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PubMed2002

Efficient construction of a diabody using a refolding system: anti-carcinoembryonic antigen recombinant antibody fragment.

Recombinant fragments of the variable region of antibodies are useful in many experimental and clinical applications. However, it can be difficult to obtain these materials in soluble form after their expression in bacteria. Here, we report an efficient procedure for preparing several variable-domain fragments (Fv), single-chain Fv (scFv), and a diabody (the smallest functional bispecific antibody) of anti-carcinoembryonic antigen (CEA) antibody by overexpression in Escherichia coli in inclusion bodies, using a refolding system to obtain renatured proteins. Two types of refolded Fv were prepared: (i) Heavy and light chains of the immunoglobulin variable regions (VH and VL, respectively) were coexpressed with a dicistronic expression vector (designated Fv(co)); (ii) VH and VL were expressed separately, mixed stoichiometrically, and refolded (designated Fv(mix)). All samples refolded with high efficiency; Fv(co), Fv(mix), scFv, and the bispecific diabody bound to several CEA-positive cell lines, exactly as did soluble Fv fragments secreted by E. coli (Fv(sol)) and the parent IgG. The refolded fragments inhibited binding of the parent IgG to CEA-positive cell lines, indicating that their epitope is identical to that of IgG. The bispecific diabody, which combined variable-region fragments of anti-CEA antibody with variable-region fragments of anti-CD3 antibody, was also prepared using the refolding system. This refolded diabody could bind to lymphokine-activated killer cells. In addition, its cytotoxicity toward human bile duct carcinoma TFK-1 and other several other CEA-positive cell lines was concentration-dependent. Taken together, our results suggest that a refolding procedure can be used to prepare various functional antibody fragments (Fv, scFv, and diabody).

Animals↗
PubMed1991

Characterization and location of the L-proline activating fragment from the multifunctional gramicidin S synthetase 2.

Gramicidin S synthetase 2 (GS2) derived from Bacillus brevis is a multifunctional single polypeptide (Mr 280,000) with a 4'-phosphopantetheine residue covalently bound to the enzyme. When GS2 was treated with trypsin or chymotrypsin, fragments with some activity were liberated. The molecular mass of the L-proline activating fragment was 114 kDa on SDS-PAGE. This fragment, when incubated with gramicidin S synthetase 1 (GS1) in the presence of phenylalanine and proline, produced D-Phe-L-Pro dipeptide. The fragment accepted D-phenylalanine from GS1 in the absence of L-proline. The L-proline activating fragment was shown to lack pantothenic acid by microbiological assay. On the other hand, the L-leucine activating fragment, which was partially purified, contained a large amount of pantothenic acid, although it did not form the D-Phe-L-Pro dipeptide. These results indicate that the L-proline activating site is located near an acceptor site for D-phenylalanine on GS2, but that it is not adjacent to a 4'-phosphopantetheine group. The N-terminal sequence (15 amino acid residues) of the L-proline activating fragment obtained by trypsin treatment was identical with that of GS2, indicating that the L-proline activating site is located at the N-terminus of the native synthetase. The N-terminal sequence of GS2 has been matched with the amino acid sequence deduced from the nucleotide sequence 71 bp downstream of the stop codon of the GS1 gene except that the first initiator methionine was not detected.

Amino Acid Isomerases↗
PubMed1976

Amino acid sequence of an active fragment of potato proteinase inhibitor IIa.

The complete amino acid sequence of an active fragment of potato proteinase inhibitor IIa has been established by the Edman degradation procedure and the carboxypeptidase technique. Sequence analyses were carried out on the reduced and carboxymethylated active fragment and its tryptic peptides. To aid in the alignment of some tryptic peptides, the partial sequences of two fragments obtained by selective tryptic cleavage of the reactive site peptide bond of inhibitor IIa at acidic pH, with subsequent reduction and carboxymethylation, were also analyzed. The active fragment consisted of 45 amino acid residues including 6 half-cystine residues. Degradation of the intact active fragment by subtilisin [EC 3.4.21.14.] at pH 6.5. yielded 3 cystine-containing peptides. Sequence analyses of these peptides revealed that the 3 disulfide linkages were located between Cys(10) and Cys(24), Cys(14) and Cys(35), and Cys(20) and Cys(43). The reactive site peptide bond of inhibitor IIa, a Lys-Ser bond, was located between positions 32 and 33 of the active fragment. The overall sequence of the active fragment was quite different from those of potato chymotrypsin inhibitor I (subunit A) and potato carboxypeptidase inhibitor.

Amino Acid Sequence↗
PubMed1977

Amino acid sequence of an active fragment of potato proteinase inhibitor IIb.

The amino acid sequence of an active fragment of potato proteinase inhibitor IIb was determined by the Edman degradation procedure and the carboxypeptidase technique. Analyses were carried out on peptides derived from the reduced and carboxymethylated active fragment by digestion with trypsin and chymotrypsin. The active fragment consisted of a single polypeptide chain of 40 amino acid residues including 6 half-cystine residues. Degradation of the intact active fragment by trypsin and subtilisin at pH 6.3--6.4 yielded 3 cystine-containing peptides, and sequence analyses of these peptides revealed that the three disulfide linkages are located between Cys(2) and Cys(16), Cys(6) and Cys(28), and Cys(12) and Cys(38). The reactive site peptide bond of inhibitor IIb, a Lys-Ser bond, is located between positions 26 and 27. The overall sequence of the active fragment is compared with that of an active fragment of inhibitor IIa and the "structure-specificity" relationships of both are discussed. Correlation of the fragments to a naturally-occurring low molecular weight inhibitor is also discussed.

Amino Acid Sequence↗
PubMed2002

An engineered IN-1 F(ab) fragment with improved affinity for the Nogo-A axonal growth inhibitor permits immunochemical detection and shows enhanced neutralizing activity.

The myelin axonal growth inhibitor NI-220/250 (Nogo-A) has attracted considerable attention in elucidating the mechanisms that account for the lack of plasticity in the adult central nervous system. The cognate monoclonal antibody IN-1, which was obtained prior to the molecular characterization of its Nogo-A antigen, has played a crucial role in this respect. However, this murine IgM/kappa antibody does not only provide an inappropriate format for in vivo studies, its low antigen affinity has also hampered the thorough structure-function analysis of its neutralizing effect toward the Nogo-A inhibitor on a molecular basis. We describe here the affinity maturation of a bacterially produced functional IN-1 F(ab) fragment via protein engineering. A soluble fragment of Nogo-A derived from the central exon 3 of its gene, which was prepared by secretion into the periplasm of Escherichia coli, served as a target in these experiments. After repeated cycles of site-directed random mutagenesis and screening, the mutant II.1.8 of the IN-1 F(ab) fragment was obtained, carrying five side chain substitutions within CDR-L3. Its dissociation constant for the complex with the recombinant Nogo-A fragment was determined in surface plasmon resonance measurements as approximately 1 microM. The affinity of the unmutated IN-1 F(ab) fragment was 8-fold lower. The engineered F(ab) fragment appeared to be well suited for the specific detection of Nogo-A in immunochemical assays and for the histochemical staining of myelin-rich tissue sections. Most importantly, its concentration-dependent neutralizing effect on the Nogo-A inhibitory activity was significantly enhanced in cell culture. This study confirms Nogo-A to be the antigen of the IN-1 antibody and it demonstrates increased potential of the engineered F(ab) fragment as a reagent for promoting axonal regeneration in vivo.

Amino Acid Substitution↗
PubMed1995

Introduction of lysine residues on the light chain constant domain improves the labelling properties of a recombinant Fab fragment.

Europium chelates provide a non-radioactive alternative for sensitive labelling of antibodies for diagnostic immunoassays. Lysine residues at antibody surfaces are ready targets for labelling by an isothiocyanate derivative of the europium chelate (Eu3+). Here the labelling efficiency of a recombinant anti-human alpha-fetoprotein (hAFP) Fab fragment has been improved by increasing its lysine content by protein engineering. Molecular modelling was used to identify three light chain constant domain surface arginine residues, R154, R187 and R210, which were mutated to lysine residues. The mutations did not influence the affinity of the lysine-enriched Fab fragment and its labelling efficiency was found to be approximately 40% higher than that of the wild-type Fab fragment. With low degree of labelling, the affinities of the two Fab fragments were identical and comparable with that of the original monoclonal anti-hAFP IgG. With a higher degree of labelling the affinities of both Fab fragments decreased more than that of the intact IgG since more lysine residues are available for labelling in the additional heavy chain constant domains of the larger molecule. Electrostatic adsorption and covalent immobilization of the Fab fragments were characterized by BIAcore and the lysine-enriched Fab fragment was found to be more efficiently immobilized to an activated carboxymethyl surface.

Amino Acid Sequence↗
PubMed2005

Functional humanization of an anti-CD30 Fab fragment for the immunotherapy of Hodgkin's lymphoma using an in vitro evolution approach.

CD30, the so-called Reed-Sternberg antigen, constitutes a promising cell-specific target for the treatment of Hodgkin's lymphoma. Starting from the previously characterized cognate HRS3 mouse monoclonal antibody, the bacterially produced functional Fab fragment was humanized by grafting the CDRs from the mouse antibody framework on to human immunoglobulin consensus sequences. This procedure led to a 10-fold decreased antigen affinity, which surprisingly was found to be mainly due to the VH domain. To improve the antigen-binding activity, an in vitro evolution strategy was employed, wherein random mutations were introduced into the humanized VH domain by means of error-prone PCR, followed by a filter sandwich Escherichia coli colony screening assay for functional Fab fragments using a recombinant extracellular domain of the CD30 antigen. After three cycles of in vitro affinity maturation, the optimized Fab fragment huHRS3-VH-EP3/1 was identified, which carried four exchanged residues within or close to the VH CDRs and had an affinity that was almost identical with that of the murine HRS3 Fab fragment. The resulting humanized Fab fragment was fully functional with respect to CD30 binding both in ELISA with the recombinant antigen and in FACS experiments with CD30-positive L540CY cells. In the light of the previously successful clinical application of an alphaCD30 x alphaCD16 bispecific mouse quadroma antibody derived from HRS3, the humanized Fab fragment comprises an important step towards the construction of a fully recombinant therapeutic agent. The combination of random mutagenesis and colony filter screening assay that was successfully applied here should be generally useful as a method for the rapid functional optimization of humanized antibody fragments.

Amino Acid Sequence↗
PubMed1995

Biodistribution of murine and chimeric Fab fragments of the monoclonal antibody A7 in human pancreatic cancer.

Much recent research has focused on the use of monoclonal antibodies (MAbs) in the immunodetection of solid tumors. Fab fragments of MAbs are more suitable for immunoscintigraphy than intact MAbs. Recently, human-mouse chimeric antibodies have been developed in an effort to reduce human antimouse antibody (HAMA) production by murine MAbs in humans. In this study, 125I-labeled murine and chimeric Fab fragments of the MAb A7 were injected i.v. into nude mice bearing a human pancreatic cancer (HPC-YS) xenograft. The radioactivity in tumors and in normal tissues was subsequently measured. The tumor tissue/blood ratio (T/B) of 125I-labeled murine and chimeric Fab fragments of MAb A7 increased with time in a similar manner and reached 9.68 +/- 2.54 and 10.49 +/- 1.50, respectively, 24 h after injection. Moreover, the T/Bs of 125I-labeled murine and chimeric Fab fragments of MAb A7 were greater than the T/B of intact MAb A7. When mice bearing tumors that did not react with MAb A7 were studied, 125I-labeled murine and chimeric Fab fragments did not localize specifically to the tumors. These results suggests that chimeric Fab fragments of MAb A7 are useful carriers of radionuclides for the immunodetection of human pancreatic cancer, with equivalent activity to murine Fab fragments and less theoretical potential to induce a HAMA response.

Animals↗
PubMed1996

Restriction fragment length polymorphism of genes of the alpha 2(XI) collagen, bone morphogenetic protein-2, alkaline phosphatase, and tumor necrosis factor-alpha among patients with ossification of posterior longitudinal ligament and controls from the Japanese population.

STUDY DESIGN: The present study analyzed the restriction fragment length polymorphism patterns of alpha 2(XI) collagen, bone morphogenetic protein-2, alkaline phosphatase, and tumor necrosis factor-alpha genes in patients with ossification of the posterior longitudinal ligament. This study investigates the genetic polymorphism of bone-induced factors in patients with ossification of the posterior longitudinal ligament and compares it with healthy control subjects. OBJECTIVES: To clarify the genetic markers linked to ossification of the posterior longitudinal ligament. SUMMARY OF BACKGROUND DATA: Ossification of the posterior longitudinal ligament is a genetic disease associated with abnormal calcium metabolism involving the posterior longitudinal ligament. Previous genetic studies have not identified the pathologic mechanism of ossification of the posterior longitudinal ligament. Histopathologic studies of ossification of the posterior longitudinal ligament and the animal model, the spinal hyperostotic mouse, have revealed an increase in Type XI collagen and bone morphogenetic protein-2 expression. METHODS: Eighteen Japanese patients with ossification of the posterior longitudinal ligament and 51 healthy, unrelated control subjects were investigated for the restriction fragment length polymorphism patterns of COL11A2, bone morphogenetic protein-2, alkaline phosphatase, and tumor necrosis factor-alpha, genes with various restriction endonucleases. RESULTS: The gene frequencies of COL11A2 obtained with BamHl (10.0 kb fragment) and HindIII (19.0 kb fragment) observed in patients with ossification of the posterior longitudinal ligament were higher compared with control subjects (0.43 and 0.14, respectively). These differences were statistically significant (BamHl P = 0.018; Hindlll P = 0.046). Two new restriction fragment length polymorphism patterns were detected of the bone morphogenetic protein-2 gene with Mspl and Taql and one already known restriction fragment length polymorphism pattern of the tumor necrosis factor-alpha gene with Ncol. However, they were not significantly different from the control subjects. CONCLUSIONS: Seven restriction fragment length polymorphisms of COL11A2 gene were identified. Two of them (BamHl, 10.0/10.0 kb genotype; HindIII, 19.0/19.0 kb genotype) were significantly different in patients with ossification of the posterior longitudinal ligament.

Alkaline Phosphatase↗
PubMed1990

Anti-CD3 F(ab')2 fragments are immunosuppressive in vivo without evoking either the strong humoral response or morbidity associated with whole mAb.

The use of anti-CD3 monoclonal antibodies to treat organ allograft rejection has been complicated by (1) the morbidity associated with the initial dose, (2) the humoral response of the patients against the mAbs, and (3) the generalized immunosuppression induced by the mAbs. We investigated the potential of F(ab')2 fragments of the anti-murine-CD3 mAb, 145-2C11, to avoid these complications in the murine model. Both whole mAb and F(ab')2 fragments induced T cell depletion. However, injection of F(ab')2 fragments of anti-CD3 mAb did not cause T cell activation, and did not induce the morbidity and mortality observed following injection of whole mAb. The humoral response against the F(ab')2 fragments was significantly reduced compared with the response against the whole mAb. Furthermore, repeated administration of F(ab')2 fragments of anti-CD3 mAb resulted in prolongation of allogeneic skin graft survival superior to that seen following treatment with a single dose of whole mAb. Finally, while T cells from mice treated with whole mAb displayed profound suppression of in vitro CTL generation, T cells from mice treated with F(ab')2 fragments had significant in vitro CTL function. These results suggest that the use of F(ab')2 fragments of anti-CD3 mAb may offer significant advantages over whole mAb for the induction and maintenance of immunosuppression.

Animals↗
PubMed1994

T cell-stimulatory fragments of foot-and-mouth disease virus released by mild treatment with cathepsin D.

Cathepsin D and cathepsin B are endosomal/lysosomal proteases that are thought to play a role during in vivo antigen processing, releasing fragments for binding to major histocompatibility complex class II products and subsequent presentation to T cells. Here we treated purified foot-and-mouth disease virus (FMDV) strain A10Holland with both enzymes. Cathepsin D, but not cathepsin B, was shown to release fragments from reduced or non-reduced FMDV under mild conditions in vitro. Twenty-eight predominant cathepsin D-released fragments were purified by HPLC and identified by amino acid composition analysis and sequencing. The unseparated set of fragments produced (the digest) was able to stimulate T cells from eight vaccinated cattle. With respect to the response to intact virus the extent of the response to the digest differed between animals: four animals could be classified as good responders, three as intermediate responders and one as a low responder. Subsequently, we investigated the proliferative T cell response to a large set of synthetic peptides in detail for two animals, one belonging to the group of good responders, the other being the low responder. The peptides covered all 28 cathepsin D-released fragments analysed and also several sequences not recovered from the digest. In this way seven T cell sites could be identified, five of which coincided with cathepsin D-released fragments. The other two T cell sites were VP2[54-72], being a homologue of a T cell site identified for FMDV strain O1K and the N terminus of VP4. Whether the most dominantly recognized T cell site was recovered from the digest or not was shown to be related to the good or low response to the digest. These findings suggest a role for cathepsin D in the release of some but not all T cell-stimulatory fragments from FMDV.

Amino Acid Sequence↗
PubMed2003

Reducing the computational complexity of protein folding via fragment folding and assembly.

Understanding, and ultimately predicting, how a 1-D protein chain reaches its native 3-D fold has been one of the most challenging problems during the last few decades. Data increasingly indicate that protein folding is a hierarchical process. Hence, the question arises as to whether we can use the hierarchical concept to reduce the practically intractable computational times. For such a scheme to work, the first step is to cut the protein sequence into fragments that form local minima on the polypeptide chain. The conformations of such fragments in solution are likely to be similar to those when the fragments are embedded in the native fold, although alternate conformations may be favored during the mutual stabilization in the combinatorial assembly process. Two elements are needed for such cutting: (1) a library of (clustered) fragments derived from known protein structures and (2) an assignment algorithm that selects optimal combinations to "cover" the protein sequence. The next two steps in hierarchical folding schemes, not addressed here, are the combinatorial assembly of the fragments and finally, optimization of the obtained conformations. Here, we address the first step in a hierarchical protein-folding scheme. The input is a target protein sequence and a library of fragments created by clustering building blocks that were generated by cutting all protein structures. The output is a set of cutout fragments. We briefly outline a graph theoretic algorithm that automatically assigns building blocks to the target sequence, and we describe a sample of the results we have obtained.

Algorithms↗
PubMed1975

Neutralizing activities of early and late IgG fragments from rabbits immunized with herpes simplex virus.

Rabbits immunized with herpes virus were bled periodically and bivalent and univalent fragments of IgG from each serum sample were prepared by enzymatic digestion. The 2-week F(ab')2 showed a low neutralizing activity only after addition of anti-IgG. F(ab')2 of the 4-week serum retained almost all of the neutralizing activity of IgG, while its univalent fragments demonstrated none even when tested with anti-IgG. In contrast to these early IgG fragments, univalent fragments of the 9-week and 20-week IgG neutralized the virus to considerable extents in the absence of anti-IgG; after addition of anti-IgG the activity equaled that of intact IgG in the cases of Fab' and Fab-II, though the activity of Fab-I was relatively low. Three three univalent fragments were all sensitive to heating at 70 C and to ultraviolet irradiation, whereas intact IgG resisted these treatments. F(ab')2 was resistant to the heating and less sensitive to ultraviolet irradiation than univalent fragments. Neutralization kinetic curve experiments to test blocking effects of IgG fragments against the neutralization by intact IgG suggested that the early Fab' did combine with the virus and that the late Fab' exerted a higher blocking effect than the early Fab'.

Animals↗
PubMed1994

Development and characterization of chimeric anti-carcinoembryonic antigen monoclonal antibodies and their Fab fragments.

In an attempt to reduce the immunogenicity of two different murine anti-carcinoembryonic antigen (CEA) monoclonal antibodies (MAbs), KM10 and A10, we produced recombinant mouse/human chimeric MAbs and the respective Fab fragments carrying the variable regions of the murine MAbs. Chimeric A10 Fab fragment was expressed in Escherichia coli, and produced in large quantities in a mini-jar fermentation system. In competitive binding assays, chimeric MAbs and their Fab fragments showed identical specificity to human CEA epitopes, as compared to the parental MAbs or Fab fragments. Both chimeric Fab fragments exhibited strong immunohistochemical reactivity with various gastrointestinal carcinomas and no reactivity with CEA-related antigens, such as NCA (nonspecific cross-reacting antigen) or BGPI (biliary glycoprotein I). Furthermore, chimeric KM10 MAb elicited substantially higher antibody-dependent cellular cytotoxicity than the murine MAb. Complement-dependent cytotoxicity in vitro was much weaker with chimeric KM10 MAb. These results indicate that chimeric MAbs or Fab fragments could potentially replace the parental murine antibodies or their Fab fragments in therapy or diagnosis of human gastrointestinal carcinomas.

Animals↗
PubMed1988

Expression of a biologically active diphtheria toxin fragment B in Escherichia coli.

The toxB gene of Corynebacterium diphtheriae bacteriophage beta encoding the B fragment of diphtheria toxin was cloned into an inducible expression vector. When expressed in Escherichia coli, fragment B was not proteolysed and was indistinguishable, by immunological criteria, from wild-type C. diphtheriae-derived fragment B. Soluble fragment B was partially purified from the cytoplasm by saline precipitation steps and was shown to compete with the wild-type diphtheria toxin for binding to receptors of sensitive eukaryotic cells. A complete diphtheria toxin was reconstituted by formation of the disulphide bridge between purified fragment A and recombinant fragment B, which migrates at the expected Mr on Western blots and which was able to block protein synthesis by ADP-ribosylation of elongation factor-2, thereby indicating that the recombinant fragment B had retained its biological activity.

Animals↗
PubMed1978

Studies on IgM polymerization: reassociation to non-covalently and covalently linked Fc5mu fragments.

Fc5mu fragments were purified from a trypsin digest of native IgM by gel filtration and isoelectric focusing. Polyacrylamide gel electrophoresis of Fc5mu fragments in sodium dodecyl sulphate disclosed a major and a minor band with molecules of 320,000 and 285,000 daltons, respectively. The mu chain fragments showed a molecular weight of 34,500. After reduction of the Fc5mu fragments to free mu chain fragments and J chain removal of the reducing agent by dialysis for 24 h under nitrogen in the presence of Zn ions gave non-covalently linked Fc5mu fragments. This shows that the non-covalent interactions operating between the mu chains of non-covalently linked native IgM are present in the C-terminal part of the mu chains. Additional dialysis in the presence of Zn and Cu ions resulted in the formation of covalently linked Fc5mu fragments.

Alkylation↗
PubMed1985

Binding of human IgA fragments to protein A-Sepharose studied with an ELISA method.

An enzyme-linked immunosorbent assay method was developed to investigate the binding of IgA fragments to protein A. The method proved to be specific and highly sensitive. Contamination with IgG did not interfere with the detection of IgA binding to protein A, and less than 10 ng of IgA could be detected. Four of nine IgA proteins tested bound to protein A to different extents. The binding was not disturbed by reduction and alkylation of the IgA proteins. Four-chain F(abc)2 and F(ab')2 fragments of the protein A-reactive IgA proteins also bound to protein A. On reduction and alkylation these fragments formed two-chain Fabc and Fab' fragments. Of these, Fabc did not bind, whereas both Fab' and IgA1-protease-produced Fab fragments did bind to protein A. These results demonstrate that the Fab fragment has a binding site for protein A. It is suggested that the protein A binding site is located on the CH1 domain of the IgA1 molecule. On Fabc fragments this binding site may be blocked because of structural alterations.

Binding Sites, Antibody↗
PubMed1983

Domain characteristics of the cyanogen bromide fragment 121-316 of thermolysin.

The molecule of thermolysin was shown by X-ray crystallography to be composed of two structural domains of equal size comprising residues 1-157 and 158-316. In order to explore the possibility that these domains correspond to globular fragments able to refold autonomously, we have investigated the conformational and stability properties of fragment 121-316, which was obtained by limited chemical cleavage of thermolysin with cyanogen bromide. As judged by far-ultraviolet circular dichroism measurements, in aqueous solution under neutral conditions the fragment maintains a relative amount of helical structure which is comparable to that exhibited by the corresponding region in native thermolysin. The secondary structure attained by the fragment appears remarkably stable to the denaturing action of heat. By measuring the temperature dependence of the dichroic signal at 220 nm a Tm near 74 degrees was obtained. Immunodiffusion analyses indicated that the fragment recognizes and precipitates antibodies raised in rabbits using native thermolysin as immunogen. The overall conformational and immunochemical data indicate that fragment 121-316 of thermolysin is able to refold into a stable structure of native-like characteristics independently of the rest of the molecule. The results of this study complement those previously reported for fragment 206-316 (Vita, C., Fontana, A., Seeman, J.R. & Chaiken, I.M. (1979) Biochemistry 18, 3023-3031).

Amino Acids↗