Microsecond molecular dynamics simulations of Mg²?- and K?-bound E1 intermediate states of the calcium pump.

ABSTRACT: We have performed microsecond molecular dynamics (MD) simulations to characterize the structural dynamics of cation-bound E1 intermediate states of the calcium pump (sarcoendoplasmic reticulum Ca²?-ATPase, SERCA) in atomic detail, including a lipid bilayer with aqueous solution on both sides. X-ray crystallography with 40 mM Mg²? in the absence of Ca²? has shown that SERCA adopts an E1 structure with transmembrane Ca²?-binding sites I and II exposed to the cytosol, stabilized by a single Mg²? bound to a hybrid binding site I'. This Mg²?-bound E1 intermediate state, designated E1•Mg²?, is proposed to constitute a functional SERCA intermediate that catalyzes the transition from E2 to E1•2Ca²? by facilitating H?/Ca²? exchange. To test this hypothesis, we performed two independent MD simulations based on the E1•Mg²? crystal structure, starting in the presence or absence of initially-bound Mg²?. Both simulations were performed for 1 µs in a solution containing 100 mM K? and 5 mM Mg²? in the absence of Ca²?, mimicking muscle cytosol during relaxation. In the presence of initially-bound Mg²?, SERCA site I' maintained Mg²? binding during the entire MD trajectory, and the cytosolic headpiece maintained a semi-open structure. In the absence of initially-bound Mg²?, two K? ions rapidly bound to sites I and I' and stayed loosely bound during most of the simulation, while the cytosolic headpiece shifted gradually to a more open structure. Thus MD simulations predict that both E1•Mg²? and E•2K+ intermediate states of SERCA are populated in solution in the absence of Ca²?, with the more open 2K+-bound state being more abundant at physiological ion concentrations. We propose that the E1•2K? state acts as a functional intermediate that facilitates the E2 to E1•2Ca²? transition through two mechanisms: by pre-organizing transport sites for Ca²? binding, and by partially opening the cytosolic headpiece prior to Ca²? activation of nucleotide binding.

SUBMITTER: Espinoza-Fonseca LM 

PROVIDER: S-EPMC3997511 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature