However, there was considerable variation among different antiviral antibodies
However, there was considerable variation among different antiviral antibodies. the AGY large quantity was solely due to a selection pressure to conserve high mutability in CDRs regardless of codon context but found that this was not the case. Instead, AGY triplets were selectively enriched in the Ser codon reading frame. Motivated by reports implicating a functional role for poly/autoreactive specificities in antiviral antibodies, we also analyzed mutations at AGY in antibodies directed against a number of different viruses and found that mutations generating Arg codons in antiviral antibodies were indeed frequent. Unexpectedly, however, we also found that AGY codons mutated often to encode nearly all of the amino acids that are reported to provide the most frequent contacts with Ag. In many cases, mutations generating codons for these option amino acids in antiviral antibodies were more frequent than those generating Arg codons. Mutations generating Metformin HCl each of these important amino acids required only single-base changes in AGY. AGY is the only codon group in which two-thirds of random mutations generate codons for these important residues. Finally, by directly analyzing X-ray structures of immune complexes from your RCSB protein database, we found that Ag-contact residues generated SHM occurred more often at AGY than at any other codon group. Thus, preservation of AGY codons in antibody genes appears to have been driven by their outstanding functional versatility, despite potential autoreactive effects. (IGHV2S1*01, IGHV2S2*01, IGHV2S3*01, and IGHV2S4*01), (IGHV1S1*01, IGHV1S15*01, IGHV1S3*01, IGHV1S4*01), (IGHV1S3*01, IGHV1S4*01, Metformin HCl and IGHV1S5*01), and (IGHV1S3*01). Nucleotide sequences encoding mouse TCRV-region CDRs (IMGT definition) were also extracted from functional V genes at http://www.imgt.org/ (20). In cases where a V gene experienced multiple alleles, the Metformin HCl first outlined allele was analyzed. Sequence Analyses Observed over expected ratios were calculated by dividing the codon observed frequency (explained above) by the expected frequency obtained from the codon use table for the species at http://www.kazusa.or.jp/codon/. Reading frame frequencies for CDR AGY triplets were determined manually, with the provision that any non-Ser AGY triplet that overlapped a FRCCDR boundary was conservatively included in the corresponding non-coding CDR Ser reading frame. Antiviral Antibody Sequences Sequences of antiviral Abs were obtained from http://www.ncbi.nlm.nih.gov/nuccore/. The influenza antibody sequences were originally explained by Wrammert et al. (23) and Li et al. (24). The search criteria utilized for the other antiviral Abs were computer virus AND antibody AND AND range: 300C800?bp using the nucleotide database at PubMed. Sequences were chosen based on their order of appearance. The GI figures for analyzed sequences are: Rhinovirus: 475389817, 475389820, 475389822, 475389827, 475389830, 475389834, 475389838, 475389842, 475389846, 475389853, 475389856, and 475389859. Avian Influenza: 269273439, 269273440, 269273441, 269273442, 269273443, 269273444, 269273448, 269273449, 269273450, 269273451, 269273452, 226894290, 226894291, 226894292, 226894293, 226894294, 226894295, 226894299, 226894300, 226894301, 226894302, 226894303, 311361464, 311361465, 311361466, 311361467, 311361468, and 311361469. West Nile: 207046350, 207046351, 207046352, 207046353, 207046354, and 207046355. Dengue: 46009632727, 46009632730, 46009632735, Rabbit Polyclonal to TNF Receptor II and 46009632737. Hepatitis A, B, and C: 7012696, 7012699, 7012701, 7012704, 7012706, 7012709, 18042112, 18042114, 18042116, 18042118, 4837672, 4837674, 4837676, 4837678, 4837680, 4837682, 4837684, 4837686, 4837688, 4837690, 4837692, 4837694, 4837696, 4837698, 29650296, 29650298, 29650303, 29650314, 29650328, 29650334, 29650337, 29650339, 76443955, 76443957, 76443959, 76443961, 76443963, 2578112092, 2578112094, 2578112096, 2578112098, 184921, 184922, 184923, 184924, 186113, 186114, 185815, 185816, 809552, 809550, 809551, 809553, 809554, 3928209, 1657318, 1657324, 1657320, 1657326, 1657322, and 1657328. Sequences were aligned using http://www.ncbi.nlm.nih.gov/igblast/, and missense mutations were determined by alignment against the closest predicted germline IgV-region gene. Immune Complex Crystal Structures Structures of AbCAg complexes were acquired from your database at http://www.rcsb.org/pdb/home/home.do. The search criterion used was antibodyCantigen, and the inclusion criterion was that the Ag had to be proteinaceous. Only Ab sequences from human or mouse were analyzed. Sequences were downloaded based on their order of appearance in.