Structural Diversity of Ultralong CDRH3s in Seven Bovine Antibody Heavy Chains.

Jinhui Dong,James E Crowe,Peter A Larsen,Jessica A Finn,Timothy P L Smith

doi:10.3389/fimmu.2019.00558

Abstract

Antigen recognition by mammalian antibodies represents the most diverse setting for protein-protein interactions, because antibody variable regions contain exceptionally diverse variable gene repertoires of DNA sequences containing combinatorial, non-templated junctional mutational diversity. Some animals use additional strategies to achieve structural complexity in the antibody combining site, and one of the most interesting of these is the formation of ultralong heavy chain complementarity determining region 3 loops in cattle. Repertoire sequencing studies of bovine antibody heavy chain variable sequences revealed that bovine antibodies can contain heavy chain complementarity determining region 3 (CDRH3) loops with 60 or more amino acids, with complex structures stabilized by multiple disulfide bonds. It is clear that bovine antibodies can achieve long, peculiarly structured CDR3s, but the range of diversity and complexity of those structures is poorly understood. We determined the atomic resolution structure of seven ultralong bovine CDRH3 loops. The studies, combined with five previous structures, reveal a large diversity of cysteine pairing variations, and highly diverse globular domains.

Highlights

The highly stable immunoglobulin fold is the universal protein scaffold structure for functionally diverse antibodies, enabling mammalian hosts to resist highly diverse pathogens using structures with hypervariable loops displayed on canonical frameworks
Heavy chain sequences of bovine antibodies with ultralong CDRH3s were obtained from a collection of sequences that we reported previously [23]
We used a collection of bovine antibody heavy chain variable gene sequences we had obtained previously from the blood of domestic cows (Bos taurus) using single-molecule long-read sequencing techniques [23]

Summary

Introduction

The highly stable immunoglobulin fold is the universal protein scaffold structure for functionally diverse antibodies, enabling mammalian hosts to resist highly diverse pathogens using structures with hypervariable loops displayed on canonical frameworks. Principally the limited size of mammalian genomes, all vertebrates except the jawless fish use variable (V), diversity (D), and joining (J) gene segment recombination including non-templated V-D and D-J junctional diversification and heavy/light chain pairing to dramatically diversify the primary antibody repertoire. B cells produce heavychain-only antibodies (HCAbs), in addition to conventional antibodies with heavy/light chain paired configuration These HCAbs contain some unusual structural features that allow camelids to diversify their antibody repertoires further, including use of various interloop disulfide bonds, an increased surface area of the paratopes, and reshaping of paratopes [6]. Potential non-canonical disulfide bonds within CDRH3, and between CDRH2 and CDRH3 were suggested because of high probability of presence of cysteine residues in CDRH3 and CDRH2, adding potential structural diversity of the antibodies

Methods

Results

Conclusion