Tracing cytoplasmic Ca ²⁺ ion and water access points in the Ca ²⁺-ATPase

Sarco(endo)plasmic reticulum Ca ²⁺-ATPase (SERCA) transports two Ca ²⁺ ions across the membrane of the sarco(endo)plasmic reticulum against the concentration gradient, harvesting the required energy by hydrolyzing one ATP molecule during each transport cycle. Although SERCA is one of the best structurally characterized membrane transporters, it is still largely unknown how the transported Ca ²⁺ ions reach their transmembrane binding sites in SERCA from the cytoplasmic side. Here, we performed extended all-atom molecular dynamics simulations of SERCA. The calculated electrostatic potential of the protein reveals a putative mechanism by which cations may be attracted to and bind to the Ca ²⁺-free state of the transporter. Additional molecular dynamics simulations performed on a Ca ²⁺-bound state of SERCA reveal a water-filled pathway that may be used by the Ca ²⁺ ions to reach their buried binding sites from the cytoplasm. Finally, several residues that are involved in attracting and guiding the cations toward the possible entry channel are identified. The results point to a single Ca ²⁺ entry site close to the kinked part of the first transmembrane helix, in a region loaded with negatively charged residues. From this point, a water pathway outlines a putative Ca ²⁺ translocation pathway toward the transmembrane ion-binding sites.