Reaching the full potential of cryo-EM reconstructions with molecular dynamics simulations at 310 K: Actin filaments as an example

Abstract

Cryo-electron microscopy (cryo-EM) structures of multi-protein complexes such as actin filaments help explain the mechanisms of assembly and interactions with partner proteins. Yet, rapid cooling during freezing may not preserve the conformations at physiological temperature. All-atom molecular dynamics simulations starting with cryo-EM reconstructions can provide additional insights. For example, at 310 K the states of ADP-actin filaments consistent with higher entropy favor partly twisted subunits and smaller rotations along short-pitch helix than the cryo-EM reconstructions, while cryogenic temperatures favor flattened conformations. In the active site, the positions of Q137 and the catalytic water 1 and activating water 2 optimal for in line attack on the {gamma}-phosphate of ATP are very rare at 310 K, explaining in part the slow rate of ATP hydrolysis in filaments. This favorable arrangement of the waters is not observed in simulations of actin monomers. At 310 K subunits in ADP-Pi-actin filaments have their backdoor gates open 60% of the time for phosphate release, a conformation not observed by cryo-EM. Rare fluctuations open binding sites for cofilin and phalloidin. The twisted conformations of pointed end subunits and interactions of the D-loop of the penultimate subunit explain the slow association of new subunits. The terminal subunit at the barbed end is tethered to its neighbor along the long-pitch helix but transiently dissociates from its lateral neighbor. These effects of subfreezing temperatures on actin filaments are surely not an isolated example, so MD simulations of structures of other frozen proteins will be informative. Significance statementFunctionally important properties of proteins are tightly linked to their conformations at physiological temperatures. While cryo-EM reconstructions and crystal structure of frozen proteins provide a molecular resolution of protein structures, they might differ from the conformations at physiological temperature. Using the actin filament as a case study, we find cryo-EM reconstructed structures correspond to low entropy conformations that differ from the ensemble of structures in molecular dynamics simulations at 310 K. The fluctuations of subunit dihedral angles, short-pitch rotations and some side chains explain functionally important properties of actin filaments, including the slow rates of ATP hydrolysis and phosphate release as well as the slow binding of the protein cofilin and cyclic peptide phalloidin.