Computational design of Periplasmic binding protein biosensors guided by molecular dynamics
Fig 2
RMSD of molecular dynamics simulations of Maltose Binding Protein (MBP) in apo and holo forms.
A, B: Holo simulations were generated from the starting point of the MBP/maltose complex crystal structure. A) Individual traces for 10x100ns MBP holo simulations. B) The mean, minimum, and maximum RMSD values for the MBP holo simulations. C, D: Apo simulations were generated from the starting point of the MBP/maltose complex crystal structure with maltose removed. C) Individual traces for 10x200ns MBP apo simulations. D) The mean, minimum, and maximum RMSD values for the MBP apo simulations. E) Final poses of MBP in representative holo/closed (purple) and apo/open (orange) simulations, chosen for RMSD close to the mean-of-means for each condition. Maltose is shown in the holo structure in green.