Actin is a major structural protein of the eukaryotic cytoskeleton and enables cell motility.
Here, we present a model of the actin filament (F-actin) that incorporates the global structure
of the recently published model by Oda et al. but also conserves internal stereochemistry. A
comparison is made using molecular dynamics simulation of the model with other recent F-
actin models. A number of structural determents such as the protomer propeller angle, the
number of hydrogen bonds and the structural variation among the protomers are analyzed.
The MD comparison is found to reflect the evolution in quality of actin models over the last
six years. In addition, simulations of the model are carried out in states with both ADP or
ATP bound and local hydrogen-bonding differences characterized. The results point to the
significance of a direct interaction of Gln137 with ATP for activation of ATPase activity after
the G-to-F-actin transition.
In many fields of physics, chemistry and biology the characterization of dynamical processes
between states or species is of fundamental interest. The central mathematical function in such sit-
uations is the committor probability - a generalized reaction coordinate that measures the progress
of the process of interest as the probability of proceeding towards the target state rather than re-
lapsing to the source state. Here, we present methodology for the efficient computation of com-
mittor probabilities for large-scale systems, such as, for example simuations of biomolecular fold-
ing. A method is derived for computing the committor for discrete state spaces using eigenvectors
with expressions for the sensitivity and a Bayesian error model for the committor. The concepts
are illustrated on two examples of diffusive dynamics with a very large number of states: a two-
dimensional model potential with three minima, and a three-dimensional model representing
protein-ligand binding. The method can finally be used to compute committor probabilities in-
cluding error estimations for medium and large system sizes allowing access to the apparatus of
transition path theory and its applications.