Open AccessStructural and energetic analysis of metastable intermediate states in the E1P–E2P transition of Ca 2+ -ATPase
Author(s) -
Chigusa Kobayashi,
Yasuhiro Matsunaga,
Jaewoon Jung,
Yuji Sugita
Publication year - 2021
Publication title -
proceedings of the national academy of sciences of the united states of america
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.011
H-Index - 771
eISSN - 1091-6490
pISSN - 0027-8424
DOI - 10.1073/pnas.2105507118
Subject(s) - chemistry , protonation , crystallography , dissociation (chemistry) , ion , umbrella sampling , biophysics , molecule , endoplasmic reticulum , transition state , metastability , transmembrane domain , cytoplasm , molecular dynamics , membrane , biochemistry , computational chemistry , biology , organic chemistry , catalysis
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.