The In Silico Prediction of Hotspot Residues that Contribute to the Structural Stability of Subunit Interfaces of a Picornavirus Capsid

Figures

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  Figure 1. Flow diagram of the methodology used in the study. Theiler’s murine encephalomyelitis virus (TMEV) subcomplexes representing the different subunit interfaces of TMEV were extracted from the homology model of the TMEV GDVII capsid generated previously [37,38]. The complexes were submitted to five tools for hotspot prediction. The prediction of protein interactions was performed using PIC and jsPISA. Hotspot residues and their interacting partners were mapped to the capsid complexes using PyMOL. Finally, ENDscript2 was used to assess the conservation of individual hotspot residues across the picornavirus family.

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  Figure 2. TMEV GDVII capsid subcomplexes for subunit interface hotspot and residue–residue interaction prediction. The respective subcomplexes were extracted from the biological assembly of TMEV GDVII in PyMOL. (A) The intraprotomer complex, consisting of a single protomer of the capsid. (B) The interprotomer complex, comprising two adjacent protomers within a pentamer. (C) The first complex of the interpentamer interface, consisting of two opposing protomers from two adjacent pentamers. (D) The second complex of the interpentamer interface, consisting of two adjacent protomers from two adjacent pentamers. Capsid proteins: VP1 (blue); VP2 (green); VP3 (red); and VP4 (yellow). The intraprotomer, interprotomer and interpentamer interfaces are denoted by black dashed lines. The five-fold, three-fold and two-fold axes are indicated by white pentagons, triangles and rectangles, respectively.

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  Figure 3. Hotspot residues and their interacting partners at the intraprotomer interfaces of the TMEV capsid. (A) Structure of the picornavirus capsid showing a single protomer. The intraprotomer interfaces between the three main capsid proteins are indicated by dashed black lines. (B) Structural cartoon mapping of predicted hotspot residues (shown as grey spheres) at the intraprotomer interfaces. (C) Schematic network of hotspot residues and the contacts made with their residue binding partners at the intraprotomer interfaces. Hotspot residues are outlined in black. Residues without outlines are non-hotspot partner residues. VP1 residues (blue); VP2 residues (green); VP3 residues (red); VP4 residues (yellow). Noncovalent interactions between hotspots and partners are shown as solid lines: hydrogen bonds (black lines); hydrophobic (purple lines); aromatic (orange lines); aromatic–sulphur (turquoise lines); cation–pi (blue lines); ionic (green lines) interactions.

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  Figure 4. Radial map of the conservation of TMEV intraprotomer residues identified as hotspots across respective picornavirus species. The individual TMEV capsid proteins were submitted to ENDScript2 for conservation analysis. The degree of conservation for each TMEV hotspot was compared in nine representative picornaviruses across four genera. Identity of viruses: 1) Cardiovirus B (SAFV; PDB: 5CFC/5A8F); 2) Cardiovirus A (EMCV; PDB: 2MEV); 3) Senecavirus (SVV-1; PDB: 3CJI); 4) Equine Rhinitis A Virus (ERAV; PDB: 2WFF); 5) Foot-and-mouth disease virus (FMDV; PDB: 5ACA); 6) Enterovirus A (EV-71; PDB: 3VBS); 7) Enterovirus B (CAV-9; PDB: 1D4M); 8) Rhinovirus A (HRV-3; PDB: 1RHI); 9) Rhinovirus B (HRV-2; PDB: 1FPN). Full alignments are available in Supplementary Figures S1–S4.

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  Figure 5. Hotspot residues and their interacting partners at the interprotomer interfaces of the TMEV capsid. (A) Structure of the picornavirus capsid showing two protomers within a pentamer that form the interprotomer interface (dashed black line). (B) Structural cartoon mapping of predicted hotspot residues (shown as grey spheres) at the interprotomer interfaces. (C) Network of hotspot residues and the contacts made with their residue binding partners at the interprotomer interface. Hotspot residues are outlined in black; partner non-hotspots are not outlined. VP1 residues (blue); VP2 residues (green); VP3 residues (red); VP4 residues (yellow). Noncovalent interactions between hotspots and partners are shown as solid lines: hydrogen bonds (black lines); hydrophobic (purple lines); aromatic (orange lines); aromatic–sulphur (turquoise lines); and cation–pi (blue lines) interactions.

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  Figure 6. Radial map of the conservation of TMEV interprotomer residues identified as hotspots across respective picornavirus species. The individual TMEV capsid proteins were submitted to ENDScript2 for conservation analysis. The degree of conservation for each TMEV hotspot was compared in eight representative picornaviruses across four genera. Identity of viruses: 1) Cardiovirus B (SAFV; PDB: 5CFC/5A8F); 2) Cardiovirus A (EMCV; PDB: 2MEV); 3) Senecavirus (SVV-1; PDB: 3CJI); 4) Equine Rhinitis A Virus (ERAV; PDB: 2WFF); 5) Foot-and-mouth disease virus (FMDV; PDB: 5ACA); 6) Enterovirus A (EV-71; PDB: 3VBS); 7) Enterovirus C (PV-1; PDB: 2PLV); 8) Rhinovirus A (HRV-3; PDB: 1RHI). Full alignments are available in Supplementary Figures S1–S4.

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  Figure 7. Schematic network of hotspot residues and their interacting partners at the interpentamer interfaces of the TMEV GDVII capsid. (A) Structure of the picornavirus capsid showing four protomers from two pentamers that form the interpentamer interface (dashed black line). (B) Structural cartoon mapping of predicted hotspot residues (shown as grey spheres) at the interpentamer interfaces. (C) Network of hotspot residues and the contacts made with their residue binding partners at the interpentamer interface. Hotspot residues are outlined in black; partner non-hotspots are not outlined. VP1 residues (blue); VP2 residues (green); VP3 residues (red); VP4 residues (yellow). Noncovalent interactions between hotspots and partners are shown as solid lines: hydrogen bonds (black lines); hydrophobic (purple lines); cation–pi (blue lines); and ionic (green lines) interactions.

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  Figure 8. Radial map of the conservation of TMEV interpentamer residues identified as hotspots across respective picornavirus species. The individual TMEV capsid proteins were submitted to ENDScript2 for conservation analysis. The degree of conservation for each TMEV hotspot was compared across nine representative picornaviruses across four genera. Identity of viruses: 1) Cardiovirus B (SAFV; PDB: 5CFC/5A8F); 2) Cardiovirus A (EMCV; PDB: 2MEV); 3) Senecavirus (SVV-1; PDB: 3CJI); 4) Equine Rhinitis A Virus (ERAV; PDB: 2WFF); 5) Foot-and-mouth disease virus (FMDV; PDB: 5ACA); 6) Enterovirus A (EV-71; PDB: 3VBS); 7) Enterovirus C (PV-1; PDB: 2PLV); 8) Enterovirus D (EV-D68; PDB: 4WM7); 9) Rhinovirus B (HRV-B14; PDB: 1R08). Full alignments are available in Supplementary Figures S1–S4.