Large-scale analysis of somatic hypermutations in antibodies reveals which structural regions, positions and amino acids are modified to improve affinity

Anat Burkovitz, Inbal Sela-Culang, Yanay Ofran

Research output: Contribution to journalArticlepeer-review

35 Scopus citations

Abstract

The principles of affinity maturation of antibodies (Abs), which underlies B cell-mediated immunity, are still under debate. It is unclear whether the antigen (Ag) binding site is a preferred target for mutations, and what the role of activation-induced deaminase (AID) hotspots is in this process. Here we report a structural analysis of 3495 residues that have been replaced through somatic hypermutations (SHMs) in 196 Abs. We show that there is no correlation between the propensity of an amino acid to be in AID hotspot and the probability that it is replaced during the SHM process. Although AID hotspots may be necessary to enable SHMs, they are not a major driving force in determining which residues are mutated. We identified Ab positions that are highly mutated and significantly affect binding. The effect of mutation on binding energy is a major factor in determining which structural regions of the Ab are mutated. There is a clear preference for mutations at the Ag-binding site. However, positions outside this region that also affect binding are often preferred targets for SHMs. As for amino acid preferences, a general trend during SHM is to make Ab-Ag interfaces more similar to protein-protein interfaces in general. In different regions of the Ab, there are different sets of preferences for amino acid substitution. This mapping improves our understanding of Ab affinity maturation and may assist in Ab engineering.

Original languageEnglish
Pages (from-to)306-319
Number of pages14
JournalFEBS Journal
Volume281
Issue number1
DOIs
StatePublished - 1 Jan 2014
Externally publishedYes

Keywords

  • affinity
  • affinity maturation
  • antibody
  • antigen
  • somatic hypermutations

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

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