Fig 1.
Structural properties of the MID1 Bbox1 domain.
(A) The ensemble of 13 structures generated from NMR-derived restraints (PDB code: 2FFW). (B) Magnitude of the fluctuation represented as eigenvectors of the Bbox1 ensemble of structures. The conformational fluctuations indicate both magnitude and directions (arrows) and are derived from PCA analysis. (C) The fluctuations of the average NMR structure are shown as a function of residue number. (D) Zoomed-in snapshot of the small cavity near residue A130. The blue dots represent the solvent accessible surface.
Fig 2.
Effects of mutating of residue A130.
(A) Homology modeling of Bbox1 structures highlighting the position and packing of side chain of A130 (i) compared to those of the T130 (ii) and V130 (iii). (B) Backbone RMSDs for WT (blue), A130T (red), and A130V (orange) during the MD simulations.
Fig 3.
Structural analysis of the MD simulation results.
(A) Backbone RMSFs for WT (blue), A130T (red), and A130V (orange) during the MD simulations. (B) Time evolution of the secondary structural elements, based on DSSP classification, of the wild type and mutant proteins. (C) The angle formed by the Cα atoms of D129, A130, and V131. (D) The angle fluctuations for WT (blue), A130T (red), and A130V (orange) during the MD simulations with the corresponding histogram to the side.
Table 1.
Apparent average pKa values of residue C142 during the multiple MD simulations for the native protein and two mutants (A130T and A130V).