Conformational effects of ligand binding on the beta 2 subunit of Escherichia coli tryptophan synthase analyzed with monoclonal antibodies

Pseudo-native motifs in the noncovalent heme-apocytochrome c complex. Evidence from antibody binding studies by enzyme-linked immunosorbent assay and microcalorimetry

When beef heart apocytochrome c is unfolded, it folds upon noncovalent heme binding (Dumont, M. E., Corin, A. F., and Campbell, G.A. (1994) Biochemistry, 33, 7368-7378). Here, the conformation of the heme-apocytochrome noncovalent complex is compared with that of holocytochrome c. A purification method was designed for obtaining in large amounts apocytochrome c that was shown by amino acid analysis and mass spectroscopy to be chemically intact. The apoprotein and its noncovalent complex were characterized by absorption, fluorescence, circular dichroism, and sedimentation velocity, confirming previous reports. Sedimentation-diffusion equilibrium showed that the apoprotein and its noncovalent complex with heme were monomeric. Surprisingly, whereas apocytochrome c was quite soluble, the noncovalent complex slowly formed heavy aggregates, thus precluding experiments at the concentrations needed for structural studies. Two monoclonal antibodies that bind strongly to distinct antigenic sites on native holocytochrome were used to probe the noncovalent complex conformation. For both antibodies, the affinity for the noncovalent complex was only about 5-10-fold smaller than that for native holocytochrome c, and about 50-100-fold larger than that for apocytochrome c. These results indicate that the noncovalent complex, although not entirely native, carries some pseudo-native structural motifs.

Analysis of thermal stability of soya globulins using monoclonal antibodies

The epitopes of two monoclonal antibodies (Mabs), one raised to soya glycinin (IFRN 0025) and one to beta-conglycinin (IFRN 0089), have been defined. The epitope of 0025 corresponds to residues 86-104 of the acidic polypeptide of glycinin A1aB1b and lies at the C terminus of the proteolytic intermediate known as glycinin-T, whilst that of 0089 corresponds to residues 78-84 in the acidic extension present in the alpha' subunit of beta-conglycinin. As the Mabs bind to synthetic peptides corresponding to the epitope regions both epitopes can be considered as being continuous in nature. The regions recognised correspond to surface loops, which are probably flexible in nature. Both Mabs were used to investigate thermally induced conformational changes in soya globulins. Thermally treated glycinin was recognised more strongly than native protein, possibly due to disruption of the disulphide bond joining the acidic and basic polypeptides. Disruption could increase epitope accessibility, as could the conformational changes associated with denaturation. The binding of anti-beta-conglycinin Mab 0089 was unaffected by heating, suggesting that its epitope remains on the surface of the aggregates formed on heating. This study demonstrates that Mabs with defined specificities can be sensitive probes for monitoring local conformational changes within a protein molecule during thermal denaturation.

Selection of monoclonal antibodies for probing of functional intermediates in incision of UV-irradiated DNA by Uvr(A)BC endonuclease from Escherichia coli

Monoclonal antibodies (mAbs) were generated that recognize UvrA and UvrB proteins. These proteins are components of the Uvr(A)BC endonuclease, which initiates nucleotide excision repair in Escherichia coli. mAbs, which can be used for probing of structural intermediates of Uvr(A)BC endonuclease functioning, were selected for their ability to: (i) recognize different epitopes; (ii) have a high-affinity for native antigenic protein; (iii) preserve functionality of the Uvr protein in immunocomplex. The adherence of anti-Uvr mAbs with these criteria was verified by additivity and competition tests, and by their influence on the ATPase activities of UvrA and UvrB*, the functionally active proteolytic fragment of UvrB. Two out of twelve anti-UvrA and seven out of thirteen anti-UvrB/anti-UvrB* hybridoma lines were shown to satisfy these criteria. Recognition of UvrA and UvrB deletion mutant proteins by mAbs was used to map their epitopes. Epitopes of A2D1 and A2B1 mAbs were mapped to regions of amino acids 230-281 and 560-680 of UvrA, respectively. Epitopes of anti-UvrB/UvrB* mAbs were assigned to the following amino acid regions of UvrB: B2A1, 8-61; B2C5 and B*2E3, 171-278; B2E2, 631-673; B3C1, 1-7 and/or 62-170; B*2B9, 473-630; B*3E11, 379-472. The ability of selected mAbs to neutralize the incision function of Uvr(A)BC was analyzed. The results are discussed in terms of the applicability of these mAbs to probe the structures of intermediates in the functioning of Uvr(A)BC.

A monoclonal antibody to avidin dissociates quaternary structure and curtails biotin binding to avidin and streptavidin

An anti-avidin mAb, viz., H12G4, is shown to release bound biotin in a dose-dependent manner from holoavidin and holostreptavidin and inhibit the binding of ligand to the two apoproteins. The release of biotin by this mAb is accompanied by quenching of ligand-induced enhanced fluorescence of the FITC-avidin conjugate. In terms of mechanism of release of bound biotin, we demonstrate that on binding to the Fab fragment of the mAb, the native tetrameric holoavidin undergoes dissociation progressively with time to monomers with no bound biotin associated with the latter. Based on the immunoreactivity associated with defined overlapping fragments of avidin obtained by chemical cleavage, the epitope recognized by mAb H12G4 has been localized to residues 58-96 of the primary sequence. By pepscan method of epitope mapping, this mAb is shown to identify a minimal core sequence of 87RNGK90 in avidin and a corresponding sequence of 84RNAH87 in streptavidin.

Generation of a monoclonal antibody that recognizes the amino-terminal decapeptide of the B-subunit of Escherichia coli heat-labile enterotoxin. A new probe for studying toxin assembly intermediates

Cholera toxin and the related Escherichia coli heat-labile enterotoxin are hexameric proteins comprising one A-subunit and five B-subunits. In this paper we report the generation and characterization of a monoclonal antibody, designated LDS47, that recognizes and precipitates in vivo assembly intermediates of the B-subunit (EtxB) of E. coli heat-labile enterotoxin. The monoclonal antibody is unable to precipitate native B-subunit pentamers, thus making LDS47 a useful probe for studying the early stages of enterotoxin biogenesis. The use of LDS47 to monitor the in vivo turnover of newly synthesized B-subunits in the periplasm of E. coli demonstrated that (i) the turnover of unassembled B-subunits followed an apparent first order process and (ii) it occurred concomitantly with the assembly of native B-pentamers (k = 0.317 +/- 0.170 min-1; t1/2 = 2.2 min). No other proteins were co-precipitated with the newly synthesized B-subunits; a finding that implies that unassembled B-subunits do not stably associate with other periplasmic proteins prior to their assembly into a macromolecular complex. The use of overlapping synthetic peptides corresponding to the entire EtxB polypeptide demonstrated that the epitope recognized by LDS47 is located within the amino-terminal decapeptide of the B-subunit. From the x-ray structural analysis of the toxin (Sixma, T., Kalk, K., van Zanten, B., Dauter, Z., Kingma, J., Witholt, B., and Hol, W. G. J. (1993) J. Mol. Biol. 230, 890-918), this region appears to resemble a curved finger that clasps the adjacent B-subunit. Thus, this region might be expected to be exposed in the unfolded or unassembled subunit, but to become partially buried upon assembly and thus inaccessible to recognition by the monoclonal antibody.

Measurement of the dissociation rate constant of antigen/antibody complexes in solution by enzyme-linked immunosorbent assay

A reliable, convenient ELISA based method has been developed for measuring the dissociation rate constants of antigen/antibody complexes in solution. Its rationale is as follows: a solution containing the preformed antigen/antibody complex is diluted well below the equilibrium dissociation constant to initiate the dissociation and, at various times after the dilution, the amount of dissociated antibody contained in an aliquot is determined by a classical ELISA, using a brief incubation of the solution in antigen coated wells. To test the validity of this method, the dissociation rate constants for several antigen/antibody complexes were compared with those obtained by classical fluorescence based methods. The good agreement between both sets of data validates the ELISA procedure. The present method offers several advantages. It uses only minute amounts of sample which need not be purified; it requires no radioactive or fluorescent labelling of the antibody or antigen, and it can, in principle, be applied to any type of complex between macromolecules if an ELISA test can be set up to detect quantitatively one of the macromolecules.

Nicking of the tryptophan synthase beta 2-subunit at Glu-296 prevents the conformational change undergone on binding the alpha-subunit

Using a monoclonal antibody as conformational probe it has been shown that the weakly active nicked-beta 2 dimer of tryptophan synthase generated by proteolytic cleavage at Glu-296, does not undergo on association with alpha subunit a conformational change known to occur in intact beta 2 subunit. This alpha induced conformational change is also prevented in intact beta 2 by the coenzyme pyridoxal-5'-phosphate when the substrate L-serine is absent.

Methods for measurement of antibody/antigen affinity based on ELISA and RIA

Various enzyme-linked immunosorbent assay or radioimmunoassay methods are currently used to quantify the antibody-antigen interaction. Only those based on indirect competition--enzyme-linked immunosorbent assay or radioimmunoassay--can provide the real thermodynamic affinity of the antibody for its antigen. They can be applied to a variety of experimental situations, some of which are reviewed here.

In vitro gene expression for the localization of antigenic determinants: application to the E. coli tryptophan synthase beta 2 subunit

Gene expression of the beta subunit of E. coli tryptophan synthase in an E. coli cell-free transcription-translation system proceeds by pauses and produces a discrete but quite continuous pattern of nascent chains starting from the N terminus and ranging in size up to the 44 kDa end product corresponding to the completed beta chains. Using specific immunoadsorption of [35S]Met radiolabelled nascent chains by different monoclonal antibodies directed against the beta 2 subunit of E. coli tryptophan synthase, the size of the smallest N-terminal fragment reacting with each antibody has been determined by SDS electrophoretic analysis of the immunoadsorbed polypeptides. The immunoadsorption assay is performed in solution under conditions avoiding the usual drawbacks of solid phase immunoassay. This approach, in combination with the results obtained with a DNA fragment library permitted us to localize the antigenic determinants recognized by the monoclonal antibodies. The proposed method could help to localize rapidly the C-terminal boundary of an epitope, before starting systematic and precise mapping by other approaches. Moreover, the method described may be of general interest for the rapid production of a large set of C-terminal truncated polypeptides for studies of antigen-antibody recognition.

Investigating protein conformation, dynamics and folding with monoclonal antibodies

Monoclonal antibodies with thoroughly characterized target specificities can be used as powerful probes of protein conformation. In addition to providing information on the relative arrangement of the domains in the native molecule, they can also be used to monitor both early and late stages of protein folding and conformational changes related to enzyme action.

Identification of cellular proteins binding to the scrapie prion protein

The scrapie prion protein (PrPSc) is an abnormal isoform of the cellular protein PrPc. PrPSc is found only in animals with scrapie or other prion diseases. The invariable association of PrPSc with infectivity suggests that PrPSc is a component of the infectious particle. In this study, we report the identification of two proteins from hamster brain of 45 and 110 kDa (denoted PrP ligands Pli 45 and Pli 110) which were able to bind to PrP 27-30, the protease-resistant core of PrPSc on ligand blots. Pli 45 and Pli 110 also bound PrPC. Both Pli's had isoelectric points of approximately 5. The dissociation rate constant of the Pli 45/PrP 27-30 complex was 3 x 10(-6) s-1. Amino acid and protein sequence analyses were performed on purified Pli 45. Both the composition and the sequence were almost identical with those predicted for mouse glial fibrillary acidic protein (GFAP). Furthermore, antibodies to Pli 45 reacted with recombinant GFAP. The identification of proteins which interact with the PrP isoforms in normal and diseased brain may provide new insights into the function of PrPC and into the molecular mechanisms underlying prion diseases.

Monoclonal antibodies as probes for monitoring the denaturation process of bovine beta-lactoglobulin

Five monoclonal antibodies (MAbs) of different idiotypes were produced against bovine beta-lactoglobulin (beta-LG). Among them, MAbs 61B4 and 62A6 reacted preferentially to native beta-LG, while MAbs 21B3 and 31A4 reacted more strongly to the reduced carboxymethylated (denatured) beta-LG than to the native material. These two types of MAb were used to analyze the denaturation process of a beta-LG molecule during heating. The binding affinity of MAbs 21B3 and 31A4 with beta-LG was increased by increasing the heating temperature, the transition temperature being 67-68 degrees C, while that of MAbs 61B4 and 62A6 was reduced by increasing the temperature, this transition temperature being about 80 degrees C. Epitopes recognized by MAbs 31A4 and 61B4 were shown to be included in the segments, Lys8-Trp19 (mostly in the random-coil region) and Thr125-Lys135 (helical region), respectively. The heat-induced conformational change of the beta-LG molecule is, therefore, likely to start in random-coil region as Lys8-Trp19, and to be followed by a structural change in a helical region as Thr125-Lys135. This study demonstrates that MAb is a useful probe to monitor local conformational changes of a protein molecule during denaturation.

New properties of Bacillus subtilis succinate dehydrogenase altered at the active site. The apparent active site thiol of succinate oxidoreductases is dispensable for succinate oxidation

Mammalian and Escherichia coli succinate dehydrogenase (SDH) and E. coli fumarate reductase apparently contain an essential cysteine residue at the active site, as shown by substrate-protectable inactivation with thiol-specific reagents. Bacillus subtilis SDH was found to be resistant to this type of reagent and contains an alanine residue at the amino acid position equivalent to the only invariant cysteine in the flavoprotein subunit of E. coli succinate oxidoreductases. Substitution of this alanine, at position 252 in the flavoprotein subunit of B. subtilis SDH, by cysteine resulted in an enzyme sensitive to thiol-specific reagents and protectable by substrate. Other biochemical properties of the redesigned SDH were similar to those of the wild-type enzyme. It is concluded that the invariant cysteine in the flavoprotein of E. coli succinate oxidoreductases corresponds to the active site thiol. However, this cysteine is most likely not essential for succinate oxidation and seemingly lacks an assignable specific function. An invariant arginine in juxtaposition to Ala-252 in the flavoprotein of B. subtilis SDH, and to the invariant cysteine in the E. coli homologous enzymes, is probably essential for substrate binding.

Polypeptide-antibody binding mechanism: conformational adaptation investigated by equilibrium and kinetic analysis

The mechanism of polypeptide-antibody binding was analysed by kinetic and equilibrium studies to find out whether or not the binding of an antibody to a large protein or a polypeptide antigen behaves as a one-step reaction or involves conformational adaptation. Three monoclonal antibodies recognizing 3 distinct epitopes on the C-terminal domain (F2) of Escherichia coli tryptophan synthase beta 2 subunit were used. The dissociation equilibrium constant (KD), the association rate constant (kon) and the dissociation rate constant (koff) of these antibodies for the native beta 2 subunit, its C-terminal fragment (F2) and different polypeptides obtained by chemical cleavage of the F2 fragment were measured. It was found that for some polypeptide-antibody complexes, binding could not be described as a one-step association-dissociation reaction, thus indicating the existence of conformational adaptation upon antibody-antigen complex formation. It was also shown that differences in affinities of a given antibody for its epitope carried by different polypeptides were mainly due to differences in the dissociation rate constant (koff) and not in the association rate constant (kon). Moreover, the immunoreactivity of various polypeptides obtained by cleavage of the F2 fragment enabled us to localize the 3 epitopes on the beta chain in light of the 3-dimensional structure of tryptophan synthase described recently by Hyde et al. (1988).

A physical-chemical and immunological comparison shows that native and renatured Escherichia coli tryptophan synthase beta 2 subunits are identical

An acid-denaturation of the beta 2 subunit of Escherichia coli tryptophan synthase has been recently described. In the present study, renaturation yield of acid-denaturated beta 2, and the influence of temperature, protein concentration and presence of ligands are investigated. It is also demonstrated that 3 forms of the protein are obtained at the end of the renaturation process: one is fully active, and is identical to native beta 2, as indicated by some of its chemical and physical properties, as well as by its immunological reactivity towards monoclonal antibodies specific for the native protein. A second form is composed of high molecular weight insoluble and inactive aggregates. A third form consists of low molecular weight soluble and inactive aggregates. The results obtained for the immunochemical reactivity of these small aggregates indicate that they are formed with partly correctly folded beta monomers assembled by specific but incorrect quaternary interactions. The capacity of monoclonal antibodies to detect such incorrect structures and to characterize renatured proteins is particularly emphasized.

Size-exclusion high-performance liquid chromatography in analysis of protein and peptide epitopes

Size-exclusion HPLC provides direct observation of antibody-antigen interactions in free solution without chemical modification of either component. HPLC data collection systems are now a routine resource in both academic and industrial research laboratories. Monoclonal antibodies are, in principle, homogeneous reagents whose interactions with epitope are suitable for unambiguous quantitative characterization. HPLC-based methods, therefore, have the potential to contribute significantly to efficient quantitative characterization of monoclonal antibodies in studies directed to the fundamental physiological roles of these molecules as well as to the optimized selection and quality control of these reagents in biotechnical applications such as represented by the immunodiagnostic industry. In many cases, HPLC-based methods may represent the simplest and most rapid approach for evaluation of relative epitope specificities and affinity/kinetic characteristics of interaction.

Epitope localization in antigen-monoclonal-antibody complexes by small-angle X-ray scattering. An approach to domain organization in the beta 2 subunit of Escherichia coli tryptophan synthase

Each polypeptide chain of the beta 2 subunit of Escherichia coli tryptophan synthase (EC 4.2.1.20) is made of two domains, F1 (N-terminal) and F2 (C-terminal). To determine the relative position of these domains in the native protein, complexes between beta 2 and Fab fragments from two monoclonal antibodies, one specific for F1 (68-1) and the other for F2 (93-6), have been prepared and purified. Small-angle X-ray scattering measurements have been made on solutions of each complex. From the experimental scattering curves obtained, computer modeling leads to structural models of the two beta 2-Fab complexes. Though relatively low, the resolution of these models allows the localization on beta 2 of the antigenic sites recognized by the two antibodies, to show that the C-terminal F2 domains lie at the distal ends of the elongated beta 2 protein, and to show how steric hindrance prevents beta 2, though structurally and functionally dimeric, from binding more than one Fab 93-6 fragment per dimer.

Conformational changes induced by domain assembly within the beta 2 subunit of Escherichia coli tryptophan synthase analysed with monoclonal antibodies

The effects of domain assembly on the conformation of the F1 (N-terminal) and F2 (C-terminal) domains of the beta 2 subunit of Escherichia coli tryptophan synthase (EC 4.2.1.20) were analysed using six monoclonal antibodies which recognize six different epitopes of the native beta 2 subunit (five carried by the F1 domain and one carried by the F2 domain). For this purpose, the affinity constant of each monoclonal antibody for the isolated domains F1 or F2, the associated domains in the trypsin-nicked apo-beta 2 and in the native apo-beta 2 subunits were determined, both with the intact immunoglobulin and the Fab fragment. It was found that the association of the F1 and F2 domains within beta 2 is accompanied by structural changes of the two domains, as detected by variations of their affinity constants for the monoclonal antibodies.