Fig. 5.
Abp2DRBD pocket dynamics. (A) Aligned structures of the two molecules of Abp1DRBD (molecule A—orange and molecule B—wheat), Abp2DRBD (blue), and Abp2DRBD R86E (red), focused on the anterior binding pocket loop. (B) Number of unique conformational states in Abp2DRBD WT (black), R86E (red), K34A (brown) and shared between WT/R86E (yellow), WT/K34A (magenta), K34A/R86E (red), and WT/K34A/R86E (green), depicted in C. (C) Network representation of the shared state-space between variants, as determined by FAST simulations of Abp2DRBD WT, R86E, and K34A. Nodes represent distinct conformational states, with node size proportional to the equilibrium population. Edges represent conditional transition probabilities within 2 ns. Distances between nodes roughly track with their kinetic distance. (D) Probability of observing a particular loop opening distance for each variant, determined with a Markov model from the FAST simulations. (E) Binding of WT vs. K34A against fibrinogen.