Figure 3.
PSMB10 G209R results in a less stable immunoproteasome assembly in silico. (A) 20S immunoproteasome structure (PDB 6E5B) highlighting PSMB10 (in blue) and neighboring β subunits PSMB1 (green), PSMB3 (light brown), PSMB4 (yellow), and PSMB9 (dark brown) of the inner rings of the assembled immunoproteasome. (B) Zoomed views of the immunoproteasome subunits surrounding PSMB10 residue G209 (upper panel) and G209R (lower panel) suggesting major clashes with R19 within PSMB10 and R211 and D213 of PSMB1. (C) Overall protein RMSD over the 100-ns MDS production run for PSMB10 WT (blue) and PSMB10 G209R (red). (D and E) (D) Residue backbone atom RMSF and (E) difference RMSF (PSMB10 G209R minus PSMB10 WT at each residue). The dotted lines denote two standard deviations (±2σ) from the average difference RMSF, and residues outside these values were considered to have the most significant changes in residue dynamics and corresponded to four protein regions (1–4, red shading). (F) Protein–protein docking of representative structures of PSMB10 WT (left, zoomed-in view) is accomplished with minimal clashes with its neighboring proteins. In contrast, PSMB10 G209R docking results in severe clashes with PSMB3 and PSMB1 (right, zoomed-in view). (G) Potential energy calculation for the 10 docked complexes for each protein reveals significantly reduced complex stability with PSMB10 G209R resulting from the identified steric clashes with neighboring subunits (t test, **P < 0.002). Refer to the image caption for details. Panel A: Structural model shows immunoproteasome highlighting P S M B 10 and neighboring subunits within assembled complex. Panel B: Zoomed structural views compare wild type and G 209 R mutation showing steric clashes with adjacent residues. Panel C: Line graph shows R M S D over time comparing P S M B 10 wild type and G 209 R stability. Panel D: Line graph shows R M S F across residues indicating differences in backbone flexibility between variants. Panel E: Difference R M S F plot highlights regions with significant dynamic changes between wild type and mutant protein. Panel F: Docking models compare wild type and mutant interactions showing increased steric clashes in G 209 R variant. Panel G: Scatter plot shows reduced complex stability and altered potential energy in the mutant compared to wild type.

PSMB10 G209R results in a less stable immunoproteasome assembly in silico. (A) 20S immunoproteasome structure (PDB 6E5B) highlighting PSMB10 (in blue) and neighboring β subunits PSMB1 (green), PSMB3 (light brown), PSMB4 (yellow), and PSMB9 (dark brown) of the inner rings of the assembled immunoproteasome. (B) Zoomed views of the immunoproteasome subunits surrounding PSMB10 residue G209 (upper panel) and G209R (lower panel) suggesting major clashes with R19 within PSMB10 and R211 and D213 of PSMB1. (C) Overall protein RMSD over the 100-ns MDS production run for PSMB10 WT (blue) and PSMB10 G209R (red). (D and E) (D) Residue backbone atom RMSF and (E) difference RMSF (PSMB10 G209R minus PSMB10 WT at each residue). The dotted lines denote two standard deviations (±2σ) from the average difference RMSF, and residues outside these values were considered to have the most significant changes in residue dynamics and corresponded to four protein regions (1–4, red shading). (F) Protein–protein docking of representative structures of PSMB10 WT (left, zoomed-in view) is accomplished with minimal clashes with its neighboring proteins. In contrast, PSMB10 G209R docking results in severe clashes with PSMB3 and PSMB1 (right, zoomed-in view). (G) Potential energy calculation for the 10 docked complexes for each protein reveals significantly reduced complex stability with PSMB10 G209R resulting from the identified steric clashes with neighboring subunits (t test, **P < 0.002).

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