Biomedical subjects
Publications and source records attributed to E A Padlan.
A survey of the base usage in genes coding for human antibodies reveals that more (A+T) and less (C+G) are found in the segments coding for the complementarity-determining regions, while the opposite is true for the segments coding for framework and constant regions. The possibility that this bias in base usage may contribute to hypermutation is explored.
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To evaluate the potential for dimerization through a particular T cell receptor (TCR) domain, we have cloned the cDNA encoding a TCR V alpha from a hybridoma with specificity for the human immunodeficiency virus (HIV) envelope glycoprotein 120-derived peptide P18-110 (RGPGRAFVTI) bound to the murine major histocompatibility complex (MHC) class I molecule, H-2Dd. This cDNA was then expressed in a bacterial vector, and protein, as inclusion bodies, was solubilized, refolded, and purified to homogeneity. Yield of the refolded material was from 10 to 50 mg per liter of bacterial culture, the protein was soluble at concentrations as high as 25 mg/ml, and it retained a high level of reactivity with an anti-V alpha 2 monoclonal antibody. This domain was monomeric both by size exclusion gel chromatography and by sodium dodecyl sulfate polyacrylamide gel electrophoresis. Circular dichroism spectra indicated that the folded V alpha domain had secondary structure similar to that of single immunoglobulin or TCR domains, consisting largely of beta sheet. Conditions for crystallization were established, and at least two crystal geometries were observed: hexagonal bipyramids that failed to diffract beyond approximately 6 A, and orthorhombic crystals that diffracted to 2.5 A. The dimerization of the V alpha domain was investigated further by solution nuclear magnetic resonance spectroscopy, which indicated that dimeric and monomeric forms of the protein were about equally populated at a concentration of 1 mM. Thus, models of TCR-mediated T cell activation that invoke TCR dimerization must consider that some V alpha domains have little tendency to form homodimers or multimers.
The three-dimensional structure of the Fab of TR1.9, a high-affinity IgG1, kappa human autoantibody to thyroid peroxidase, was determined crystallographically to a resolution of 2.0 A. The combining site was found to be relatively flat, like other antibodies to large proteins. Sequence differences from the most closely related germline genes mainly occur at positions occupied by residues with outward-pointing side chains. An increased deformability of the second and third complementarity-determining regions of the heavy chain may result from the replacement of two germline asparagines and the presence of several glycines, and may allow "induced fit" in the binding to antigen. Four exposed charged residues, resulting from the use of a particular D (diversity) and J (joining) segments in the assembly of the heavy chain, may contribute to the high affinity of antigen binding. The crystal structure of TR1.9 Fab is the first for a human IgG high-affinity autoantibody.
We have investigated the capacity of N- and C-terminally truncated and chimeric human (h) IgE-derived peptides to inhibit the binding of 125I-labeled hIgE, and to engage cell lines expressing high and low affinity receptors (Fc-epsilon-RI/II). The peptide sequence Pro343-Ser353 of the hC-epsilon-3 domain is common to all h-epsilon-chain peptides that recognize hFc-epsilon-RI. This region in IgE is homologous to the A loop in C-gamma-2 that engages the rat neonatal IgG receptor. Optimum Fc-epsilon-RI occupancy by hIgE occurs at pH 6.4, with a second peak at 7.4. N- or C-terminal truncation has little effect on the association rate of the ligands with this receptor. Dissociation markedly increases following C-terminal deletion, and hFc-epsilon-RI occupancy at pH 6.4 is diminished. His residue(s) in the C-terminal region of the epsilon-chain may thus contribute to the high affinity of interaction. Grafting the homologus rat epsilon-chain sequence into hIgE maintains hFc-epsilon-RI interaction without conferring binding to rat Fc-epsilon-RI. hFc-epsilon-RII interaction is lost, suggesting that these residues also contribute to hFc-epsilon RII binding. h-epsilon-chain peptides comprising only this sequence do not block hIgE/hFc-epsilon-RI interaction or engage the receptor. Therefore, sequences N- or C-terminal to this core peptide provide structures necessary for receptor recognition.
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A murine monoclonal antibody H67 was characterized for the binding specificity, which showed that H67 recognizes a disulfide-bond-dependent conformational epitope of common a antigenic determinant on the hepatitis B surface antigen. The result suggested that this antibody may have the potential of replacing hepatitis B immune globulin in the prevention of hepatitis B virus (HBV) infection. Therefore, we have constructed the humanized antibody HuS10 by grafting the complementarity determining regions and some framework amino acid residues of H67 onto the most homologous human antibody variable regions, 21/28 for heavy chain variable region and B1 and J kappa 2 for light chain variable region, followed by combining with human constant regions C gamma 1 and C kappa. The affinity of the HuS10 was the same as that of the H67, 8 x 10(8) x 10(8)M-1, and the HuS10 neutralized the in vitro infection of adult human hepatocyte primary culture by adr or ayw subtype of HBV. The neutralization assay showed that the HuS10 had approximately 2,000-times higher specific activity than commercially available polyclonal HBIG. These results suggest that the humanized antibody will be useful in the prevention or treatment of HBV infection.
Antigen-specific T-cell responses require antigenic peptides presented on the cell surface by the major histocompatibility complex (MHC) molecules. The structural characteristics of these peptides are being defined. It is now known that the majority of peptides that associate with MHC Class I are 8-10 residues long, with allotype-specific binding motifs containing up to three anchor positions. This is consistent with the presence of six pockets and the close-ended structure of the MHC Class I peptide binding groove. In contrast to peptides associated with MHC Class I, those associated with MHC Class II are 10-34 residues in length and are commonly presented in nested sets with extensions or truncations at the N- or C-terminal ends. Binding motifs for MHC Class II appear to contain up to four anchor positions, with more loosely defined amino acid preferences. The expression of histocompatibility proteins in cells that do not load peptides but fold them correctly has permitted the X-ray analysis of the three-dimensional structure of Class I and Class II complexes with single defined peptides. The differences in length between the Class I and Class II sequences can be ascribed to small structural differences between the two binding sites and the positioning of key residues, that make hydrogen bonds to the bound peptides. Recent advances in mass spectrometry are making possible the analysis and sequencing of subpicomolar quantities of MHC-bound peptides and the estimation of the size of the total population of peptides. The sequence information derived from this technique, in conjunction with X-ray crystallographic analysis of MHC complexes involving single, defined peptides, may provide a new approach towards the development of useful reagents for therapeutic intervention.
Monoclonal antibody (MAb) CC49 reacts with tumor-associated glycoprotein (TAG)-72, a human pancarcinoma antigen. In clinical trials, radiolabeled CC49 has shown excellent tumor localization; however, many of the patients receiving MAb CC49 develop a human antimouse antibody response. In an attempt to prevent this antiimmunoglobulin response, we have developed a humanized CC49 (HuCC49) by grafting the MAb CC49 hypervariable regions onto the variable light (VL) and variable heavy (VH) frameworks of the human MAbs LEN and 21/28' CL, respectively, while retaining those murine framework residues that may be required for the integrity of the antigen combining-site structure. The HuCC49 MAb was compared with native murine CC49 (nCC49) and chimeric CC49 (cCC49), using a variety of assays. SDS-PAGE analysis under nonreducing conditions showed that the HuCC49 MAb has virtually identical mobility to that of cCC49. Under reducing conditions, the HuCC49 yielded two bands of approximately 25-28 and approximately 50-55 kDa, characteristic of heavy and light immunoglobulin chains. In competition radioimmunoassays, HuCC49 completely inhibited the binding of 125I-labeled nCC49 to TAG-72, although 23- to 30-fold more HuCC49 was required to achieve a level of competition similar to those of cCC49 and nCC49. The relative affinity of HuCC49 was 2- to 3-fold less than those of the cCC49 and nCC49 MAbs, respectively. The plasma clearance in mice of HuCC49 was virtually identical to that of cCC49. Biodistribution studies demonstrated equivalent tumor-targeting of HuCC49 and cCC49 to human colon carcinoma xenografts. These studies thus suggest that HuCC49 and genetically modified molecules, such as sFv and domain-deleted immunoglobulins developed by using the HuCC49 variable region as a cassette, may be potentially useful in both diagnostic and therapeutic clinical trials in patients with TAG-72-positive tumors.
The successful identification of the residues that contact ligand has important implications, especially in view of the increasing use of antibodies in various medical and industrial applications. Analysis of the crystallographically derived, three-dimensional structures of five antibody-antigen complexes and of the available amino acid sequence data on antibody variable regions reveals that the residues that contact antigen are in the main also the most variable. It is proposed that a good first guess of the identity of the specificity-determining residues can be made from an examination of the variability values at sequence positions. New boundaries for the complementarity-determining regions are proposed.
B3(Fv)-PE38 is a recombinant single-chain immunotoxin in which the Fv region of carcinoma-specific antibody B3 is fused to a truncated form of Pseudomonas exotoxin (PE). The efficacy of monoclonal antibody B3 and B3 immunotoxins in cancer therapy and diagnosis may be limited by the human anti-mouse response. Here we describe the humanization of the Fv of B3(Fv)-PE38 by "framework exchange." The variable domains of the heavy (VH) and light (VL) chains were aligned with their best human homologs to identify framework residues that differ. Initially, 11 framework residues in VH and six in VL were changed by site-specific mutagenesis to human residues and introduced simultaneously into a preassembled single-chain Fv expression cassette. Six VH and five VL residues that differ were not changed because they were buried, in the interdomain interface, or previously found to result in decreased affinity when mutated. This basic design resulted in some 20-fold loss of activity. Changing VL residues at the interdomain interfacial position 100 and at the buried position 104 to the human sequence increased the activity 8-fold. Changing VH residue at position 82b from the human sequence back to that of the mouse restored the activity 2- to 3-fold to the full binding and cytotoxic activity of the mouse sequence. Humanized B3(Fv)-PE38 lost immunogenic epitopes recognized by sera from monkeys that had been immunized with B3(Fv)-PE38.
We are studying murine mAbs against two carbohydrate epitopes, 3-fucosyllactosamine (Le(x), CD15) and galactosylgloboside. The VH domains of both panels of Ab are encoded by VH441, a member of the X24 family of Ig genes. To evaluate the contribution of the heavy chain CDR3 to the affinity of the anti-3-fucosyllactosamine Ab, CDR3-H of PMN6, a low affinity Ab, was replaced by the CDR3 of PM81, a higher affinity Ab. The affinity of the chimeric 6/81 Ab was increased when the heavy chain was paired with the PM81 light chain, but not when paired with another light chain (M5), which differs from PM81 light chain by three amino acids. To evaluate the contribution of somatic mutations to the binding of GalGb4, the 3A9 VH sequence, which contains three amino acid substitutions, was replaced by a germ-line sequence encoded by either VH441 or VHX24. The chimeric Ab, 441/3A9 and X24/3A9, bound Ag as well as the wild-type 3A9 Ab. Computer models of the Fv fragments of PM81 and 3A9 were compared with the crystal structure of the Fv fragment of J539, a galactan-binding myeloma protein that is encoded by the same VH and VK genes as 3A9. The surfaces of 3A9 and J539 have shallow pockets that are potential Ag-binding sites. Replacement of CDR3-H Tyr99, which is a prominent component of the pocket, by Ala abolished the binding of Ag. In contrast, the Fv surface of PM81 contains a large cleft rather than a pocket. These models indicate how the same VH gene segment can be used to encode Abs that exhibit different specificities.
The structure of carbonmonoxide Glycera hemoglobin has been determined to 1.5 A resolution by X-ray diffraction. The model, including ordered solvent, has been refined by the method of restrained least-squares to an R-value of 0.146. The positions of 1104 protein atoms and the oxygens of 155 water molecules have been determined with an estimated r.m.s. error of 0.10 to 0.13 A. The r.m.s. errors in protein geometry are 0.027 A for bond distances, 0.038 A for angle distances and 0.012 A for deviations of planar groups from their least-squares planes. The iron lies exactly in the plane of the heme nitrogens and the heme is very slightly domed toward the proximal side. The carbon-oxygen bond in the carbon monoxide ligand is bent 7.9 degrees away from the normal to the plane of the heme nitrogens. The ligand is in close contact with, and slightly removed from the heme normal by distal residues Leu 58(E7) and Val62(E11). Comparison of the CO structure with the 1.5 A deoxy structure shows that the majority of the rather small structural changes occurring upon ligation are mediated by movement of the heme due to shortening of the five iron to nitrogen bonds. There is very little empty space inside the molecule, and no direct channel from the solvent into the heme pocket; however, rotation of the side-chain of the distal leucine residue Leu 58(E6) could provide a ligand pathway.
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The structures of the various regions of an antibody molecule are analysed and correlated with biological function. The structural features which relate to potential applications are detailed.
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We have previously constructed a chimeric version of KC4G3, a murine antibody that reacts with several human epithelial cancers and binds to the human breast epithelial mucin. We have now successfully humanized KC4G3 using positional consensus data, previously compiled after examining several other antibody structures, listing residues in the VH and V kappa frameworks that could influence antigen binding. We have previously showed that a fraction of the kappa chains of murine and chimeric KC4G3 migrates abnormally on SDS-PAGE most likely due to N-linked glycosylation in V kappa. The glycosylation signal has now been removed from V kappa, as a consequence of humanization. As expected, the humanized kappa chain migrates normally on SDS-PAGE. We detected no significant differences either in the affinities (1.6 x 10(9) M-1 vs. 1.4 x 10(9) M-1, respectively) or in the ability to compete for antigen binding, between the murine and the humanized antibodies. The humanized version is an IgG1, kappa immunoglobulin produced by mouse myeloma SP2/0-Ag14 cells and is designated HuKC4v2. The HuKC4v2 frameworks conform to the V kappa II and VHIII human consensus in all but six positions in V kappa and three positions in VH.