Comparison of the Internal Dynamics of Metalloproteases Provides New Insights on Their Function and Evolution
Fig 1
Thermolysin PC, ED and NM modes.
(A) Visual representation of residue-level PC1 mode vectors (black, scale 2.05), NM1 mode vectors (green, scale 1.47) and ED3 mode vectors from Sim1 (red, scale 3.17). Inset: Details of active site region. Colored ribbons corresponding to the top of the active site pocket (residues 105–177 in blue and 210–230 in green). Active site residues H142, H146 and E166 in green and catalytic E143 in cyan sticks representation. (B) Square fluctuations as a function of residue index (1.316) obtained for PC1. Top bars correspond to residue coloring as presented in (A), with catalytic E143 represented as cyan circle. (C) Projection of thermolysin crystal structures along PC1 and PC2. Structures were grouped into bound (red) and unbound (black) groups; unbound reference structure (PDB ID: 1L3F) used in PCA, EDA and NM calculations (green). (D) Square fluctuations as a function of residue index obtained for ED3 from Sim1 and ED1 from Sim2. (E) Cross-projection of crystal structures along PC1 and ED3 from Sim1 (r = 0.94). (F) Square fluctuations as a function of residue index obtained for NM1 from calculated thermolysin ANM and respective variants. (G) Cross-projection of crystal structures along PC1 and NM1 (r = 0.95).