Structural Elucidation of the Mechanistic Basis of Degeneracy in the Primary Humoral Response

Abstract

The mechanistic basis for efficient combating of the infinite range of foreign Ags by the limited repertoire of naive Abs expressed on primary B cell surfaces during their first encounter was addressed through elegantly designed crystallographic analyses. Resolution of the discrepancy arising from the limited number of possible germline Ab receptors on primary B cells for recognizing the unlimited pool of possible Ags has been attempted by invoking the degenerate recognition potential of the germline Abs. Structural analyses of germline mAb BBE6.12H3 in an Ag-free state, as well as bound to four different peptide Ags, established the correlation of its degenerate specificity with conformational versatility of the paratope. Six distinct paratope topologies observed for a single germline mAb provided a quantitative description of the primary Ag recognition repertoire at the tertiary structural level. Each of the four different peptide Ags was bound specifically to a distinct conformation of the paratope, which was also different from that of the Ag-free states of the same germline mAb. A minimal conserved motif in the pristine Ag-combining site essential for multispecificity and Ag binding-mediated change in the elbow angle of Fab was also discernible. It is proposed that the generation of a primary Ab repertoire involves large, yet finite, germline Ab clones, each capable of adopting discrete conformations, which in turn exhibit diverse binding modes.

Comment on Three X-ray Crystal Structure Papers

“…Additional strong support for the existence of the bound ligands can be seen in the structural analyses of germline Ab BBE6.12H3 in ligand-free state and in the states bound to four different peptide ligands (1). Abs often have induced fit on binding of the Ag, reflected in terms of structural changes in the Ab, particularly in elbow angle and conformations of the CDRs (11)(12)(13)(14).…”

Adjustable Locks and Flexible Keys: Plasticity of Epitope–Paratope Interactions in Germline Antibodies

“…The structure of Ppy bound to the mAb BBE6.12H3 (PDB code 2Y07) has been reported previously (4). A comparative analysis of the 36-65-Ppy and BBE6.12H3-Ppy paratopes revealed distinct topologies and charge distributions (Figs.…”

“…Therefore, it is interesting to address the structural mechanisms adopted by germline encoded BCRs for Ag recognition. Previous structural studies have provided insights on how germline Ab pluripotency may enhance the BCR repertoire diversity (4,5,(8)(9)(10). Comparative analysis of degeneracy in interactions of germline versus affinity-matured Abs with antigenic targets would contribute further to the understanding of the structural mechanisms operating in the configuration of B cell immune responses.…”

“…We have previously explored mechanistic details of mAb BBE6.12H3 binding to these peptides (4). Further analyses of the same peptides bound to the germline mAb 36-65 have allowed us to compare the recognition of a flexible Ag by independent germline Abs.…”

Response to Comment on Three X-ray Crystal Structure Papers

“…Additional strong support for the existence of the bound ligands can be seen in the structural analyses of germline Ab BBE6.12H3 in ligand-free state and in the states bound to four different peptide ligands (1). Abs often have induced fit on binding of the Ag, reflected in terms of structural changes in the Ab, particularly in elbow angle and conformations of the CDRs (11)(12)(13)(14).…”