Akademik Veri Yönetim Sistemi
Turkish Journal of Biology, cilt.47, sa.6, ss.423-436, 2023 (SCI-Expanded, Scopus, TRDizin)
Background/aim: In recent years, single-domain antibodies, also known as nanobodies, have emerged as an alternative to full immunoglobulin Gs (IgGs), due to their various advantages, including increased solubility, faster clearance, and cheaper production. Nanobodies are generally derived from the variable domain of the camelid heavy-chain-only immunoglobulin Gs (hcIgGs). Due to the high sequence homology between variable heavy chains of camelids (VH Hs) and humans (VH s), hcIgGs are ideal candidates for nanobody development. However, further examination is needed to understand the structural differences between VH s and VH Hs. This analysis is essential for nanobody engineering to mitigate potential immunogenicity, while preserving stability, functionality, and antigen specificity. Materials and methods: We obtained the VH and VH H sequences of various camelid and non-camelid mammalian antibodies from public databases and used multiple sequence alignment based on the Chothia numbering scheme. Aligned sequences were subjected to diverse analyses encompassing paratope length, binding prediction, motif, disulfide bridge, salt bridge profiling, and physicochemical characteristic distribution. Logistic Regression coupled with the Boruta-Random Forest algorithm facilitated the comprehensive examination of physicochemical properties. Results: Our findings revealed longer, less variable paratope sequences in VH Hs, along with specific antigen binding residues with increased binding potential compared to VH s. Although the VH s showed more heterogeneous noncanonical disulfide bond patterns, the VH Hs had a higher number of noncanonical disulfide bridges. Intriguingly, a typical salt bridge between the 94th and 101st positions in the VH s had a very low encounter rate in the VH Hs. Surprisingly, we also identified notable differences in the physicochemical patterns of mostly conserved frameworks (FWs), especially the FW2 and FW3 regions, between VH s and VH Hs. Conclusion: Our findings point to possible key sites in VH Hs as candidate residues for nanobody engineering efforts.