
The monoclonal anti-progesterone antibody DB3 binds progesterone with nanomolar affinity (Ka approximately 10(9) M-1), suggesting high specificity. However, DB3 also cross-reacts with similar affinity with a subgroup of structurally distinct, progesterone-like steroids. Crystals of the unliganded Fab' and various steroid-Fab' complexes are isomorph...
Citations
... The international community has also come up with a proposal called Minimum Information About a Protein Affinity Reagent (MIAPAR), which aims to establish a stronger connection between antibody producers and users. MIAPAR-compliant data include information such as the production/purification process, experimental evidence, updated protocols, and other relevant details (7,9). ...
... Extrapolating from a structural analysis of the placental AP, a model for the protein structure of TNAP was developed, which implies that the enzyme contains two Zn 2+ ions and one Mg 2+ ion in its active center [9]. The function of an additionally identified Ca 2+ site is still unclear [10]. ...
... In the last years, it became evident that biologics have a broad potential in a number of medical indication area like oncology or inflammation. [1] As parenterals, most biologics are applied as infusions or via the sub-cutaneous route. [2,3] The necessary dosages of antibody biologics are often very high, reaching amounts of up to several 100 of milligrams per application. As a consequence, protein concentrations >100 mg/mL are required for sub-cutaneous application. For example, I ...
... An alternative strategy in such cases has been the use of biomolecular scaffolds that can incorporate the properties of the receptor binding site. mAbs are prime candidates for such a role since their affinity and specificity can be naturally tailored and have indeed been used in varied scenarios to elucidate functionally relevant ligand-receptor interactions, constrain flexible molecules in their biologically active forms [21,22] and in few cases capture metabolites in their transition states [23]. Earlier studies from our laboratory demonstrated that an otherwise flexible peptide antigen could be held in a single conformation by three independent mAbs [24]. ...
... For instance, the Fc fraction of IgG, which rheumatoid factor targets, contains multiple 'SSV' motifs, which we also observed in peptides preferentially bound in older donors. While rheumatoid factor doesn't bind these motifs in co-crystals with IgG Fc (primarily binding to CH2 and CH3 domains) [43,44], it is intriguing that multiple diserine motifs may stabilize interaction to enhance autoantibody avidity. ...
... Ribosome display is a cell-free method that overcomes some of limitations in phage display technique such as transformation steps which increases library capability [9] or enable expression of toxic proteins without affecting growth rate of the host [10][11][12][13]. Ribosome display, as a rapid and robust technique, was first used by Hanes and Plueckthun [14,15], simultaneously by He and Taussig [16], for affinity selection of single chain antibodies. Thereafter, it has been widely used for in vitro selection of different functional molecules (scFvs, sdAbs, DARPins, Affibodies, etc.) against targets of interest [17][18][19][20][21][22][23][24][25][26][27][28][29][30][31] and also for affinity maturation of phage displayed selected binders [17,[32][33][34]. ...
... The proteins once expressed become rapidly immobilized on the capture slide, creating a protein array that can be duplicated several times. DAPA has been extended to print arrays of 116 different proteins (Stoevesandt, Vetter et al. 2011). It has also been optimized using different array support coatings, which increase its sensitivity towards the printed proteins (Schmidt, Cook et al. 2013). ...
... In fact, Hopp and Woods assigns R, K, D, E, and Q as amino acids with the highest hydrophilicity index values [26]. Other investigators are aware of the immunogenic nature of these side chains [27] and PE was partially deimmunized by mutating combinations of only these residues [7]. Thus, using the known X-ray crystallographic structure of DT390, we identified 24 potential amino acids (R, K, D, E, and Q) located in prominent positions on the molecular surface. ...
... Many of the conventional antibody/antigen-based ELISA-based assays are highly speci c, however, they lack the level of sensitivity needed for detection of disease at an early stage. One of the main reasons is poor or insu cient alignment and distribution of the antibodies on the sensor substrate that limits the number of antibody-antigen binding events 18 . To address this challenge nanoparticles (NPs) have been used to effectively in regulate the alignment and distribution of antibodies on its surface to enhance sensitivity and improve interaction with the substrate. ...
... Indeed, in mice in which both Ig-κ and Ig-λ are ablated, there is almost a complete lack of mature B cells [59]. The only LC-less B cells that do survive express at the cell surface HC, in which the C H 1 domain is deleted [60], highlighting that the C H 1 domain is key for ER retention of the HC, and for eliciting (UPR-driven) HC toxicity, which is in line with our findings in the HeLa-μ s model [9]. Also the recombination and SHM of the Ig-κ or Ig-λ locus often result in aberrant LCs that provoke proteotoxic ER stress [61], which, analogously, could be co-opted as a counter-selection criterion for defective B cell clones. ...















































































