Sequence and structure statistics of the nanobody database and molecular dynamics simulation analysis of the nanobody VHH

Abstract

Antibodies are immunoglobulins produced in vivo by immune cells stimulated by exogenous molecules, and nano-antibodies are a class of molecules that are similar to conventional antibodies but smaller in size. Originally discovered as an antibody in camelidsand cartilaginous fishes, they are called heavy chain antibodies due to the lack of light and heavy chain constant regions in the CH1 region except for the retained heavy chain, and their binding region to the antigen consists of the heavy chain variable region only, making them the smallest antibodies available with complete antibody functional properties. In this experiment, we analyzed the commonalities and differences of the nanobodies by extracting all their amino acid sequences, performed protein modeling of the relevant nanobodies of coronaviruses among them, and then analyzed the data of RMSD and RMSF by using molecular dynamics simulation, and finally predicted and analyzed the protein conformation and the structures of VHH at all levels.