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D R Bundle

Publications and source records attributed to D R Bundle.

At least 37 records · Page 2Linked to original sources
PubMed1996

Synthesis and conformational studies of the tyvelose capped, Lewis-x like tetrasaccharide epitope of Trichinella spiralis.

Chemical synthesis and high resolution NMR studies are reported for the tetrasaccharide epitope and constituent structures that occur as terminal elements of Trichinella spiralis cell surface glycans. The 2-(trimethylsilyl)ethyl and methyl glycosides of Lewis-x type trisaccharides, in which beta GalNAc replaces beta Gal were synthesized from monosaccharide synthons utilizing thioglycoside and halide-ion glycosylation methods. The unique 3,6-dideoxy-beta-D-arabinohexopyranosyl residue that caps the structure was introduced to selectively protected 2-(trimethylsilyl)ethyl and methyl trisaccharide glycosides by utilizing an insoluble silver zeolite catalyst and a glycosyl halide. In separate reactions not only were the principal targets obtained but also the corresponding alpha-linked tetrasaccharides. A comparison of the NMR spectra of the methyl tetrasaccharide glycosides showed that at the site of the alpha-linked tyvelose structure, specific GalNAc resonances (C-1, C-2, C-3) possess uncharacteristically wide 13C (8-21 Hz) and 1H lines. The beta-linked tetrasaccharide glycoside, that represents the native parasite epitope, exhibited only narrow line widths (3 Hz, 13C). Since NOE derived distance constraints for the alpha-linked tyvelose structure were not consistent with the existence of unusual glycosidic conformers, the origin of the limited number of wide lines was attributed to local rigidity in the GalNAc residue, at the site of tyvelose glycosylation.

Animals↗
PubMed1995

Expression of a recombinant human glycosyltransferase from a synthetic gene and its utilization for synthesis of the human blood group B trisaccharide.

A 1034-bp synthetic gene encoding the human blood group B glycosyltransferase, which catalyzes the transfer of galactose from UDP-Gal to Fuc alpha(1-2)Gal beta-OR to give the blood group B determinant Gal alpha(1-3)[Fuc alpha(1-2)]Gal beta-OR (where R is a glycoprotein or glycolipid), has been expressed in Escherichia coli by replacing its membrane-anchoring domain with an ompA bacterial secretory signal. The active enzyme was purified from the periplasm using UDP-hexanolamine affinity chromatography and used in the synthesis of preparative amounts of the human blood group B trisaccharide antigen. The substrate specificity and kinetics of the recombinant enzyme were comparable to the enzyme from human sera. Thus we have achieved the construction of a completely synthetic glycosyltransferase gene and its successful expression.

ABO Blood-Group System↗
PubMed1995

Basis for selection of improved carbohydrate-binding single-chain antibodies from synthetic gene libraries.

A technique is described for the simultaneous and controlled random mutation of all three heavy or light chain complementarity-determining regions (CDRs) in a single-chain Fv specific for the O polysaccharide of Salmonella serogroup B. Sense oligonucleotides were synthesized such that the central bases encoding a CDR were randomized by equimolar spiking with A, G, C, and T at a level of 10% while the antisense strands contained inosine in the spiked regions. Phage display of libraries assembled from the spiked oligonucleotides by a synthetic ligase chain reaction demonstrated a bias for selection of mutants that formed dimers and higher oligomers. Kinetic analyses showed that oligomerization increased association rates in addition to slowing dissociation rates. In combination with some contribution from reduced steric clashes with residues in heavy-chain CDR2, oligomerization resulted in functional affinities that were much higher than that of the monomeric form of the wild-type single-chain Fv.

Amino Acid Sequence↗
PubMed1995

Long-range 4J and 5J, including interglycosidic correlations in gradient-enhanced homonuclear COSY experiments of oligosaccharides.

Gradient-enhanced, two-dimensional, homonuclear correlation techniques (GCOSY) of carbohydrates provide numerous correlations based on 4J and 5J long-range interactions. Intraresidue correlations, involving all 1H resonances of a given pyranose ring with its anomeric proton, are consistently observed in alpha-pyranosyl residues at approximately 5 to 10 times lower intensities than vicinal 3J correlation cross peaks. beta-Anomers, pyranosyl residues with axial H1 protons, show very few such effects. Both alpha and beta anomers do, however, exhibit interresidue 4J correlations across the glycosidic linkage as shown for several linear and branched oligosaccharides ranging from three to five residues and are especially useful for spectral assignments in the envelope of pyranosyl ring protons located in the typically very crowded 3 to 4 ppm region. These effects depend on the strength and duration of the applied gradients.

Carbohydrates↗
PubMed1995

Bifunctional fusion proteins consisting of a single-chain antibody and an engineered lanthanide-binding protein.

The combination of an antibody fragment with a lanthanide chelating protein has desirable characteristics for fluorescence-based immunoassays and tumor radioimmunotherapy. As a model for this design, a fusion protein consisting of a single-chain antibody linked to an engineered version of oncomodulin, a protein with two Ca(2+)-binding motifs (the CD and EF loops), was produced by secretion from Escherichia coli in good yield. The single-chain antibody was specific for a Salmonella O-polysaccharide. The CD loop of oncomodulin had been redesigned to bind lanthanide ions with high affinity. The fusion protein was shown to have antigen-binding activity that was comparable to that of the unfused single-chain antibody, to bind Tb3+ with very high affinity and to give strong, sensitized Tb3+ luminescence via excitation of the tryptophan residue in the CD loop. A second fusion protein containing a 30-residue helix-loop-helix motif as the lanthanide-binding component was also prepared, but showed considerably lower solubility. Competition for Tb3+ binding by a series of metal chelators indicated that the affinities of the oncomodulin and 30 residue fusions for Tb3+ were approximately 10(11) M-1 and 10(7) M-1, respectively. Time-resolved lanthanide luminescence photography of electrophoresis gels demonstrated that the helix-loop-helix Ca(2+)-binding could be used to specifically visualize the scFv fragment.

Amino Acid Sequence↗
PubMed1994

Exploring the mimicry of polysaccharide antigens by anti-idiotypic antibodies. The crystallization, molecular replacement, and refinement to 2.8 A resolution of an idiotope-anti-idiotope Fab complex and of the unliganded anti-idiotope Fab.

The monoclonal antibody YsT9.1 is specific for the lipopolysaccharide A antigen of Brucella abortus. A complex formed between the Fab of YsT9.1 (Ab1) and the Fab of its antidiotopic monoclonal antibody T91AJ5 (Ab2) has been crystallized, and data have been collected to 2.8 A resolution. The space group is monoclinic P2(1), with one molecule per asymmetric unit. The structure was solved using a limited Patterson-correlation search over the asymmetric-unit of rotation space, and has been refined to an R-factor of 0.174. The complex is a head-to-head dimer, with the contact between the two Fabs almost completely restricted to their hypervariable loops. The interactions between the two Fabs in the complex are dominated by tyrosine residues, not only in the formation of hydrogen bonds, but in their participation in an aromatic ring network that spans the two Fv domains. The anti-idiotope was found to be unable to carry an internal image of the antigen and induce polysaccharide-specific "anti-anti-idiotopes" (Ab3) because the polysaccharide binding cleft on the Ab1 is too narrow and deep to allow comprehensive contact with the binding site of Ab2. The antibody T91AJ5 therefore is a class gamma anti-idiotope. The contact surfaces of the two Fabs are highly complementary; however, they are distinctly different in character. Each Fab has two separate binding surfaces of approximately equal size, but while the two binding surfaces of Ab1 are partitioned between the light and heavy chains, the two binding surfaces of Ab2 are shared between the chains, with the heavy chain responsible for about 60% of the total binding area. The structure of the unliganded Fab of Ab2 has also been solved by molecular replacement, and refined to an R-factor of 0.152 at 2.8 A resolution. This Fab crystallizes in the orthorhombic space group P2(1)2(1)2(1), with one molecule per asymmetric unit. The second hypervariable loop of the heavy chain of the Ab2 Fab is observed to undergo a significant and necessary conformational rearrangement in going from the unliganded to complexed form, and thus complex formation is an example of "induced fit" of antigen to antibody. The unliganded Ab1 Fab packs in the standard head-to-tail fashion observed for other Fabs. This mode of packing is precluded in the complex, by its head-to-head nature, and it is found to pack in tilted layers with most intermolecular contacts made between adjacent Ab2 Fab molecules.(ABSTRACT TRUNCATED AT 400 WORDS)

Antibodies, Anti-Idiotypic↗
PubMed1994

Structure of a single-chain antibody variable domain (Fv) fragment complexed with a carbohydrate antigen at 1.7-A resolution.

We describe here the 1.7-A resolution structure of a single-chain antibody variable domain (scFv) molecule, based on the carbohydrate-binding antibody Se155-4, complexed with the trisaccharide ligand alpha-D-Gal(1-->2)[alpha-D-Abe(1-->3)]alpha-D-Manp1-->OMe, where Abe is abequose. The scFv expressed in Escherichia coli has the variable region light chain to heavy chain polarity with the domains connected by a 19-residue linker. Although the linker is partially disordered in the crystal, the packing of the molecules suggests a monomeric state of the scFv. The carbohydrate adopts a different conformation about the Man-Gal linkage than was observed previously in the Fab-trisaccharide complex. Instead of a direct hydrogen bond between O2Abe and O2Gal, these two atoms are bridged by a water molecule in the present complex.

Amino Acid Sequence↗
PubMed1994

Molecular recognition of a Salmonella trisaccharide epitope by monoclonal antibody Se155-4.

The binding site of monoclonal antibody Se155-4, which has been the object of successful crystallographic and antibody-engineering studies, is shown by solid-phase immunoassays to be complementary to a branched trisaccharide, alpha-D-Galp(1-->2) [alpha-D-Abep(1-->3)]-alpha-D-Manp(1, rather than to the tetrasaccharide repeating unit alpha-D-Galp(1-->2) [alpha-D-Abep(1-->3)]-alpha-D-Manp(1-->4) alpha-L-Rhap(1- of the bacterial antigen. Specificity for the 3,6-dideoxy-D-xylo-hexose (3,6-dideoxy-D-galactose) epitope present in Salmonella paratyphi B O-antigens was ensured by screening hybridoma experiments with glycoconjugates derived from synthetic oligosaccharides. Detailed epitope mapping of the molecular recognition by modified and monodeoxy oligosaccharide derivatives showed that complementary surfaces and three antibody-saccharide hydrogen bonds are essential for full binding activity. Both hydroxyl groups of the 3,6-dideoxy-D-galactose residue were obligatory for binding and consistent with the directional nature of their involvement in carbohydrate-protein hydrogen bonds; related tetrasaccharides built from the isomeric 3,6-dideoxyhexoses, 3,6-dideoxy-D-glucose, paratose, and 3,6-dideoxy-D-mannose, tyvelose were not bound by the antibody. Titration microcalorimetry measurements were consistent with the hydrogen-bonding map inferred from the crystal structure and suggest that the displacement of water molecules from the binding site accounts for the favorable entropy that accompanies binding of the native trisaccharide determinant. The protein sequences determined for the antibody VL and VH domains reveal somatic mutation of the VL germ line gene, implying that this antibody-binding site results from a mature antibody response.

Amino Acid Sequence↗
PubMed1994

Solution structure of a trisaccharide-antibody complex: comparison of NMR measurements with a crystal structure.

NMR and crystallography have been used to study antigen conformational changes that occur in a trisaccharide-Fab complex in solution and in the solid state. NOE buildup rates from transferred NOE experiments show that the antigenic determinant of a Salmonella lipopolysaccharide, represented by the trisaccharide methyl glycoside alpha-D-Galp(1-->2 [alpha-D-Abep(1-->3)]- alpha-D-Manp1-->OMe (1), undergoes a protein-induced conformational shift about the Gal-->Man glycosidic linkage when it is bound by a monoclonal antibody in aqueous solution. The same trisaccharide was crystallized with Fab, and a solved structure at 2.1-A resolution revealed that the conformation of the trisaccharide ligand was similar to that seen in a dodesaccharide-Fab complex [Cygler et al. (1991) Science 253, 442-445), where the Gal-Man linkage also experienced a similar conformational shift. Distance constraints derived from the TRNOE buildup curves are consistent with two bound trisaccharide conformations, one of which correlates with the ligand conformation of the crystalline Fab-trisaccharide complex. In this bound conformation, short interatomic distances between Abe O-2 and Gal O-2 permit an oligosaccharide intramolecular hydrogen bond. Despite its relatively low energy, a preponderance of this conformer could not be detected in aqueous or DMSO solutions of free trisaccharide by either 1H or 13C NMR experiments. In DMSO, a different intramolecular hydrogen bond between Abe O-2 and Man O-4 was observed due to a solvent-induced shift in the conformational equilibria (relative to aqueous solution). Molecular modeling of the trisaccharide in the binding site and as the free ligand suggested that the protein imposes an induced fit on the antigen, primarily resulting in a shift of the Gal-Man phi torsional angle. This reduces the interproton separation between Abe H-3 and Gal H-1 with a marked increase in the intensity of the previously weak NOEs between the protons of the noncovalently linked galactose and abequose residues. The impact of the conformational shift on gross trisaccharide topology is sufficiently small that binding modes inferred from functional group replacements are not impaired.

Antibodies, Monoclonal↗
PubMed1994

Selection of antibody single-chain variable fragments with improved carbohydrate binding by phage display.

A single-chain variable fragment (Fv) version of a murine monoclonal antibody, Se155-4, specific for Salmonella serogroup B O-polysaccharide, was used as a model system for testing monovalent phage display as a route for enhancing the relatively low affinities that typify anti-carbohydrate antibodies. Random single-chain Fv mutant libraries generated by chemical and error-prone polymerase chain reaction methods were panned against the serogroup B lipopolysaccharide. Panning of a randomly mutated heavy chain variable domain library indicated selection for improved serogroup B binders and yielded six mutants, five of which showed wild type activity by enzyme immunoassay. Two of these were apparently selected on the basis of better functional single-chain Fv yield in Escherichia coli. A heavy chain mutation (Ile77-->Thr) in one mutant, 3B1, appeared to have a particularly dramatic effect, resulting in yields of approximately 120 mg/liter of functional periplasmic product. The sixth mutant, 4B2, had complementarity determining region 1 (CDR1) and CDR2 mutations and demonstrated 10-fold improved binding, by enzyme immunoassay, relative to the wild type. Extensive analysis of antigen-antibody interactions indicated that the improved binding properties of 4B2 were attributable to a higher association rate constant and interaction with an epitope that is larger than the trisaccharide recognized by the wild type. None of the mutations involved known trisaccharide contact residues; this was consistent with analysis of wild type and mutant single-chain Fvs by titration microcalorimetry. Examination of the structure indicated that two mutations in the heavy chain CDR2 provided improved surface complementarity between the protein and the extended epitope encompassing 2 additional hexose residues. However, introduction of only the CDR2 mutations into the wild type structure failed to confer the improved binding properties of 4B2, indicating an indirect effect by the more distant mutations. Panning of randomly mutated light chain variable domain and full-length single-chain Fv mutant libraries did not yield mutants with improved assembly or binding properties.

Antibodies, Monoclonal↗
PubMed1994

Modulation of antibody affinity by synthetic modifications of the most exposed pyranose residue of a trisaccharide epitope.

When the Salmonella trisaccharide epitope, methyl 3-O-(3,6-dideoxy-alpha-D-xylo-hexopyranosyl)-2-O-(alpha-D-galactopyra nos yl)- alpha-D-mannopyranoside 12 is bound by a monoclonal antibody Se155.4, the 3,6-dideoxy-alpha-D-hexose is completely buried, while the galactopyranosyl mannopyranosyl units lay across the protein surface. Crystallography of an antibody complexed with 12 also shows that the galactose residue is the most exposed saccharide. A simplified strategy to synthesize 12 and analogues modified at the galactose residue is described. Monosaccharide building blocks containing benzyl ether and ester protecting groups were used for efficient assembly of trisaccharides that can be deprotected by a single hydrogenolysis step, or occasionally preceded by a transesterification stage. Glycosylation of methyl 2-O-benzoyl-4,6-di-O-benzyl-alpha-D- mannopyranoside 4 by 2,4-di-O-benzyl-3,6-dideoxy-D-xylo-hexopyranosyl chloride 8 affords after transesterification the disaccharide acceptor 10. This disaccharide serves as a universal acceptor for glycosylation by glycosyl donors that lead, following facile deprotection, to the alpha- and beta-D-galacto, alpha- and beta-D-gluco, and 2-amino-2-deoxy-alpha-D-galacto trisaccharides 12, 14, 17, 18 and 21. Only a small change in binding energy delta (delta G) occurs when the alpha-D-galactopyranosyl residue of 12 is replaced by either an alpha-D-glucopyranosyl 17 or a 2-amino-2-deoxy alpha-D-galactopyranosyl unit 21. Whereas binding of the beta-D-glucopyranose congener 18 was tolerated by the antibody, the beta-D-galactopyranose analogue 14, showed a 250 fold loss of affinity.(ABSTRACT TRUNCATED AT 250 WORDS)

Antibodies, Monoclonal↗
PubMed1994

Effect of C lambda-C kappa domain switching on Fab activity and yield in Escherichia coli: synthesis and expression of genes encoding two anti-carbohydrate Fabs.

We have used a strategy of hybrid gene synthesis and constant domain shuffling to construct and functionally express in Escherichia coli genes encoding two anti-carbohydrate Fabs, one specific for a Brucella cell-surface polysaccharide and the second for the human blood group A determinant. Very similar VL amino acid sequences made possible the simultaneous synthesis of the two corresponding genes. A class switching approach was used in Fd and light chain gene assembly. The two independently synthesized VH genes were fused to a previously made sequence encoding the C(gamma 1)1 domain as an alternative to synthesis of the natural C gamma 2b 1 and C mu 1 sequences. The VL genes were initially coupled to a synthetic C kappa gene. When these light chain and the above Fd genes, each preceded by the ompA signal sequence, were expressed from two-cistron DNA, yields of functional periplasmic Fab were low and, in each instance, limited by light chain availability. Replacement of the C kappa domains with a C lambda 1 domain resulted in a significant increase in the amount of soluble periplasmic light chain and functional Fab for both the Brucella and blood group A antibodies. The C kappa and C lambda 1 forms of each of the Brucella and blood group A Fabs, with His5 fusions at the C-termini of the Fd chains, were purified by immobilized metal affinity chromatography.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1993

Synthesis of chlorodeoxy trisaccharides related to the Shigella flexneri Y polysaccharide.

Chloromethoxylation of di-O-acetyl-L-rhamnal has been employed as a convenient route to methyl 3,4-di-O-acetyl-2-chloro-2-deoxy-alpha-L-rhamnopyranoside 7, which was converted into an ethyl thioglycoside 10, suitable for use as a glycosyl donor. It and a disaccharide analogue 20 were effective donors in N-iodosuccinimide-triflic acid promoted glycosylations of a 2-acetamido-2-deoxy-D-glucopyranoside acceptor 22. Chlorodeoxy saccharides have previously been shown to be suitable derivatives to probe oligosaccharide-protein interactions, and this synthetic strategy provided three monochlorodeoxy trisaccharide congeners of the native Shigella flexneri epitope 2, alpha-L-Rhap-(1-->3)-alpha-L-Rhap-(1-->3)-beta-D-GlcNAcp+ ++-(1-->O)-Me.

Carbohydrate Conformation↗