Fig. 3

(A) Root-mean-square deviation RMSD (Å) distributions calculated for the peptide backbone in Ahx-SV and Ahx-PQ and the corresponding epitopes in the hCG protein. Data was collected from the analysis of 150 ns MD simulations in pre-polymerization mixtures (Ahx-SV and Ahx-PQ) or water (full hCG), using the coordinates of the SV and PQ epitopes in the 1HRP crystallographic structure as reference models. (B) Peptide radius of gyration R_g (Å) for the SV and PQ sequences in Ahx-SV, Ahx-PQ, and the full hCG protein calculated from 150 ns MD trajectories. (C) Structural representations of the backbone conformations achieved by the SV and PQ sequences in Ahx-SV, Ahx-PQ, and the full hCG protein throughout 150 MD trajectories. Structures are displayed from MD trajectories aligned to the first and last amino acids of each sequence. (D) Heatmaps for the frequency of secondary structure assignations according to DSSP analysis on SV and PQ sequences in Ahx-SV, Ahx-PQ, and the full hCG protein throughout 150 MD trajectories.