PMC:5118421 / 19083-20187 JSONTXT

{"project":"TEST0","denotations":[{"id":"27920779-118-124-3100240","span":{"begin":215,"end":217},"obj":"[\"15860590\", \"20882016\", \"23940276\"]"},{"id":"27920779-165-171-3100241","span":{"begin":388,"end":390},"obj":"[\"15529369\"]"}],"text":"An abundance of CDR codons that are prone to mutate to encode antinuclear Ab seemed paradoxical. However, there is speculation that a modest degree of autoreactivity may be beneficial to antiviral immune responses (37–39). For example, some viruses display host-derived nuclear material on their capsids that might enhance B cell activation or antibody efficacy due to an avidity effect (40). Therefore, we sought to determine if Arg residues are frequently generated via SHM in antiviral Ab. At first, we examined somatic mutations in broadly neutralizing antibodies (bNAbs) against HIV. Although we found that somatic mutations in AGY codons frequently produced Arg codons in these Abs, the results were not easily interpreted because overall mutation frequencies were extremely high, and in many cases CDR boundaries could not be defined due to insertions and deletions. Therefore, we extended our analysis to 298 published sequences of human antibodies against eight other virus species or subspecies. This analysis revealed frequent somatic mutations converting AGY Ser codons in CDRs to Arg codons."}

{"project":"2_test","denotations":[{"id":"27920779-15860590-34707963","span":{"begin":215,"end":217},"obj":"15860590"},{"id":"27920779-20882016-34707963","span":{"begin":215,"end":217},"obj":"20882016"},{"id":"27920779-23940276-34707963","span":{"begin":215,"end":217},"obj":"23940276"},{"id":"27920779-15529369-34707964","span":{"begin":388,"end":390},"obj":"15529369"}],"text":"An abundance of CDR codons that are prone to mutate to encode antinuclear Ab seemed paradoxical. However, there is speculation that a modest degree of autoreactivity may be beneficial to antiviral immune responses (37–39). For example, some viruses display host-derived nuclear material on their capsids that might enhance B cell activation or antibody efficacy due to an avidity effect (40). Therefore, we sought to determine if Arg residues are frequently generated via SHM in antiviral Ab. At first, we examined somatic mutations in broadly neutralizing antibodies (bNAbs) against HIV. Although we found that somatic mutations in AGY codons frequently produced Arg codons in these Abs, the results were not easily interpreted because overall mutation frequencies were extremely high, and in many cases CDR boundaries could not be defined due to insertions and deletions. Therefore, we extended our analysis to 298 published sequences of human antibodies against eight other virus species or subspecies. This analysis revealed frequent somatic mutations converting AGY Ser codons in CDRs to Arg codons."}

{"project":"MyTest","denotations":[{"id":"27920779-15860590-34707963","span":{"begin":215,"end":217},"obj":"15860590"},{"id":"27920779-20882016-34707963","span":{"begin":215,"end":217},"obj":"20882016"},{"id":"27920779-23940276-34707963","span":{"begin":215,"end":217},"obj":"23940276"},{"id":"27920779-15529369-34707964","span":{"begin":388,"end":390},"obj":"15529369"}],"namespaces":[{"prefix":"_base","uri":"https://www.uniprot.org/uniprot/testbase"},{"prefix":"UniProtKB","uri":"https://www.uniprot.org/uniprot/"},{"prefix":"uniprot","uri":"https://www.uniprot.org/uniprotkb/"}],"text":"An abundance of CDR codons that are prone to mutate to encode antinuclear Ab seemed paradoxical. However, there is speculation that a modest degree of autoreactivity may be beneficial to antiviral immune responses (37–39). For example, some viruses display host-derived nuclear material on their capsids that might enhance B cell activation or antibody efficacy due to an avidity effect (40). Therefore, we sought to determine if Arg residues are frequently generated via SHM in antiviral Ab. At first, we examined somatic mutations in broadly neutralizing antibodies (bNAbs) against HIV. Although we found that somatic mutations in AGY codons frequently produced Arg codons in these Abs, the results were not easily interpreted because overall mutation frequencies were extremely high, and in many cases CDR boundaries could not be defined due to insertions and deletions. Therefore, we extended our analysis to 298 published sequences of human antibodies against eight other virus species or subspecies. This analysis revealed frequent somatic mutations converting AGY Ser codons in CDRs to Arg codons."}