Amino acid sequence of residues 1-98 of the K-2Kb murine major histocompatibility alloantigen: comparison with H-2Kb and H-2db reveals extensive localized differences

A structural somatic variant of the Kk antigen is generated by point mutation

We have previously selected structural variants of the Kk antigen from a (C3 X D2)F1 T-cell lymphoma. Those mutants were identified by the loss of certain epitopes defined by monoclonal antibodies. The variant Kk molecule from HK13.S3 cells is no longer recognized by 40% of the trinitrophenyl-specific, Kk-restricted cytotoxic T lymphocytes. Here we report on the primary structure of the altered Kk molecules from the cell line HK13.S3. Comparison with the parental Kk reveals a single base pair exchange, GCG to GTG, that results in an alanine to valine exchange in position 40 of the protein. This observation emphasizes that minor structural alterations in class I molecules may have a strong effect on the H-2-restricted T-cell response.

A program for prediction of protein secondary structure from nucleotide sequence data: application to histocompatibility antigens

A computer program is described which, given a nucleotide or an amino acid sequence, outputs protein secondary structure prediction curves as well as hydrophobicity and charged-residue profiles. The program allows for cumulative averaging of properties (secondary structure propensities, hydrophobicity and charge profiles) from several homologous primary structures, a novel concept shown to improve the predictive accuracy. The use of the program is demonstrated on a set of nucleotide and amino acid sequences from human and murine histocompatibility antigens of class I and II. The last extracellular domains of both class I and II antigens (alpha 3 of class I, alpha 2 and beta 2 of class II) and the beta 2-microglobulin domain are predicted to consist of seven anti-parallel beta-strands, in accord with previous claims of homology between these domains and the constant domains of immunoglobulin chains. The remaining extracellular domains are all proposed to form an anti-parallel, four-stranded beta-sheet with one of its faces being covered by alpha-helices and/or structureless segments ("open face sandwiches").

Amino acid sequence analysis of the H-2Kk alloantigen: complete sequence of residues 1-98 and partial sequence from 99 to 263

The H-2Kk molecule was purified by immunoprecipitation from the glycoprotein fraction of Nonidet P-40 extracts of RDM 4 mouse tumor cells. Cyanogen bromide cleavage of the major papain fragment yielded three peptides, the largest of which consisted of three disulfide-linked peptides which could be separated after reduction and alkylation. These peptides were readily aligned by their homology to similar fragments derived from other H-2 class I molecules. Amino acid sequence analyses of the two nondisulfide-linked peptides, peptide E (residues 1-52) and peptide D (53-98), yielded the following NH2-terminal sequence for the H-2Kk molecule: [sequence in text]. Comparison of this sequence with those of other H-2 class I molecules revealed that: (1) Lys-19, Val-55, Glu-56, Asn-63 and Ile-73 are unique to the H-2Kk molecule; and (2) H-2Kk shares 79-83% homology in this region with other mouse class I molecules. Partial NH2-terminal amino acid sequences are also reported for the three disulfide-linked peptides. Several discrepancies from previously reported partial sequences of the H-2Kk molecule were detected.

Identification of the cloned gene for the murine transplantation antigen H-2Kb by hybridization with synthetic oligonucleotides

The H-2K(b) gene is a member of the large major histocompatibility complex class I gene family. Since many members of this family cross-hybridize with class I cDNA probes, the cloned H-2K(b) gene was identified by hybridization with specific oligonucleotide probes. This clone was definitively shown to encode the H-2K(b) polypeptide by partial DNA sequencing and by serological and tryptic peptide analyses of the expressed product.

Identification of the cloned gene for the murine transplantation antigen H-2Kb by hybridization with synthetic oligonucleotides

The H-2K(b) gene is a member of the large major histocompatibility complex class I gene family. Since many members of this family cross-hybridize with class I cDNA probes, the cloned H-2K(b) gene was identified by hybridization with specific oligonucleotide probes. This clone was definitively shown to encode the H-2K(b) polypeptide by partial DNA sequencing and by serological and tryptic peptide analyses of the expressed product.

Amino acid sequence of the cytoplasmic segment of the h-2Kd (H2.31) murine major histocompatibility antigen

The primary structure of the carboxy-terminal portion of the H-2Kd murine major histocompatibility antigen has been determined using radiosequencing methodology. The two peptides encompassing the entire cytoplasmic portion of the H-2Kd molecule were isolated from cyanogen bromide digests of the detergent solubilized molecule. These two peptides are not present in CNBr digests of papain-solubilized H-2Kd. Alignment of the two CNBr peptides was deduced from tryptic overlap peptides derived from the whole molecule. Alignment with the corresponding region of the H-2Kb antigen shows 90% homology and supports the assignment of this segment of H-2Kd as the C-terminal. The sequence obtained in this study is (Met)-Arg-Arg-Asn-Thr-Gly-Gly-Lys-Gly-Val-Asn-Tyr-Ala-Leu-Ala-Pro-Gly-Ser-Gln- Thr-Ser-Asp-Leu-Ser-Leu-Pro-Asp-Pro-Lys-Val-Met-Val-His-Asp-Pro-His-Ser-Leu- Ala. These data allow extensive comparisons with the protein sequences deduced from the 3' ends of H-2d haplotype cDNA and genomic clones as well as with the homologous regions of H-2Kb and H-2Db.

Spontaneous H-2 mutants provide evidence that a copy mechanism analogous to gene conversion generates polymorphism in the major histocompatibility complex

The analysis of H-2K products from spontaneously generated major histocompatibility complex (MHC) mutants and of the primary structure of other class I antigens suggests the genetic hypothesis that diversity in the MHC results from a copy mechanism analogous to gene conversion. The hypothesis was tested by making precise structural predictions about three partially characterized MHC mutants (bm1, bm3, and bm8). The predictions were based on consensus sequences among class I genes that differ from H-2Kb in the same region of the molecule as do the Kb mutants. In two cases (bm3 and bm8) we successfully predicted the correct amino acid substitution at positions known to be altered but for which the specific nature of the substitution had not been determined. In two additional cases (bm1 and bm8) we predicted and found both new mutation sites and the specific amino acid substitutions. The positions and identifications of the variant amino acids were determined by radiolabeled amino acid sequence analysis and DNA restriction endonuclease analysis. The interaction of MHC genes through a copy mechanism to generate diversity permits the introduction of multiple nucleotide base substitutions into class I sequences by a single genetic event. Such a mechanism may account in part for the large structural divergence among alleles of MHC loci and the high degree of MHC polymorphism among wild mice.

Primary structure of the H-2Db alloantigen. II. Additional amino acid sequence information, localization of a third site of glycosylation and evidence for K and D region specific sequences

The complete amino acid sequence of the CNBr fragment comprising residues 229-284 of the murine major histocompatibility complex antigen H-2Db has been determined using radiochemical methodology. The sequence was determined by N-terminal sequence analysis of the intact CNBr fragment and by sequence determinations of peptides derived from this fragment by trypsin and staphylococcal V8 protease cleavage. In addition to the amino acid assignments for H-2Db, it was possible to assign the linkage position of the third N-linked glycosyl unit to the asparagine at residue 256. Additional amino acid sequence assignments have also been made for three other CNBr fragments that span residues 99-138, 139-228, and 308-331 of the H-2Db molecule. The total protein sequence information available (222 of 338 residues) agrees in every comparable position with the protein sequence derived from the cDNA clone (pH203) isolated by Reyes and co-workers (1982b), which strongly suggests that this clone encodes H-2Db. Combination of the protein sequence with that deduced from the cDNA clone provides the complete H-2Db protein sequence. Comparison of this sequence with other available protein sequence information for murine class I molecules has revealed protein sequences that may be unique to either K or D region molecules.

Amino acid sequence of the carboxyl-terminal hydrophilic region of the H-2Kb MHC alloantigen. Completion of the entire primary structure of the H-2Kb molecule

The amino acid sequence of the COOH-terminal hydrophilic region of the H-2Kb histocompatibility antigen was determined. The sequence was completed by analyses of four CNBr fragments obtained from the intact molecule as well as tryptic peptides. This region was composed of 39 amino acid residues with a cluster of basic residues at the NH2 terminus and localized positions 308-346 of the H-2Kb molecule. These sequence data, together with those reported for the NH2-terminal 284 residues [Martinko, J. M., Uehara, H., Ewenstein, B. M., Kindt, T. J., Coligan, J. E., & Nathenson, S. G. (1980) Biochemistry 19, 6188-6193] and for the intramembranous segment [Uehara, H., Coligan, J. E., & Nathenson, S. G. (1981) Biochemistry (preceding paper in this issue)], provided the complete primary structure of the H-2Kb molecule. This is the first histocompatibility antigen for which the entire primary structure is determined.