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Abe K, Ozako M, Inukai M, Matsuyuki Y, Kitayama S, Kanai C, Nagai C, Gopalasingam CC, Gerle C, Shigematsu H, Umekubo N, Yokoshima S, Yoshimori A. Deep learning driven de novo drug design based on gastric proton pump structures. Commun Biol 2023; 6:956. [PMID: 37726448 PMCID: PMC10509173 DOI: 10.1038/s42003-023-05334-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/08/2023] [Indexed: 09/21/2023] Open
Abstract
Existing drugs often suffer in their effectiveness due to detrimental side effects, low binding affinity or pharmacokinetic problems. This may be overcome by the development of distinct compounds. Here, we exploit the rich structural basis of drug-bound gastric proton pump to develop compounds with strong inhibitory potency, employing a combinatorial approach utilizing deep generative models for de novo drug design with organic synthesis and cryo-EM structural analysis. Candidate compounds that satisfy pharmacophores defined in the drug-bound proton pump structures, were designed in silico utilizing our deep generative models, a workflow termed Deep Quartet. Several candidates were synthesized and screened according to their inhibition potencies in vitro, and their binding poses were in turn identified by cryo-EM. Structures reaching up to 2.10 Å resolution allowed us to evaluate and re-design compound structures, heralding the most potent compound in this study, DQ-18 (N-methyl-4-((2-(benzyloxy)-5-chlorobenzyl)oxy)benzylamine), which shows a Ki value of 47.6 nM. Further high-resolution cryo-EM analysis at 2.08 Å resolution unambiguously determined the DQ-18 binding pose. Our integrated approach offers a framework for structure-based de novo drug development based on the desired pharmacophores within the protein structure.
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Affiliation(s)
- Kazuhiro Abe
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, Aichi, 464-8601, Japan.
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan.
- Center for One Medicine Innovative Translational Research (COMIT), Nagoya University, Nagoya, Aichi, 464-8601, Japan.
| | - Mami Ozako
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Miki Inukai
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Yoe Matsuyuki
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Shinnosuke Kitayama
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Chisato Kanai
- INTAGE Healthcare, Inc., 3-5-7, Kawaramachi Chuo-ku, Osaka, 541-0048, Japan
| | - Chiaki Nagai
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | | | - Christoph Gerle
- RIKEN SPring-8 Center, Kouto, Sayo-gun, Hyogo, 679-5148, Japan
| | - Hideki Shigematsu
- Japan Synchrotron Radiation Research Institute (JASRI), SPring-8, 1-1-1 Kouto, Sayo, Hyogo, 679-5148, Japan
| | - Nariyoshi Umekubo
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Satoshi Yokoshima
- Graduate School of Pharmaceutical Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan.
| | - Atsushi Yoshimori
- Institute for Theoretical Medicine, Inc., 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, 251-0012, Japan.
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Petrov VV. Functioning of Yeast Pma1 H+-ATPase under Changing Charge: Role of Asp739 and Arg811 Residues. BIOCHEMISTRY. BIOKHIMIIA 2017; 82:46-59. [PMID: 28320286 DOI: 10.1134/s0006297917010059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The plasma membrane Pma1 H+-ATPase of the yeast Saccharomyces cerevisiae contains conserved residue Asp739 located at the interface of transmembrane segment M6 and the cytosol. Its replacement by Asn or Val (Petrov et al. (2000) J. Biol. Chem., 275, 15709-15716) or by Ala (Miranda et al. (2011) Biochim. Biophys. Acta, 1808, 1781-1789) caused complete blockage of biogenesis of the enzyme, which did not reach secretory vesicles. It was proposed that a strong ionic bond (salt bridge) could be formed between this residue and positively charged residue(s) in close proximity, and the replacement D739A disrupted this bond. Based on a 3D homology model of the enzyme, it was suggested that the conserved Arg811 located in close proximity to Asp739 could be such stabilizing residue. To test this suggestion, single mutants with substituted Asp739 (D739V, D739N, D739A, and D739R) and Arg811 (R811L, R811M, R811A, and R811D) as well as double mutants carrying charge-neutralizing (D739A/R811A) or charge-swapping (D739R/R811D) substitutions were used. Expression of ATPases with single substitutions R811A and R811D were 38-63%, and their activities were 29-30% of the wild type level; ATP hydrolysis and H+ transport in these enzymes were essentially uncoupled. For the other substitutions including the double mutations, the biogenesis of the enzyme was practically blocked. These data confirm the important role of Asp739 and Arg811 residues for the biogenesis and function of the enzyme, suggesting their importance for defining H+ transport determinants but ruling out, however, the existence of a strong ionic bond (salt bridge) between these two residues and/or importance of such bridge for structure-function relationships in Pma1 H+-ATPase.
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Affiliation(s)
- V V Petrov
- Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino, Moscow Region, 142290, Russia.
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Sakai H, Fujii T, Takeguchi N. Proton-Potassium (H+/K+) ATPases: Properties and Roles in Health and Diseases. Met Ions Life Sci 2016; 16:459-83. [DOI: 10.1007/978-3-319-21756-7_13] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Petrov VV. Point mutations in the extracytosolic loop between transmembrane segments M5 and M6 of the yeast Pma1 H+-ATPase: alanine-scanning mutagenesis. J Biomol Struct Dyn 2013; 33:70-84. [PMID: 24256122 DOI: 10.1080/07391102.2013.849619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Membrane-spanning segments M4, M5, M6, and M8 of the H(+)-, Ca(2+)-, and K(+), Na(+)-ATPases, which belong to the P2-type pumps are the core through which cations are transported. M5 and M6 loop is a short extracytoplasmic stretch of the seven amino acid residues (714-DNSLDID) connecting two of these segments, M5 and M6, where residues involved in the formation of the proton-binding site(s) are located. In the present study, we have used alanine-scanning mutagenesis to explore the structural and functional relationships within this loop of the yeast plasma membrane Pma1 H(+)-ATPase. Of the 7 Ala mutants made, substitution for the most conserved residue (Leu-717) has led to a severe misfolding and complete block in biogenesis of the mutant enzyme. The replacement of Asp-714 has also caused misfolding leading to significant decrease in the expression of the mutant and loss of activity. The remaining mutants were expressed in secretory vesicles at 21-119% of the wild-type level and were active enough to be analyzed in detail. One of these mutants (I719A) showed five- to threefold decrease in both expression and ATP hydrolyzing and H(+) pumping activities and also threefold reduction in the coupling ratio between ATP hydrolysis and H(+) transport. Thus, Ala substitutions at three positions of the seven seriously affected biogenesis, folding, stability and/or functioning of the enzyme. Taken together, these results lead to suggestion that M5 and M6 loop play an important role in the protein stability and function and is responsible for proper arrangement of transmembrane segments M5 and M6 and probably other domains of the enzyme. Results for additional conserved substitutions (Asn and Glu) at Asp-714 and Asp-720 confirmed this suggestion.
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Affiliation(s)
- Valery V Petrov
- a Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences , pr. Nauki 5, Pushchino 142290 , Russia
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Chourasia M, Sastry GN. The nucleotide, inhibitor, and cation binding sites of P-type II ATPases. Chem Biol Drug Des 2012; 79:617-27. [PMID: 22260628 DOI: 10.1111/j.1747-0285.2012.01334.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
P-type ATPases constitute a ubiquitous superfamily of cation transport enzymes, responsible for carrying out actions of paramount importance in biology such as ion transport and expulsion of toxic ions from cells. The harmonized toggling of gates in the extra- and intracellular domains explain the phenomenon of specific cation binding in selective physiological states. A quantitative understanding of the fundamental aspects of ion transport mechanism and regulation of P-type ATPases requires detailed knowledge of thermodynamical, structural, and functional properties. Computational studies have made significant contributions to our understanding of biological ion pumps. Various 3D structures of Ca(2+) -ATPase between E1 and E2 transition states have given a impetus to the theorists to work on the Na(+) K(+) - and H(+) K(+) -ATPase to address important questions about their function. The current review delineates the importance of cation, nucleotide, and inhibitor binding domains, with a focus on the therapeutic potential and biological relevance of the three P-type II ATPases. This will give an insight into the ion selectivity and their conduction across the transmembrane helices of P-type II ATPases, which may pave the way to a range of fundamental questions about the mechanism and aid in the efforts of structure- and analog-based drug design.
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Affiliation(s)
- Mukesh Chourasia
- Molecular Modeling Group, Indian Institute of Chemical Technology, Hyderabad, India
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Abe K, Tani K, Nishizawa T, Fujiyoshi Y. Inter-subunit interaction of gastric H+,K+-ATPase prevents reverse reaction of the transport cycle. EMBO J 2009; 28:1637-43. [PMID: 19387495 DOI: 10.1038/emboj.2009.102] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Accepted: 03/10/2009] [Indexed: 11/09/2022] Open
Abstract
The gastric H(+),K(+)-ATPase is an ATP-driven proton pump responsible for generating a million-fold proton gradient across the gastric membrane. We present the structure of gastric H(+),K(+)-ATPase at 6.5 A resolution as determined by electron crystallography of two-dimensional crystals. The structure shows the catalytic alpha-subunit and the non-catalytic beta-subunit in a pseudo-E(2)P conformation. Different from Na(+),K(+)-ATPase, the N-terminal tail of the beta-subunit is in direct contact with the phosphorylation domain of the alpha-subunit. This interaction may hold the phosphorylation domain in place, thus stabilizing the enzyme conformation and preventing the reverse reaction of the transport cycle. Indeed, truncation of the beta-subunit N-terminus allowed the reverse reaction to occur. These results suggest that the beta-subunit N-terminus prevents the reverse reaction from E(2)P to E(1)P, which is likely to be relevant for the generation of a large H(+) gradient in vivo situation.
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Affiliation(s)
- Kazuhiro Abe
- Department of Biophysics, Faculty of Science, Kyoto University, Kyoto, Japan
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Abstract
Gastric H,K-ATPase is an electroneutral transmembrane pump that moves protons from the cytoplasm of the parietal cell into the gastric lumen in exchange for potassium ions. The mechanism of transport against the established electrochemical gradients includes intermediate conformations in which the transferred ions are trapped (occluded) within the membrane domain of the pump. The pump cycle involves switching between the E1 and E2P states. Molecular dynamics simulations on homology models of the E2P and E1 states were performed to investigate the mechanism of K(+) movement in this enzyme. We performed separate E2P simulations with one K(+) in the luminal channel, one K(+) ion in the occlusion site, two K(+) ions in the occlusion site, and targeted molecular dynamics from E2P to E1 with two K(+) ions in the occlusion site. The models were inserted into a lipid bilayer system and were stable over the time course of the simulations, and K(+) ions in the channel moved to a consistent location near the center of the membrane domain, thus defining the occlusion site. The backbone carbonyl oxygen from residues 337 through 342 on the nonhelical turn of M4, as well as side-chain oxygen from E343, E795, and E820, participated in the ion occlusion. A single water molecule was stably bound between the two K(+) ions in the occlusion site, providing an additional ligand and partial shielding the positive charges from one another. Targeted molecular dynamics was used to transform the protein from the E2P to the E1 state (two K(+) ions to the cytoplasm). This simulation identified the separation of the water column in the entry channel as the likely gating mechanism on the luminal side. A hydrated exit channel also formed on the cytoplasmic side of the occlusion site during this simulation. Hence, water molecules became available to hydrate the ions. The movement of the M1M2 transmembrane segments, and the displacement of residues Q159, E160, Q110, and T152 during the conformational change, as well as the motions of E343 and L346, acted as the cytoplasmic-side gate.
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Morii M, Yamauchi M, Ichikawa T, Fujii T, Takahashi Y, Asano S, Takeguchi N, Sakai H. Involvement of the H3O+-Lys-164 -Gln-161-Glu-345 charge transfer pathway in proton transport of gastric H+,K+-ATPase. J Biol Chem 2008; 283:16876-84. [PMID: 18403373 DOI: 10.1074/jbc.m800563200] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Gastric H(+),K(+)-ATPase is shown to transport 2 mol of H(+)/mol of ATP hydrolysis in isolated hog gastric vesicles. We studied whether the H(+) transport mechanism is due to charge transfer and/or transfer of hydronium ion (H(3)O(+)). From transport of [(18)O]H(2)O, 1.8 mol of water molecule/mol of ATP hydrolysis was found to be transported. We performed a molecular dynamics simulation of the three-dimensional structure model of the H(+),K(+)-ATPase alpha-subunit at E(1) conformation. It predicts the presence of a charge transfer pathway from hydronium ion in cytosolic medium to Glu-345 in cation binding site 2 (H(3)O(+)-Lys-164 -Gln-161-Glu-345). No charge transport pathway was formed in mutant Q161L, E345L, and E345D. Alternative pathways (H(3)O(+)-Gln-161-Glu-345) in mutant K164L and (H(3)O(+)-Arg-105-Gln-161-Gln-345) in mutant E345Q were formed. The H(+),K(+)-ATPase activity in these mutants reflected the presence and absence of charge transfer pathways. We also found charge transfer from sites 2 to 1 via a water wire and a charge transfer pathway (H(3)O(+)-Asn-794 -Glu-797). These results suggest that protons are charge-transferred from the cytosolic side to H(2)O in sites 2 and 1, the H(2)O comes from cytosolic medium, and H(3)O(+) in the sites are transported into lumen during the conformational transition from E(1)PtoE(2)P.
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Affiliation(s)
- Magotoshi Morii
- Department of Pharmaceutical Physiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan
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9
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Guerra G, Petrov VV, Allen KE, Miranda M, Pardo JP, Slayman CW. Role of transmembrane segment M8 in the biogenesis and function of yeast plasma-membrane H(+)-ATPase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:2383-92. [PMID: 17573037 PMCID: PMC2267258 DOI: 10.1016/j.bbamem.2007.04.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2007] [Revised: 04/26/2007] [Accepted: 04/27/2007] [Indexed: 11/20/2022]
Abstract
Of the four transmembrane helices (M4, M5, M6, and M8) that pack together to form the ion-binding sites of P(2)-type ATPases, M8 has until now received the least attention. The present study has used alanine-scanning mutagenesis to map structure-function relationships throughout M8 of the yeast plasma-membrane H(+)-ATPase. Mutant forms of the ATPase were expressed in secretory vesicles and at the plasma membrane for measurements of ATP hydrolysis and ATP-dependent H(+) pumping. In secretory vesicles, Ala substitutions at a cluster of four positions near the extracytoplasmic end of M8 led to partial uncoupling of H(+) transport from ATP hydrolysis, while substitution of Ser-800 (close to the middle of M8) by Ala increased the apparent stoichiometry of H(+) transport. A similar increase has previously been reported following the substitution of Glu-803 by Gln (Petrov, V. et al., J. Biol. Chem. 275:15709-15718, 2000) at a position known to contribute directly to Ca(2+) binding in the Ca(2+)-ATPase of sarcoplasmic reticulum (Toyoshima, C., et al., Nature 405: 647-655, 2000). Four other mutations in M8 interfered with H(+)-ATPase folding and trafficking to the plasma membrane; based on homology modeling, they occupy positions that appear important for the proper bundling of M8 with M5, M6, M7, and M10. Taken together, these results point to a key role for M8 in the biogenesis, stability, and physiological functioning of the H(+)-ATPase.
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Affiliation(s)
| | | | | | | | | | - Carolyn W. Slayman
- To whom reprint requests should be addressed: Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven CT 06510; tel. (203) 737-1770; fax (203) 737-1771; e-mail,
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Chourasia M, Sastry GM, Sastry GN. Proton binding sites and conformational analysis of H+K(+)-ATPase. Biochem Biophys Res Commun 2005; 336:961-6. [PMID: 16157306 DOI: 10.1016/j.bbrc.2005.08.205] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2005] [Accepted: 08/25/2005] [Indexed: 10/25/2022]
Abstract
It is proposed that the hydronium ion, H3O+, binds to the E1 conformation of the alpha-subunit of gastric proton pump. The H3O+ binding cavities are characterized parametrically based on valence, sequence, geometry, and size considerations from comparative modeling. The cavities have scope for accommodating monovalent cations of different ionic radii. The H3O+ transport is proposed to be aided by arenes which are arranged regularly along the pump starting from N-domain through the transmembrane region. Step-by-step structural changes accompanying H3O+ occlusion are studied in detail. The observations corroborate well with earlier experimental studies.
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Affiliation(s)
- Mukesh Chourasia
- Molecular Modelling Group, Organic Chemical Sciences, Indian Institute of Chemical Technology, Hyderabad 500007, India
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Sánchez-Más J, Sánchez-Laorden BL, Guillo LA, Jiménez-Cervantes C, García-Borrón JC. The melanocortin-1 receptor carboxyl terminal pentapeptide is essential for MC1R function and expression on the cell surface. Peptides 2005; 26:1848-57. [PMID: 15993512 DOI: 10.1016/j.peptides.2004.11.030] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2004] [Accepted: 11/05/2004] [Indexed: 10/25/2022]
Abstract
The pigmentary actions of the melanocortins are mediated by the melanocortin-1 receptor (MC1R), a seven transmembrane domains receptor positively coupled to Gs and the cAMP cascade. In order to define the structure-function relationships of potentially relevant domains in MC1R, particularly its C-terminal cytosolic tail, we generated and analyzed several variants with C-terminal deletions, as well as point mutants in selected residues of the human MC1R. We show that the MC1R C-terminal pentapeptide is essential for proper receptor expression on the plasma membrane, and that residues Thr314, Cys315 and Trp317 are at least partially responsible for this effect.
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Affiliation(s)
- J Sánchez-Más
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Murcia, Apto 4021, 30100 Espinardo, Murcia, Spain
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12
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Bindu PH, Sastry GM, Murty US, Sastry GN. Structural and conformational changes concomitant with the E1–E2 transition in H+K+-ATPase: a comparative protein modeling study. Biochem Biophys Res Commun 2004; 319:312-20. [PMID: 15178408 DOI: 10.1016/j.bbrc.2004.05.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2004] [Indexed: 11/30/2022]
Abstract
Comparative modeling studies on conserved regions of the gastric H(+)K(+)-ATPase reveal that the E1-E2 conformational transition induces significant tertiary structural changes while conserving the secondary structure. The residues 516-530 of the cytoplasmic domain and TM10 within the transmembrane (TM) regions undergo maximum tertiary structural changes. The luminal regions exhibit comparatively lesser tertiary structural deviations. Residues 249-304 show maximum secondary structural deviation in the conformational transition. The Cys-815 and Cys-323 residues involved in inhibitor binding are found to have smaller buried side chain areas in the E1 conformation compared to E2. Retention of activity correlates well with the buried side chain area when selected amino acid residues in TM6 are mutated using modeling techniques with bulkier amino acid residues. Conformational specificity for ion binding is corroborated with the fraction of side chains exposed to polar atoms of the residues E345, D826, V340, A341, V343, and E822.
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Affiliation(s)
- P Hima Bindu
- Molecular Modelling Group, Organic Chemical Sciences, Indian Institute of Chemical Technology, Hyderabad 500007, India
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13
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Apell HJ. Structure-function relationship in P-type ATPases--a biophysical approach. Rev Physiol Biochem Pharmacol 2004; 150:1-35. [PMID: 12811587 DOI: 10.1007/s10254-003-0018-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
P-type ATPases are a large family of membrane proteins that perform active ion transport across biological membranes. In these proteins the energy-providing ATP hydrolysis is coupled to ion-transport that builds up or maintains the electrochemical potential gradients of one or two ion species across the membrane. P-type ATPases are found in virtually all eukaryotic cells and also in bacteria, and they are transporters of a broad variety of ions. So far, a crystal structure with atomic resolution is available only for one species, the SR Ca-ATPase. However, biochemical and biophysical studies provide an abundance of details on the function of this class of ion pumps. The aim of this review is to summarize the results of preferentially biophysical investigations of the three best-studied ion pumps, the Na,K-ATPase, the gastric H,K-ATPase, and the SR Ca-ATPase, and to compare functional properties to recent structural insights with the aim of contributing to the understanding of their structure-function relationship.
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Affiliation(s)
- H-J Apell
- Department of Biology, University of Konstanz, Fach M635, 78457 Konstanz, Germany.
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Asano S, Morii M, Takeguchi N. Molecular and Cellular Regulation of the Gastric Proton Pump. Biol Pharm Bull 2004; 27:1-12. [PMID: 14743830 DOI: 10.1248/bpb.27.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The gastric H+, K+-ATPase is a proton pump that is responsible for gastric acid secretion and that actively transports protons and K+ ions in opposite directions to generate in excess of a million-fold gradient across the membrane under physiological conditions. This pump is also a target molecule of proton pump inhibitors which are used for the clinical treatment of hyperacidity. In this review, we wish to summarize the molecular regulation of this pump based on mutational studies, particularly those used for the identification of binding sites for cations and specific inhibitors. Recent reports by Toyoshima et al (2000, 2002) presented precise three-dimensional (3-D) structures of the sarcoplasmic reticulum (SR) Ca2+-ATPase, which belongs to the same family as the gastric H+, K+-ATPase. We have studied the structure-function relationships for the gastric H+, K+-ATPase using 3-D structures constructed by homology modeling of the related SR Ca2+-ATPase, which was used as a template molecule. We also discuss in this review, the regulation of cell surface expression and synthesis control of the gastric proton pump.
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Affiliation(s)
- Shinji Asano
- Life Scientific Research Center, Toyama Medican and Pharmaceutical University, 2630 Sugitani, Toyama 930-0194, Japan.
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Asano S, Yoshida A, Yashiro H, Kobayashi Y, Morisato A, Ogawa H, Takeguchi N, Morii M. The cavity structure for docking the K(+)-competitive inhibitors in the gastric proton pump. J Biol Chem 2003; 279:13968-75. [PMID: 14699149 DOI: 10.1074/jbc.m308934200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
2-Methyl-8-(phenylmethoxy)imidazo[1,2-a]pyridine-3-acetonitrile (SCH 28080) is a reversible inhibitor specific for the gastric proton pump. The inhibition pattern is competitive with K(+). Here we studied the binding sites of this inhibitor on the putative three-dimensional structure of the gastric proton pump alpha-subunit that was constructed by homology modeling based on the structure of sarcoplasmic reticulum Ca(2+) pump. Alanine and serine mutants of Tyr(801) located in the fifth transmembrane segment of the gastric proton pump alpha-subunit retained the (86)Rb transport and K(+)-dependent ATPase (K(+)-ATPase) activities. These mutants showed 60-80-times lower sensitivity to SCH 28080 than the wild type in the (86)Rb transport activity. The K(+)-ATPase activities of these mutants were not completely inhibited by SCH 28080. The sensitivity to SCH 28080 was dependent on the bulkiness of the side chain at this position. Therefore, the side chain of Tyr(801) is important for the interaction with this inhibitor. In the three-dimensional structure of the E(2) form (conformation with high affinity for K(+)) of the gastric proton pump, Tyr(801) faces a cavity surrounded by the first, fourth, fifth, sixth, and eighth transmembrane segments and fifth/sixth, seventh/eighth, and ninth/tenth loops. SCH 28080 can dock in this cavity. However, SCH 28080 cannot dock in the same location in the E(1) form (conformation with high affinity for proton) of the gastric proton pump due to the drastic rearrangement of the transmembrane helices between the E(1) and E(2) forms. These results support the idea that this cavity is the binding pocket of SCH 28080.
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Affiliation(s)
- Shinji Asano
- Life Scientific Research Center, Faculty of Pharmaceutical Sciences, Toyama Medical & Pharmaceutical University, Toyama, Japan.
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Abstract
The Na+/K+ ATPase asymmetrically distributes sodium and potassium ions across the plasma membrane to generate and maintain the membrane potential in many cell types. Although these pumps have been hypothesized to be involved in various human neurological disorders, including seizures and neurodegeneration, direct genetic evidence has been lacking. Here, we describe novel mutations in the Drosophila gene encoding the alpha (catalytic) subunit of the Na+/K+ ATPase that lead to behavioral abnormalities, reduced life span, and severe neuronal hyperexcitability. These phenotypes parallel the occurrence of extensive, age-dependent neurodegeneration. We have also discovered that the ATPalpha transcripts undergo alternative splicing that substantially increases the diversity of potential proteins. Our data show that maintenance of neuronal viability is dependent on normal sodium pump activity and establish Drosophila as a useful model for investigating the role of the pump in human neurodegenerative and seizure disorders.
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Abstract
Overlapping neural, hormonal, and paracrine pathways finely regulate gastric acid secretion. In rats and guinea pigs, most of the intrinsic neural innervation to the gastric mucosa originates in the myenteric plexus. In contrast, human stomachs have a clearly defined submucosal plexus that contains a variety of transmitters including nitric oxide, vasoactive intestinal peptide (VIP), gastrin-releasing peptide (GRP), substance P, and calcitonin gene-related peptide (CGRP). Although GRP is known to participate in meal-stimulated acid secretion by releasing gastrin in a variety of laboratory animals, recent studies were unable to demonstrate a role for endogenous GRP in meal-stimulated gastrin secretion in humans. Pituitary adenylate cyclase-activating polypeptide (PACAP), a member of the secretin-glucagon-VIP family, has been localized to gastric mucosal neurons and may participate in vagally mediated acid secretion. Two novel peptides, ghrelin and leptin, have been localized to the stomach. Peripheral administration of ghrelin stimulates and of leptin inhibits acid secretion. The binding of secretagogues to parietal cells generates changes in second messengers that regulate the translocation and activation of the proton pump, HK-ATPase. In resting cells, HK-ATPase is contained within cytoplasmic tubulovesicles in an inactive form. At stimulation, the tubulovesicles fuse with the apical canaliculi and the HK-ATPase is incorporated into the apical membrane where it actively pumps H ions in exchange for K. Acute infection with Helicobacter pylori results in hypochlorhydria, whereas chronic infection can cause either hypo- or hyperchlorhydria, depending on the distribution of the infection and the degree of corpus gastritis. Recent studies suggest that inflammatory cytokines, produced in response to the organism, can play a role in the perturbations in acid and gastrin secretion induced by H. pylori.
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Affiliation(s)
- Mitchell L Schubert
- Department of Medicine, Division of Gastroenterology, Medical College of Virginia and McGuire VAMC Richmond, Virginia 23249, USA.
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18
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Guennoun S, Horisberger JD. Cysteine-scanning mutagenesis study of the sixth transmembrane segment of the Na,K-ATPase alpha subunit. FEBS Lett 2002; 513:277-81. [PMID: 11904164 DOI: 10.1016/s0014-5793(02)02323-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The accessibility of the residues of the sixth transmembrane segment (TM) of the Bufo marinus Na,K-ATPase alpha subunit was explored by cysteine scanning mutagenesis. Methanethiosulfonate reagents reached only the two most extracellular positions (T803, D804) in the native conformation of the Na,K-pump. Palytoxin induced a conductance in all mutants, including D811C, T814C and D815C which showed no active electrogenic transport. After palytoxin treatment, four additional positions (V805, L808, D811 and M816) became accessible to the sulfhydryl reagent. We conclude that one side of the sixth TM helix forms a wall of the palytoxin-induced channel pore and, probably, of the cation pathway from the extracellular side to one of their binding sites.
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Affiliation(s)
- Saïda Guennoun
- Institute of Pharmacology and Toxicology, Bugnon 27, CH-1005, Lausanne, Switzerland
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