Structural and energetic analysis of metastable intermediate states in the E1P–E2P transition of Ca(2+)-ATPase

Sarcoplasmic reticulum (SR) Ca(2+)-ATPase transports two Ca(2+) ions from the cytoplasm to the SR lumen against a large concentration gradient. X-ray crystallography has revealed the atomic structures of the protein before and after the dissociation of Ca(2+), while biochemical studies have suggested the existence of intermediate states in the transition between E1P⋅ADP⋅2Ca(2+) and E2P. Here, we explore the pathway and free energy profile of the transition using atomistic molecular dynamics simulations with the mean-force string method and umbrella sampling. The simulations suggest that a series of structural changes accompany the ordered dissociation of ADP, the A-domain rotation, and the rearrangement of the transmembrane (TM) helices. The luminal gate then opens to release Ca(2+) ions toward the SR lumen. Intermediate structures on the pathway are stabilized by transient sidechain interactions between the A- and P-domains. Lipid molecules between TM helices play a key role in the stabilization. Free energy profiles of the transition assuming different protonation states suggest rapid exchanges between Ca(2+) ions and protons when the Ca(2+) ions are released toward the SR lumen.