Extended Data Fig. 10: Evolution of key observables during SMD simulations.
From: Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments
a, Predicted fraction pBD of Pi egress through the R177-N111 backdoor along SMD replicate 1, with neutral meH73, as obtained by classifier analysis of the enhanced sampling trajectories. b, Predicted fraction pBD of Pi egress through the R177-N111 backdoor along SMD replicate 1, with positively charged meHis73, as obtained by classifier analysis of the enhanced sampling trajectories. c, Survival analysis of the R177-N111 hydrogen bond in SMD simulations. For each protonation state of meH73, we computed the fraction of trajectories with the R177-N111 hydrogen bond still formed at time t. A distance cut-off of 0.6 nm between atoms CZ of R177 and CG of N111 was used to define a formed hydrogen bond. The solid lines represent the 2 ns-rolling average of the survival fraction. The dotted lines represent the 2 ns-rolling averages of the survival fraction ± SEM. The background overlays represent the raw values for the survival fraction ± SEM. d, Survival analysis of the rotameric state of H161. For each protonation state of meH73, we computed the fraction of trajectories with H161 in a core-like rotameric state. H161 side-chain rotameric states were defined by χ1 torsion angle being above or below 180 deg. Representation conventions are the same as for panel c. e–l. Evolution of structural observables during for all SMD simulation replicates. For clarity, 2 ns-moving averages are shown.
