Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning

doi:10.1371/journal.pcbi.1012921

Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning

Fig 5

Biophysical characterization of Nb Ab.2.

(A) Circular Dichroism (CD) spectra of Nb Ab.2 displaying characteristic signals of -structured immunoglobulin (IgG) folded domains. (B) Estimation of secondary structure components derived from the CD data using BeStSel. (C, D) left: MST binding curve illustrating the interaction between recombinant SARS-CoV-2 RBD and Nb Ab.2. right: MST binding curve demonstrating the interaction between SARS-CoV-2 VLPs and Nb Ab.2. (E) Solvent-accessible surface area obtained from different snapshots of 200-ns molecular dynamics simulations of the RBD binding site considering the free RBD (orange) and within the fully glycosylated spike protein (blue). The snapshots were recorded at every 1 ns.

doi: https://doi.org/10.1371/journal.pcbi.1012921.g005