Computational design of Periplasmic binding protein biosensors guided by molecular dynamics
Fig 3
A comparison of metrics attempting to identify regions of MBP primary sequence known to be receptive to effector protein insertion with highlighted regions of interest.
Across all figures, the residue ranges 167–173 and 335–348 are highlighted. 167–173 contains the region of interest 169–171, with flanking residues also highlighted for ease of visualisation. A) The change in backbone dihedral angle between holo and apo crystal structures (PDB 1ANF, 1OMP respectively). B) Change in backbone dihedral angle between holo and apo molecular dynamics simulations. Neither regions 167–173 nor 335–348 contain significant values for this metric. C) Difference in RMSF of each residue between holo and apo molecular dynamics simulations. D) Pearson correlation coefficient metric for all apo MBP simulations where the closed-to-open state transition was observed, filtered to only show peaks in the top percentile for mean, median, and maximum pixel value. Negative Pearson correlation coefficient indicates residues that become closer to each other throughout the closed-to-open transition, and positive values closer.