Fig 1: Hydrogen bonding distance evolution of representative key interactions in the MD trajectory of the MB59-CD59 complex. (A,B) Time evolution of H-bonding interactions involving MB59 CDR1 (A) and CDR3 (B). (C) Cartoon representation showing the H-bonding interactions on a representative structure of the trajectory (the closest to the average structure).
Fig 2: Overlay of sensorgrams obtained for the binding of the three bi-cyclic peptides to CD59 using SPR (A,C,E) and BLI (B,D,F) techniques. The curves of pm59sh are reported in (A,B), the curves of pm59md are reported in (C,D) and the curves of pm59ln are reported in (E,F).
Fig 3: Paratope and antigen predictions. (A) Paratope propensity of MB59 residues. Cartoon representation of MB59 model highlighting the scores of the paratope propensity prediction analysis. Colour scheme spans from red (highest paratope propensity score) to blue (lowest paratope propensity score). (B) CD59 sequence-based epitope prediction using BepiPred3.0; lightest yellow corresponds the highest scores. (C) Structure-based discontinuous epitope prediction using DiscoTope. Green peaks correspond to highest scores, over the threshold (-10). (D) Cartoon representation of the MB59-CD59 computed using AlphaFold2.0. High ranking epitope residues are labelled.
Fig 4: Cartoon representation of the CD59—blocking scFv, MB59. VL and VH chains are drawn in blue and lilac purple, respectively. The inset reports a scheme of scFv chain organisation.
Fig 5: RMSD and RMSF analysis from MD simulations. (A) Time evolution of RMSD (Å), computed on Cα atoms, for the MD59-CD59 and isolated chains. In (B) RMSD evolution upon removal of the linker 115–135. The colour code is indicated. (C) RMSF values, calculated on backbone Cα atoms in the equilibrated region (100–500 ns).
Supplier Page from Abcam for Recombinant Human CD59 protein