Fig 1.
Phylogenetic tree built with 87 sequences of the M protein of the PEDV from Mexico, United States of America, Europe and Asia.
The amino acid sequences of M protein were clustered into three groups related to G2a, G2b, G1 strains of PEDV. The arrows signal the two sequences chosen to generate the 3D model of the M protein. The evolutionary history was inferred using the Neighbor-Joining method. Details and references are provided in Material and Methods section.
Fig 2.
Predicted 3D models of the CV777 M and 2013MMV M proteins, generated with Robetta.
A) CV777 M protein model. B) 2013MMV M protein model. The transmembrane region is shown in red. The regions outside the viral membrane are shown in yellow. The globular region is shown in green. The blue arrows point to the N-terminal end and the white arrows point to the C-terminal end. C) Overlapping of the 3D models of CV777 M and 2013MMV M proteins. The red areas correspond to the highest RMSD value, while the green areas correspond to the lowest RMSD value. The white arrows indicate the sites with the highest RMSD, corresponding to the loops and to the N- and C-terminal ends. D) 3D model of CV777 M protein on a theoretical lipid layer obtained from the OPM server. The program added red pseudoatoms to mark the extracellular hydrophobic boundary of the lipid bilayer. E) 3D model of 2013MMV M protein on a theoretical lipid bilayer obtained from the OPM server. In this case, the server added red and blue pseudoatoms to mark the extracellular and intracellular hydrophobic boundaries of the lipid bilayer, respectively.
Fig 3.
Evaluation of the overall model quality of 3D models of the CV777 M protein and 2013MMV M protein using ProSA web.
A) Z-score plot of the 3D model of CV777 M protein. B) Plot of residue scores (Knowledge-based energy) of the 3D model of CV777 M protein. C) Z-score plot of the 3D model of 2013MMV M protein. D) Plot of residue scores of the 2013MMV M protein. The black dot in A and C represents the 3D model of the M protein.
Table 1.
Continuous B-cell epitopes of CV777 M protein.
Fig 4.
Discontinuous epitopes predicted in ElliPro from CV777, 2013MMV and SARS-CoV-2 M protein models.
A) CV777 M protein. B) 2013MMV M protein. C) SARS-CoV-2 M protein from AlphaFold. D) SARS-CoV-2 M protein from Feig lab. Predicted discontinuous epitopes are highlighted in the 3D model with different colors to represent the score. The epitope with the highest score is represented in red up to the lowest value in orange. The score decreases from the epitopes marked in green, blue, yellow, and pink. Arrows with the same color indicate discontinuous epitopes located in equivalent regions in the models. Colored residues in each epitope are indicated in S2 Table.
Fig 5.
Discontinuous epitopes predicted in DiscoTope from CV777 and 2013MMV M protein and SARS-CoV-2 protein M models.
A) CV777 M protein. B) 2013MMV M protein. C) SARS-CoV-2 M protein from AlphaFold. D) SARS-CoV-2 M protein from Feig lab. Predicted discontinuous epitopes are highlighted in the 3D model with different colors to represent the score. The epitope with the highest score is represented in red up to the lowest value in orange. The score decreases from the epitopes marked in green, blue, yellow and pink. Arrows with the same color indicate discontinuous epitopes located in equivalent regions in the models. An additional color (light blue) show residues that were not predicted in ElliPro. Colored residues in each epitope are indicated in S3 Table.
Table 2.
Continuous T cell epitopes of CV777 and 2013MMV M protein.