Junctional diversification in the generation of the precursor of a discrete immune response

Phosphocholine (PC)-specific antibodies that arise in the mouse in response to Proteus morganii (PM) and use V1-DFL16.1-JH1 are characterized by a number of recurring mutations. Most striking is an invariant A for G substitution in codon 95 of VH which results in an asparagine instead of aspartate at that position. Because of the apparent importance of this substitution in an anti-PC(PM) response, we wanted to determine the molecular basis for this base change. A cDNA library derived from pre-immune splenic B cells was examined for the frequency of VDJ containing the A substitution at 95 and the presence of additional point mutations in these sequences. Six different cDNA were isolated which contained an A substitution at the VD junction (frequency 0.00009); a seventh positive cDNA could not be examined. The V segments of four of these cDNA matched known germline genes and were, therefore, unmutated. Two others closely matched V in families whose members have not all been characterized, hence, it is not known whether the mutations observed are somatic or germline in origin. Sequences of 35 cDNA clones, containing the same V segment but differing in D, J and junctional nucleotides, revealed no mutations. These results indicate that the A substitution generated at codon 95 is most likely a product of V-DJ joining.

Identification of critical contact residues in the NC41 epitope of a subtype N9 influenza virus neuraminidase

We have examined amino acids on influenza virus neuraminidase (NA) subtype N9 (A/tern/Australia/G70c/75) which are in contact with monoclonal antibody NC41 to analyze individual interactions important for antibody recognition. The crystal structure of NA complexed with NC41 Fab1 shows antibody contacts at 19 amino acid residues on the NA surface which are localized on five polypeptide loops surrounding the enzyme active site. Fifteen mutant NA genes were constructed to encode a protein which contained a single amino acid substitution and these were tested for effects of the replacement on NC41 binding. Our data revealed that NAs with changes at 368, 400, and 434 completely lost NC41 recognition. NAs with side chains replaced at residues 346 and 373 exhibited binding reduced to less than 50% of wild-type binding. Changes in seven other contacting residues, including substituted side chains which differed considerably from wild-type NA in size and charge, had no significant effect on NC41 binding. These results indicate that only a few of the many residues which make up an epitope are crucial for interaction and provide the critical contacts required for antibody recognition. This implies that antibody escape mutants are selected only if they contain changes at these crucial sites, or changes which introduce bulky side chains that sterically prevent antibody attachment.

Mutagenesis around residue 176 on HLA-B*0702 characterizes multiple distinct epitopes for anti-HLA antibodies

Preformed antibodies against HLA-A,B,C molecules cause hyperacute rejection of transplanted allogeneic tissues. To understand better the molecular basis of hyperacute rejection, narrowly reactive anti-HLA-B*0702 monoclonal antibodies have been studied. Previous epitope mapping studies of these monoclonal antibodies by mutating B*0702 have conflicted with antibody-blocking studies. To resolve these discrepancies, we mutated B*0702 residues around the antigenically important residue 176, and measured anti-B*0702 antibody binding. Antibody MB40.2 binding is abrogated by mutations at residues 169, 180, and 182, close to residue 176 in the primary structure. However, MB40.2 binding is not affected by 12 other B*0702 mutations close to residue 176 in the tertiary structure. This suggests that MB40.2 may recognize a sequential B*0702 epitope including residues between positions 169-182. Antibody BB7.1 binding requires B*0702 alpha 2-domain residues 166 and 169. Competition for B*0702 residue 169 explains why MB40.2 and BB7.1 crossblock. Because BB7.1 binding also requires B*0702 alpha 1-domain residues, BB7.1 may contact both alpha-helices, straddling the B*0702 peptide-binding groove. Previous results showed that both MB40.2 and MB40.3 binding require B*0702 residues 176/178. However, MB40.3 binding is not affected by any of 15 other mutations near residue 176. This suggests that MB40.3 does not contact residues 176/178; rather, residues 176/178 appear to affect MB40.3 binding by subtly influencing B*0702 conformation. Thus, monoclonal antibodies influenced by a defined B*0702 region around residue 176 appear to recognize three different types of epitopes. This suggests that human alloantibodies also recognize diverse types of HLA epitopes.

Variable region differences affect antibody binding to immobilized but not soluble antigen

We have examined the antigen binding characteristics of two chimeric IgG1 antibodies that differ only in the heavy chain variable region. Antibodies 10B and B11 were expressed from two different anti-(Tyr,Glu)-Ala-Lys murine VH genes joined to human IgG1 constant region genes in a murine anti-(Tyr,Glu)-Ala-Lys heavy chain loss variant hybridoma. The binding characteristics of the antibodies to (Tyr,Glu)-Ala-Lys and to a peptide conjugate, CYYYEEEEY:BSA, were measured in solution and solid phase assays. The antibodies exhibited similar affinities and binding characteristics when assayed in solution assays. However, when we measured binding of antibodies to immobilized antigens, we found that antibody affinity depended on the epitope density in the immobilized immune complexes. The binding of antibody 10B and of B11 to immobilized (Tyr,Glu)-Ala-Lys and to CYYYEEEEY:BSA were similar at high antigen density, but antibody B11 bound less well at lower antigen density. Fab fragments of 10B bound to immobilized (Tyr,Glu)-Ala-Lys and CYYYEEEEY:BSA, but Fab fragments of B11 did not bind to (Tyr,Glu)-Ala-Lys and bound less well to CYYYEEEEY:BSA than 10B Fabs.

Cytoplasmic domain heterogeneity and functions of IgG Fc receptors in B lymphocytes

B lymphocytes and macrophages express closely related immunoglobulin G (IgG) Fc receptors (Fc gamma RII) that differ only in the structures of their cytoplasmic domains. Because of cell type-specific alternative messenger RNA splicing, B-cell Fc gamma RII contains an insertion of 47 amino acids that participates in determining receptor function in these cells. Transfection of an Fc gamma RII-negative B-cell line with complementary DNA's encoding the two splice products and various receptor mutants indicated that the insertion was responsible for preventing both Fc gamma RII-mediated endocytosis and Fc gamma RII-mediated antigen presentation. The insertion was not required for Fc gamma RII to modulate surface immunoglobulin-triggered B-cell activation. Instead, regulation of activation involved a region of the cytoplasmic domain common to both the lymphocyte and macrophage receptor isoforms. In contrast, the insertion did contribute to the formation of caps in response to receptor cross-linking, consistent with suggestions that the lymphocyte but not macrophage form of the receptor can associate with the detergent-insoluble cytoskeleton.

HLA-DR peptide-induced alloreactive T cell lines reveal an HLA-DR sequence that can be both "dominant" and "cryptic": evidence for allele-specific processing

Previously, we reported on a T cell line, ThoU6, which we obtained through stimulation of DPw3+ cells with a synthetic "DR3 peptide" with a sequence identical to the third hypervariable region of the DRB1*0301 chain. This T cell line recognizes both the synthetic peptide presented by DPw3 as well as DR3+ DPw3+ stimulator cells. This implies that the synthetic DR3 peptide has a natural counterpart in DR3-positive cells. Here we describe the recognition pattern of another T cell line that was sensitized with the same synthetic DR3 peptide. This T cell line, BieU6, shows both HLA-DRw13/Dw18 (self)-restricted recognition of the synthetic DR3 peptide and allorecognition towards DR13/Dw19, a molecule which is highly homologous to Dw18, in the absence of synthetic peptide. These results suggest that the epitope formed by the Dw18 molecule plus the synthetic DR3 peptide and recognized by T cell line BieU6 mimics the Dw19 molecule. The potential role for a Dw19-specific peptide is discussed. The inability of T cell line BieU6 to recognize Dw18+ DR3+ cells indicates that, in this case, the synthetic DR3 peptide is "cryptic", i.e. does not have a natural counterpart that is effectively presented to T cells. Mapping of the shortest peptides recognized by T cell lines ThoU6 and BieU6 indicate that these sequences are fully overlapping. We, therefore, suggest that the antigen-presenting molecules, HLA-DPw3 and HLA-Dw18, differ in their accessibility for self peptides derived from the third hypervariable region of DR molecules. These observations may be explained by allele-specific processing.

The molecular basis for reactivity of anti-Cw1 and anti-Cw3 alloantisera with HLA-B46 haplotypes

HLA haplotypes containing the HLA-B46 allele react with both anti-Cw1 and anti-Cw3 alloantisera, a pattern of reactivity defined as the Cw11 antigen and postulated to involve either a distinctive Cw11 allele or a duplicated HLA-C locus. From serological characterization of CIR cells transfected with B46 cDNA we now demonstrate that the anti-Cw3 reactivity with these haplotypes is solely due to the B46 molecule and not to an HLA-C molecule. Furthermore, isolation and characterization of HLA-C mRNA from cells expressing B46 strongly suggest that anti-Cw1 reactions are directed against the product of a conventional Cw1 allele. The antigenic cross-reactivities of B46 with B62 and Cw3 correlate with its chimaeric primary structure, which is identical to that of B62, except in the alpha 1 helix where it is identical to both Cw3 and Cw1. The structure, distribution and genetic linkage of B46 indicate it is of recent, Asian origin and is the result of a gene conversion, involving Cw1 as the donor gene and B62 as the recipient. These results demonstrate that the Cw11 antigen neither corresponds to a novel HLA-C allele nor a duplicated HLA-C locus, but to a combination of epitopes contributed by linked Cw1 and B46 alleles. The nucleotide sequence we previously and erroneously attributed to a distinct Cw11 allele is now demonstrated to encode Cw8. Isolation of the cDNA clone with this sequence from a library made from a cell homozygous for the B46 haplotype was probably an artefact of contamination.

Mutations in the third, but not the first or second, hypervariable regions of DR(beta 1*0101) eliminate DR1-restricted recognition of a pertussis toxin peptide

We have examined the role of 12 polymorphic residues of the beta-chain of the HLA-DR1 class II molecule in T cell recognition of an epitope of pertussis toxin. Murine L cell transfectants expressing wild-type or mutant DR1 molecules (containing single amino acid substitutions in DR(beta 1*0101)) were used as APC in proliferation assays involving nine DR1-restricted T cell clones specific for peptide 30-42 of pertussis toxin. Four different patterns of recognition of the mutants were found among the pertussis-specific clones. Residues in the third hypervariable region (HVR) of DR(beta 1*0101) are critically important for all the T cell clones; amino acid substitutions at positions 70 and 74 abrogated recognition by all of the T cell clones, and substitutions at positions 67 and 71 eliminated recognition by most of the clones. In contrast, most single amino acid substitutions in the first and second HVR, predicted to be located in the floor of the peptide binding groove, had little or no effect on the proliferative responses of these clones. However, the involvement of beta-chain first and second HVR residues was demonstrated by the inability of transfectants expressing wild-type DR(beta 1*0404) (DR4Dw14) or DR(beta 1*1402) (DR6Dw16) to present peptide to these clones. These beta-chains have completely different first and second HVR compared with DR(alpha,beta 1*0101) although the third HVR are identical. These results illustrate the functional importance of third HVR residues of DR(beta 1*0101) and allow definition of the molecular interactions of the DR1 molecule with the 30-42 peptide.

Somatic mutation, affinity maturation and the antibody repertoire: a computer model

Somatic mutation has been implicated as a significant and possibly primary factor in the maturation of antibody affinity in the humoral immune response. B cells stimulated by antigen experience a hyper-mutation in the gene segments that code for the antigen-binding site of the antibody, creating antibody specificities that did not exist at the time of immunization. Although most of the mutations are likely to be disadvantageous, new specificities with a higher affinity for the antigen are sometimes created. These higher-affinity cells are preferentially selected for proliferation and eventual antibody secretion, resulting in a progressively higher average affinity over time. In this paper we present the results of an investigation of somatic mutation through the use of a computer model. At the basis of the model is a large repertoire of discrete antibodies and antigens, having three-dimensional structures, that exhibit properties similar to those of the real populations. The key factor is that the binding strength between any antibody/antigen pair can be calculated as a function of the complementarity of the (a) size, (b) shape and (c) functional groups that comprise the two structures. The created repertoires are imbedded in a dynamical system model of the immune response to directly evaluate the affect of somatic mutation on affinity maturation. We also present an expanded hypothesis of clonal selection and development to explain how the mutational restrictions imposed by the genetic code and the structure of the antibody repertoire, along with antigen concentration, affinity, and probabilistic factors may interact and contribute to the expansion of specific clones as the response develops over time.

Complementary peptides as interactive sites for protein binding

The observation that pairs of peptides encoded from complementary strands of nucleic acids can bind one another suggested to us that proteins might use similar "complementary peptide" sequences to facilitate their interactions with other proteins or peptides. Here we review evidence to support this hypothesis. Investigations by us and by others showed that receptors and their ligands may use complementary peptide sequences or their analogs to facilitate binding. In addition, antibodies made against pairs of complementary peptides bind one another in an idiotypic/anti-idiotypic fashion. Taken together, these findings suggest that complementary peptide sequences may be used as recognition units by pairs of proteins which interact.

Immunogenetic model

Different and equally legitimate modes of interpreting serologic reactions will considerably change the image of reality. Some principles of such transformations are briefly outlined and applied to immunogenetic systems.