Affinity labelling of the binding site of rabbit antibody. Evidence for the involvement of the hypervariable regions of the heavy chain

Cross-linking of the anticodon of P and A site bound tRNAs to the ribosome via aromatic azides of variable length: involvement of 16S rRNA at the A site

The topography of the ribosomal decoding site was explored by affinity labeling from the 5'-anticodon base, 5-(carboxymethoxy)uridine-34, of P or A site bound tRNA1Val. A nitrophenyl azide was attached to the carboxyl group of this nucleotide via side chains varying in length from 18 to 24 A. Binding of acetylvalyl-tRNA to the P site was codon dependent and that of valyl-tRNA to the A site was both codon and elongation factor Tu (EFTu) dependent. Cross-linking to both A and P sites was irradiation, probe, codon, and, in the case of the A site, EFTu dependent. Putative P-site cross-linked aminoacyl-tRNA was reactive with puromycin. The yield of cross-linking was little affected by placement of the tRNA at the A or P site but varied considerably with the length and structure of the probe side chain. When the distance from the pyrimidine C-5 atom to the azide group was 23 A, 42-45% cross-linking was obtained at each site, but when the distance was decreased to 18 A, only 7-12% was found. Placing an S-S bond in the center of the 23-A leash decreased the A-site yield to about half, while insertion of a CONH group decreased A-site cross-linking about 8-fold. P-site cross-linking was more sensitive to mercaptan quenching (50% at 0.5 mM) than was that at the A site (50% at greater than 2.0 mM) but both were partially shielded from solvent.(ABSTRACT TRUNCATED AT 250 WORDS)

The measurement of antibody affinity: a comparison of five techniques utilizing a panel of monoclonal anti-DNP antibodies and the effect of high affinity antibody on the measurement of low affinity antibody

The affinities of 9 IgG1 monoclonal anti-dinitrophenol (DNP) antibodies for 3H-epsilon-DNP-L-lysine, 125I-HOP-DNP-L-lysine and 125I-DNP-human serum albumin (HSA) were determined. 3H-DNP-lysine was used in equilibrium dialysis and ammonium sulphate globulin precipitation assays; 125I-HOP-DNP-lysine was used in equilibrium dialysis and polyethylene glycol precipitation; and 125I-DNP5-HSA in the polyethylene glycol precipitation assay for affinity. The ranking order of the monoclonal antibodies in terms of affinity by the assays was significantly correlated. Of particular importance was the observation that the simple and widely applicable globulin precipitation assay utilizing a protein antigen produced affinity values which showed concordance with the least equivocal but cumbersome assay, equilibrium dialysis. Mixing of antibodies of high and low affinity demonstrated that even a low proportion of high affinity antibody had marked effect on measurements of the amount and affinity of a predominantly low affinity antibody preparation.

Formation and properties of a covalent complex between elongation factor Tu and Phe-tRNA bearing a photoaffinity probe on its 3-(3-amino-3-carboxypropyl)uridine residue

Escherichia coli Phe-tRNA, modified with the photoaffinity reagent 6-(2-nitro-4-azidophenylamino)caproate on the 3-(3-amino-3-carboxypropyl)uridine residue, was crosslinked to E. coli EFTu Section upon irradiation at 0 degree C with visible light at wavelengths greater than 400 nm. Crosslinking was dependent on irradiation, the photoaffinity probe, and was blocked by pre-photolysis. 1 mM-dithiothreitol completely quenched crosslinking. Binding of the tRNA to EFTu was a prerequisite for crosslinking, because neither EFTu . GDP nor AcPhe-tRNA could substitute; EFTu . GDPCP, however, was almost as active as EFTu . GTP. Crosslinking was complete in less than five minutes and was stable to at least 20 minutes of irradiation with a single 650 W tungsten lamp 4 cm away. The crosslinking yield ranged from 15% to 25%. The crosslinked complex possessed several remarkable properties. At 0.5 mM-Mg2+, the complex protected the AA-tRNA link to chemical hydrolysis, stabilized the bound GTP to dissociation or exchange, and was not adsorbed to cellulose nitrate filters. The purified crosslinked complex could be bound to ribosomes with concomitant hydrolysis of GTP. Extensive peptide bond formation with AcPhe-tRNA in the P site occurred despite the presence of the crosslinked EFTu. We conclude that hydrolysis of GTP is sufficient to release the 3' end of the Phe-tRNA from complexation with EFTu. Translocation of the A site bound complex did not occur. The crosslink site on EFTu is probably near the periphery of the molecule, because shortening the probe from 20 A to 14 A completely blocked crosslinking. A similar but shorter 8 A probe, p-azidophenacyl-4-thiouridine located on the opposite face of the tRNA, did not crosslink.

E coli tRNAPhe modified at the 3-(3-amino-3-carboxypropyl) uridine with a photoaffinity label is fully functional for aminoacylation and for ribosomal interaction

E. coli tRNAPhe was modified at its 3-(3-amino-3-carboxypropyl)uridine residue with the N-hydroxysuccinimide ester of N-(4-azido-2-nitrophenyl) glycine. Exclusive modification of this base was shown by two-dimensional TLC analysis of the T1 oligonucleotide and nucleoside products of nuclease digestion. The fully modified tRNA could be aminoacylated to the same level as control tRNA. The aminoacylated tRNA was as active as control tRNA in non-enzymatic binding to the P site of ribosomes, and in EFTu-dependent binding to the ribosomal A site. The functional activity of this photolabile modified tRNA allows it to be used to probe the A and P binding sites on ribosomes and on the other proteins that interact with tRNA. Crosslinking to the ribosomal P site has been shown.

Identification of the corticotropin binding domain of bovine serum albumin by photoaffinity labeling

The interaction of the pituitary hormone corticotropin (ACTH) with bovine serum albumin (BSA) was investigated by photoaffinity labeling with 2-nitro-4-azido-phenylsulfenyl (2,4-NAPS) derivatives of aCTH and [Trp-(SH)9]ACTH. Nearly 30 mol % of tritiated [2,4-NAPS-Trp9]ACTH was covalently bound to BSA at a molar ratio of hormone:BSA of 1.33. The [2,4-NAPS-Trp9] [3H]ACTH-BSA complex was isolated, and the CNBr fragments of the complex were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The radioactivity was predominantly associated with the amino-terminal CNBr fragment corresponding to residues 1-183 in BSA. This result was confirmed by studies of the inhibition of covalent labeling of BSA by photoreactive ACTH. 8-Anilinonaphthalenesulfonic acid which binds to the amino-terminal domain of BSA strongly inhibited the photolabeling of BSA by [2,4-NAPS-Trp9][3H]ACTH. Palmitate and progesterone, known to bind to the carboxy-terminal domains of BSA, did not inhibit the incorporation of [2,4]NAPS-Trp9][3H]ACTH into BSA. The removal of ACTH from the covalent complexes was also investigated. The release of ACTH from the [2,4]NAPSS-Trp9]ACTH--BSA complex by treatment with beta-mercaptoethanol was complete in 6 h, but only 80% of ACTH was released from [2,4]NAPS-Trp9]ACTH--BSA under these conditions.

The utility of photo-affinity labels as "mapping" reagents. A study of sub-populations of a specific rabbit antibody by using structurally related photo-affinity reagents

A specific rabbit antibody against the 4-azido-2-nitrophenyl determinant was photo-labelled by the homologous hapten epsilon-(4-azido-2-nitrophenyl)-l-lysine, and by the close structural isomer epsilon-(5-azido-2-nitrophenyl)-l-lysine. The extents of covalent labelling of the antibody-binding site were assessed by using radioactive haptens and exhaustive displacement dialysis, which leaves the unlabelled sites empty but largely intact. A single photolysis of hapten-antibody complex suffices to label those sites that are capable of being labelled. Although there is considerable overlap among sub-populations of antibody that will bind the two haptens non-covalently, sites that can be covalently labelled by one reagent cannot be labelled by the other.