Espinoza-Fonseca, L. Michel; Autry, Joseph M.; Thomas, David D.
Microsecond Molecular Dynamics Simulations of Mg2+- and K+- Bound E1 Intermediate States of the Calcium Pump
PLOS ONE, 9 Art. No. e95979, APR 23 2014

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 center dot Mg2+, is proposed to constitute a functional SERCA intermediate that catalyzes the transition from E2 to E1 center dot 2Ca(2+) by facilitating H+/Ca2+ exchange. To test this hypothesis, we performed two independent MD simulations based on the E1 center dot Mg2+ crystal structure, starting in the presence or absence of initially-bound Mg2+. Both simulations were performed for 1 mu s 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 center dot Mg2+ and E center dot 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 center dot 2K(+) state acts as a functional intermediate that facilitates the E2 to E1 center dot 2Ca(2+) 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.

DOI:10.1371/journal.pone.0095979

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