Fig. 2

Prediction of the flexibility of HEV-FMDV chimeric proteins. The different conformational models of Seq 8-P216 (a) and Seq 8-P222 (b) predicted by the CABS-flex server were superimposed and visualized by Pymol. The fluctuations of the protrusion index of the key epitope sites between the different conformations were calculated for both Seq 8-P216 (c) and Seq 8-P222 (d): the black circles represent the PI of the epitope sites in the input models; the lines represent the PI for the same residues in the 12 models predicted by the molecular dynamics simulation; the black arrows indicate the residues with a PI decrease in most of the 12 models compared to the input model. The overall exposure of HEV and FMDV epitopes in Seq 8-P216 and Seq 8-P222 chimeric proteins were computed for each model (e): the exposure is represented as the area under the curve of the protrusion index of the key-epitope sites (the method is detailed in the “Antigenicity analysis” section); circles and diamonds in red represent the overall antigenicity of the initial models; circles and diamonds in black represent the overall antigenicity of different models predicted in the molecular dynamics simulations