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标题：Structural and energetic analysis of metastable intermediate states in the E1P–E2P transition of Ca ²⁺-ATPase
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作者：Chigusa Kobayashi ; Yasuhiro Matsunaga ; Jaewoon Jung 等
期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2021
卷号：118
期号：40
DOI：10.1073/pnas.2105507118
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：Significance Ion pumps (or P-type ATPases) are membrane proteins, which transport ions through biological membranes against a concentration gradient, a function essential for many biological processes, such as muscle contraction, neurotransmission, and metabolism. Molecular mechanisms underlying active ion transport by ion pumps have been investigated by biochemical experiments and high-resolution structure analyses. Here, the transition of sarcoplasmic reticulum Ca 2+-ATPase upon dissociation of Ca 2+ is investigated using atomistic molecular dynamics simulations. We find intermediate structures along the pathway are stabilized by transient interactions between A- and P-domains as well as lipid molecules in the transmembrane helices. 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.
关键词：encalcium ion pump;protein–lipid interactions;molecular dynamics;conformational change;free energy analysis