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Ma R, Briggs JM. The tilting motion of the central core reveals the transport mechanism of the sarco/endoplasmic reticulum Ca 2+-ATPase. Int J Biol Macromol 2024; 269:132000. [PMID: 38697445 DOI: 10.1016/j.ijbiomac.2024.132000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/22/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
The sarco/endoplasmic reticulum Ca2+-ATPase (SERCA) transports two Ca2+ ions per ATP hydrolyzed from the cytoplasm to the lumen. However, how the ATP hydrolysis remotely drives the Ca2+ transport is unclear. In the SERCA1a crystal structures, the ATP hydrolysis is accompanied by the notably increasing tilting angle of the central core (CC) and the Ca2+ transport, and the CC tilting angle dramatically decreases in the E2 to E1 transition. We demonstrated that the significantly increasing tilting motion of the CC drove the Ca2+ release in the molecular dynamics simulation of the R836A variant, and the dramatic spontaneous decrease in the CC tilting angle of the E2 state triggers the restart of the SERCA1a's transport cycle. The repulsion between the phosphorylated D351 and the phosphate groups in ADP triggers the release of ADP from the SERCA1a headpiece. We proposed a novel SERCA transport mechanism in which ATP hydrolysis drives a significant tilting motion of the CC, which drives Ca2+ transport and the A domain rotational motion in the E1P-ADP-2Ca2+ to E2P transition. The dramatic spontaneous decrease in the CC tilting angle of the E2 state drives the restart of the transport cycle.
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Affiliation(s)
- Rulong Ma
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, United States of America
| | - James M Briggs
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, United States of America.
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2
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Structural and energetic analysis of metastable intermediate states in the E1P-E2P transition of Ca 2+-ATPase. Proc Natl Acad Sci U S A 2021; 118:2105507118. [PMID: 34593638 PMCID: PMC8501872 DOI: 10.1073/pnas.2105507118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 01/05/2023] Open
Abstract
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 Ca2+-ATPase upon dissociation of Ca2+ 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) Ca2+-ATPase transports two Ca2+ 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 Ca2+, while biochemical studies have suggested the existence of intermediate states in the transition between E1P⋅ADP⋅2Ca2+ 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 Ca2+ 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 Ca2+ ions and protons when the Ca2+ ions are released toward the SR lumen.
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3
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Angle change of the A-domain in a single SERCA1a molecule detected by defocused orientation imaging. Sci Rep 2021; 11:13672. [PMID: 34211016 PMCID: PMC8249593 DOI: 10.1038/s41598-021-92986-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/18/2021] [Indexed: 11/24/2022] Open
Abstract
The sarcoendoplasmic reticulum Ca2+-ATPase (SERCA) transports Ca2+ ions across the membrane coupled with ATP hydrolysis. Crystal structures of ligand-stabilized molecules indicate that the movement of actuator (A) domain plays a crucial role in Ca2+ translocation. However, the actual structural movements during the transitions between intermediates remain uncertain, in particular, the structure of E2PCa2 has not been solved. Here, the angle of the A-domain was measured by defocused orientation imaging using isotropic total internal reflection fluorescence microscopy. A single SERCA1a molecule, labeled with fluorophore ReAsH on the A-domain in fixed orientation, was embedded in a nanodisc, and stabilized on Ni–NTA glass. Activation with ATP and Ca2+ caused angle changes of the fluorophore and therefore the A-domain, motions lost by inhibitor, thapsigargin. Our high-speed set-up captured the motion during EP isomerization, and suggests that the A-domain rapidly rotates back and forth from an E1PCa2 position to a position close to the E2P state. This is the first report of the detection in the movement of the A-domain as an angle change. Our method provides a powerful tool to investigate the conformational change of a membrane protein in real-time.
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Structural Basis of Substrate-Independent Phosphorylation in a P4-ATPase Lipid Flippase. J Mol Biol 2021; 433:167062. [PMID: 34023399 DOI: 10.1016/j.jmb.2021.167062] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/13/2021] [Accepted: 05/17/2021] [Indexed: 11/21/2022]
Abstract
P4-ATPases define a eukaryotic subfamily of the P-type ATPases, and are responsible for the transverse flip of specific lipids from the extracellular or luminal leaflet to the cytosolic leaflet of cell membranes. The enzymatic cycle of P-type ATPases is divided into autophosphorylation and dephosphorylation half-reactions. Unlike most other P-type ATPases, P4-ATPases transport their substrate during dephosphorylation only, i.e. the phosphorylation half-reaction is not associated with transport. To study the structural basis of the distinct mechanisms of P4-ATPases, we have determined cryo-EM structures of Drs2p-Cdc50p from Saccharomyces cerevisiae covering multiple intermediates of the cycle. We identify several structural motifs specific to Drs2p and P4-ATPases in general that decrease movements and flexibility of domains as compared to other P-type ATPases such as Na+/K+-ATPase or Ca2+-ATPase. These motifs include the linkers that connect the transmembrane region to the actuator (A) domain, which is responsible for dephosphorylation. Additionally, mutation of Tyr380, which interacts with conserved Asp340 of the distinct DGET dephosphorylation loop of P4-ATPases, highlights a functional role of these P4-ATPase specific motifs in the A-domain. Finally, the transmembrane (TM) domain, responsible for transport, also undergoes less extensive conformational changes, which is ensured both by a longer segment connecting TM helix 4 with the phosphorylation site, and possible stabilization by the auxiliary subunit Cdc50p. Collectively these adaptions in P4-ATPases are responsible for phosphorylation becoming transport-independent.
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5
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Structural dynamics of P-type ATPase ion pumps. Biochem Soc Trans 2020; 47:1247-1257. [PMID: 31671180 DOI: 10.1042/bst20190124] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/06/2019] [Accepted: 09/16/2019] [Indexed: 02/04/2023]
Abstract
P-type ATPases transport ions across biological membranes against concentration gradients and are essential for all cells. They use the energy from ATP hydrolysis to propel large intramolecular movements, which drive vectorial transport of ions. Tight coordination of the motions of the pump is required to couple the two spatially distant processes of ion binding and ATP hydrolysis. Here, we review our current understanding of the structural dynamics of P-type ATPases, focusing primarily on Ca2+ pumps. We integrate different types of information that report on structural dynamics, primarily time-resolved fluorescence experiments including single-molecule Förster resonance energy transfer and molecular dynamics simulations, and interpret them in the framework provided by the numerous crystal structures of sarco/endoplasmic reticulum Ca2+-ATPase. We discuss the challenges in characterizing the dynamics of membrane pumps, and the likely impact of new technologies on the field.
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Danko S, Yamasaki K, Daiho T, Suzuki H. Membrane Perturbation of ADP-insensitive Phosphoenzyme of Ca 2+-ATPase Modifies Gathering of Transmembrane Helix M2 with Cytoplasmic Domains and Luminal Gating. Sci Rep 2017; 7:41172. [PMID: 28117348 PMCID: PMC5259720 DOI: 10.1038/srep41172] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/16/2016] [Indexed: 11/25/2022] Open
Abstract
Ca2+ transport by sarcoplasmic reticulum Ca2+-ATPase involves ATP-dependent phosphorylation of a catalytic aspartic acid residue. The key process, luminal Ca2+ release occurs upon phosphoenzyme isomerization, abbreviated as E1PCa2 (reactive to ADP regenerating ATP and with two occluded Ca2+ at transport sites) → E2P (insensitive to ADP and after Ca2+ release). The isomerization involves gathering of cytoplasmic actuator and phosphorylation domains with second transmembrane helix (M2), and is epitomized by protection of a Leu119-proteinase K (prtK) cleavage site on M2. Ca2+ binding to the luminal transport sites of E2P, producing E2PCa2 before Ca2+-release exposes the prtK-site. Here we explore E2P structure to further elucidate luminal gating mechanism and effect of membrane perturbation. We find that ground state E2P becomes cleavable at Leu119 in a non-solubilizing concentration of detergent C12E8 at pH 7.4, indicating a shift towards a more E2PCa2-like state. Cleavage is accelerated by Mg2+ binding to luminal transport sites and blocked by their protonation at pH 6.0. Results indicate that possible disruption of phospholipid-protein interactions strongly favors an E2P species with looser head domain interactions at M2 and responsive to specific ligand binding at the transport sites, likely an early flexible intermediate in the development towards ground state E2P.
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Affiliation(s)
- Stefania Danko
- Asahikawa Medical University, Department of Biochemistry, Midorigaoka-Higashi, Asahikawa, 078-8510, Japan
| | - Kazuo Yamasaki
- Asahikawa Medical University, Department of Biochemistry, Midorigaoka-Higashi, Asahikawa, 078-8510, Japan
| | - Takashi Daiho
- Asahikawa Medical University, Department of Biochemistry, Midorigaoka-Higashi, Asahikawa, 078-8510, Japan
| | - Hiroshi Suzuki
- Asahikawa Medical University, Department of Biochemistry, Midorigaoka-Higashi, Asahikawa, 078-8510, Japan
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Autry JM, Thomas DD, Espinoza-Fonseca LM. Sarcolipin Promotes Uncoupling of the SERCA Ca 2+ Pump by Inducing a Structural Rearrangement in the Energy-Transduction Domain. Biochemistry 2016; 55:6083-6086. [PMID: 27731980 PMCID: PMC5506494 DOI: 10.1021/acs.biochem.6b00728] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We have performed microsecond (μs) molecular dynamics simulation (MDS) to identify structural mechanisms for sarcolipin (SLN) uncoupling of Ca2+ transport from ATP hydrolysis for the sarcoplasmic reticulum Ca2+-ATPase (SERCA). SLN regulates muscle metabolism and energy expenditure to provide resistance against diet-induced obesity and extreme cold. MDS demonstrated that the cytosolic domain of SLN induces a salt bridge-mediated structural rearrangement in the energy-transduction domain of SERCA. We propose that this structural change uncouples SERCA by perturbing Ca2+ occlusion at residue E309 in transport site II, thus facilitating Ca2+ backflux to the cytosol. Our results have important implications for designing muscle-based therapies for human obesity.
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Affiliation(s)
- Joseph M. Autry
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
- Biophysical Technology Center, University of Minnesota, Minneapolis, MN 55455
| | - David D. Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
| | - L. Michel Espinoza-Fonseca
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455
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Daiho T, Yamasaki K, Danko S, Suzuki H. Glycine 105 as Pivot for a Critical Knee-like Joint between Cytoplasmic and Transmembrane Segments of the Second Transmembrane Helix in Ca2+-ATPase. J Biol Chem 2016; 291:24688-24701. [PMID: 27733680 DOI: 10.1074/jbc.m116.759704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 10/11/2016] [Indexed: 11/06/2022] Open
Abstract
The cytoplasmic actuator domain of the sarco(endo)plasmic reticulum Ca2+-ATPase undergoes large rotational movements that influence the distant transmembrane transport sites, and a long second transmembrane helix (M2) connected with this domain plays critical roles in transmitting motions between the cytoplasmic catalytic domains and transport sites. Here we explore possible structural roles of Gly105 between the cytoplasmic (M2c) and transmembrane (M2m) segments of M2 by introducing mutations that limit/increase conformational freedom. Alanine substitution G105A markedly retards isomerization of the phosphoenzyme intermediate (E1PCa2 → E2PCa2 → E2P + 2Ca2+), and disrupts Ca2+ occlusion in E1PCa2 and E2PCa2 at the transport sites uncoupling ATP hydrolysis and Ca2+ transport. In contrast, this substitution accelerates the ATPase activation (E2 → E1Ca2). Introducing a glycine by substituting another residue on M2 in the G105A mutant (i.e. "G-shift substitution") identifies the glycine positions required for proper Ca2+ handling and kinetics in each step. All wild-type kinetic properties, including coupled transport, are fully restored in the G-shift substitution at position 112 (G105A/A112G) located on the same side of the M2c helix as Gly105 facing M4/phosphorylation domain. Results demonstrate that Gly105 functions as a flexible knee-like joint during the Ca2+ transport cycle, so that cytoplasmic domain motions can bend and strain M2 in the correct direction or straighten the helix for proper gating and coupling of Ca2+ transport and ATP hydrolysis.
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Affiliation(s)
- Takashi Daiho
- From the Department of Biochemistry, Asahikawa Medical University, Midorigaoka-Higashi, Asahikawa 078-8510, Japan.
| | - Kazuo Yamasaki
- From the Department of Biochemistry, Asahikawa Medical University, Midorigaoka-Higashi, Asahikawa 078-8510, Japan
| | - Stefania Danko
- From the Department of Biochemistry, Asahikawa Medical University, Midorigaoka-Higashi, Asahikawa 078-8510, Japan
| | - Hiroshi Suzuki
- From the Department of Biochemistry, Asahikawa Medical University, Midorigaoka-Higashi, Asahikawa 078-8510, Japan
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Sahoo SK, Shaikh SA, Sopariwala DH, Bal NC, Bruhn DS, Kopec W, Khandelia H, Periasamy M. The N Terminus of Sarcolipin Plays an Important Role in Uncoupling Sarco-endoplasmic Reticulum Ca2+-ATPase (SERCA) ATP Hydrolysis from Ca2+ Transport. J Biol Chem 2015; 290:14057-67. [PMID: 25882845 DOI: 10.1074/jbc.m115.636738] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Indexed: 01/13/2023] Open
Abstract
The sarcoendoplasmic reticulum Ca(2+)-ATPase (SERCA) is responsible for intracellular Ca(2+) homeostasis. SERCA activity in muscle can be regulated by phospholamban (PLB), an affinity modulator, and sarcolipin (SLN), an uncoupler. Although PLB gets dislodged from Ca(2+)-bound SERCA, SLN continues to bind SERCA throughout its kinetic cycle and promotes uncoupling of Ca(2+) transport from ATP hydrolysis. To determine the structural regions of SLN that mediate uncoupling of SERCA, we employed mutagenesis and generated chimeras of PLB and SLN. In this study we demonstrate that deletion of SLN N-terminal residues (2)ERSTQ leads to loss of the uncoupling function even though the truncated peptide can target and constitutively bind SERCA. Furthermore, molecular dynamics simulations of SLN and SERCA interaction showed a rearrangement of SERCA residues that is altered when the SLN N terminus is deleted. Interestingly, transfer of the PLB cytosolic domain to the SLN transmembrane (TM) and luminal tail causes the chimeric protein to lose SLN-like function. Further introduction of the PLB TM region into this chimera resulted in conversion to full PLB-like function. We also found that swapping PLB N and C termini with those from SLN caused the resulting chimera to acquire SLN-like function. Swapping the C terminus alone was not sufficient for this conversion. These results suggest that domains can be switched between SLN and PLB without losing the ability to regulate SERCA activity; however, the resulting chimeras acquire functions different from the parent molecules. Importantly, our studies highlight that the N termini of SLN and PLB influence their respective unique functions.
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Affiliation(s)
- Sanjaya K Sahoo
- the Sanford Burnham Medical Research Institute at Lake Nona, Orlando, Florida 32827
| | - Sana A Shaikh
- From the Department of Physiology and Cell Biology, The Ohio State University, Columbus, Ohio 43210
| | - Danesh H Sopariwala
- From the Department of Physiology and Cell Biology, The Ohio State University, Columbus, Ohio 43210
| | - Naresh C Bal
- From the Department of Physiology and Cell Biology, The Ohio State University, Columbus, Ohio 43210
| | - Dennis Skjøth Bruhn
- the MEMPHYS, Center for Biomembrane Physics, University of Southern Denmark, Odense M 5230, Denmark, and
| | - Wojciech Kopec
- the MEMPHYS, Center for Biomembrane Physics, University of Southern Denmark, Odense M 5230, Denmark, and
| | - Himanshu Khandelia
- the MEMPHYS, Center for Biomembrane Physics, University of Southern Denmark, Odense M 5230, Denmark, and
| | - Muthu Periasamy
- the Sanford Burnham Medical Research Institute at Lake Nona, Orlando, Florida 32827 From the Department of Physiology and Cell Biology, The Ohio State University, Columbus, Ohio 43210,
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Kobayashi C, Koike R, Ota M, Sugita Y. Hierarchical domain-motion analysis of conformational changes in sarcoplasmic reticulum Ca2+
-ATPase. Proteins 2015; 83:746-56. [DOI: 10.1002/prot.24763] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Revised: 12/15/2014] [Accepted: 12/21/2014] [Indexed: 12/28/2022]
Affiliation(s)
- Chigusa Kobayashi
- Computational Biophysics Research Team, Research Division; RIKEN Advanced Institute for Computational Science; 7-1-26 Minatojima-Minamimachi, Chuo-Ku Kobe Hyogo Kobe 640-0047 Japan
| | - Ryotaro Koike
- Graduate School of Information Science; Nagoya University; Furo-Cho, Chikusa-Ku Nagoya Aichi 464-8601 Japan
| | - Motonori Ota
- Graduate School of Information Science; Nagoya University; Furo-Cho, Chikusa-Ku Nagoya Aichi 464-8601 Japan
| | - Yuji Sugita
- Computational Biophysics Research Team, Research Division; RIKEN Advanced Institute for Computational Science; 7-1-26 Minatojima-Minamimachi, Chuo-Ku Kobe Hyogo Kobe 640-0047 Japan
- RIKEN Theoretical Molecular Science Laboratory; 2-1 Hirosawa Wako-Shi Saitama 351-0198 Japan
- Laboratory for Biomolecular Function Simulation, Computational Biology Research Core; RIKEN Quantitative Biology Center; 7-1-26 Minatojima-Minamimachi, Chuo-Ku Kobe Hyogo Kobe 640-0047 Japan
- RIKEN iTHES; 2-1 Hirosawa Wako-Shi Saitama 351-0198 Japan
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