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Shahnazari M, Zakipour Z, Razi H, Moghadam A, Alemzadeh A. Bioinformatics approaches for classification and investigation of the evolution of the Na/K-ATPase alpha-subunit. BMC Ecol Evol 2022; 22:122. [PMID: 36289471 PMCID: PMC9609216 DOI: 10.1186/s12862-022-02071-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 09/29/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Na,K-ATPase is a key protein in maintaining membrane potential that has numerous additional cellular functions. Its catalytic subunit (α), found in a wide range of organisms from prokaryotes to complex eukaryote. Several studies have been done to identify the functions as well as determining the evolutionary relationships of the α-subunit. However, a survey of a larger collection of protein sequences according to sequences similarity and their attributes is very important in revealing deeper evolutionary relationships and identifying specific amino acid differences among evolutionary groups that may have a functional role. RESULTS In this study, 753 protein sequences using phylogenetic tree classification resulted in four groups: prokaryotes (I), fungi and various kinds of Protista and some invertebrates (II), the main group of invertebrates (III), and vertebrates (IV) that was consisted with species tree. The percent of sequences that acquired a specific motif for the α/β subunit assembly increased from group I to group IV. The vertebrate sequences were divided into four groups according to isoforms with each group conforming to the evolutionary path of vertebrates from fish to tetrapods. Data mining was used to identify the most effective attributes in classification of sequences. Using 1252 attributes extracted from the sequences, the decision tree classified them in five groups: Protista, prokaryotes, fungi, invertebrates and vertebrates. Also, vertebrates were divided into four subgroups (isoforms). Generally, the count of different dipeptides and amino acid ratios were the most significant attributes for grouping. Using alignment of sequences identified the effective position of the respective dipeptides in the separation of the groups. So that 208GC is apparently involved in the separation of vertebrates from the four other organism groups, and 41DH, 431FK, and 451KC were involved in separation vertebrate isoform types. CONCLUSION The application of phylogenetic and decision tree analysis for Na,K-ATPase, provides a better understanding of the evolutionary changes according to the amino acid sequence and its related properties that could lead to the identification of effective attributes in the separation of sequences in different groups of phylogenetic tree. In this study, key evolution-related dipeptides are identified which can guide future experimental studies.
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Affiliation(s)
- Marzieh Shahnazari
- grid.412573.60000 0001 0745 1259Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Zahra Zakipour
- grid.412573.60000 0001 0745 1259Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Hooman Razi
- grid.412573.60000 0001 0745 1259Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Ali Moghadam
- grid.412573.60000 0001 0745 1259Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | - Abbas Alemzadeh
- grid.412573.60000 0001 0745 1259Department of Plant Production and Genetics, School of Agriculture, Shiraz University, Shiraz, Iran
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Shahnazari M, Alemzadeh A, Zakipour Z, Razi H. Evolution and classification of Na/K ATPase α-subunit in Arthropoda and Nematoda. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2020.101015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Moraes CM, Lucena MN, Garçon DP, Pinto MR, Fabri LM, Faleiros RO, Fontes CFL, McNamara JC, Leone FA. Biochemical Characterization and Allosteric Modulation by Magnesium of (Na +, K +)-ATPase Activity in the Gills of the Red Mangrove Crab Goniopsis cruentata (Brachyura, Grapsidae). J Membr Biol 2020; 253:229-245. [PMID: 32440867 DOI: 10.1007/s00232-020-00120-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 05/02/2020] [Indexed: 11/26/2022]
Abstract
We provide a kinetic characterization of (Na+, K+)-ATPase activity in a posterior gill microsomal fraction from the grapsid crab Goniopsis cruentata. (Na+, K+)-ATPase activity constitutes 95% of total ATPase activity, and sucrose density centrifugation reveals an ATPase activity peak between 25 and 35% sucrose, distributed into two, partially separated protein fractions. The (Na+, K+)-ATPase α-subunit is localized throughout the ionocyte cytoplasm and has an Mr of ≈ 10 kDa and hydrolyzes ATP obeying cooperative kinetics. Low (VM = 186.0 ± 9.3 nmol Pi min-1 mg-1 protein and K0.5 = 0.085 ± 0.004 mmol L-1) and high (VM = 153.4 ± 7.7 nmol Pi min-1 mg-1 protein and K0.5 = 0.013 ± 0.0006 mmol L-1) affinity ATP binding sites were characterized. At low ATP concentrations, excess Mg2+ stimulates the enzyme, triggering exposure of a high-affinity binding site that accounts for 50% of (Na+, K+)-ATPase activity. Stimulation by Mg2+ (VM = 425.9 ± 25.5 nmol Pi min-1 mg-1 protein, K0.5 = 0.16 ± 0.01 mmol L-1), K+ (VM = 485.3 ± 24.3 nmol Pi min-1 mg-1 protein, K0.5 = 0.9 ± 0.05 mmol L-1), Na+ (VM = 425.0 ± 23.4 nmol Pi min-1 mg-1 protein, K0.5 = 5.1 ± 0.3 mmol L-1) and NH4+ (VM = 497.9 ± 24.9 nmol Pi min-1 mg-1 protein, K0.5 = 9.7 ± 0.5 mmol L-1) obeys cooperative kinetics. Ouabain inhibits up to 95% of ATPase activity with KI = 196.6 ± 9.8 µmol L-1. This first kinetic characterization of the gill (Na+, K+)-ATPase in Goniopsis cruentata enables better comprehension of the biochemical underpinnings of osmoregulatory ability in this semi-terrestrial mangrove crab.
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Affiliation(s)
- Cintya M Moraes
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes 3900, Ribeirão Preto, SP, 14040-901, Brazil
| | - Malson N Lucena
- Instituto de Biociências, Universidade Federal do Mato Grosso do Sul, Campo Grande, MS, Brazil
| | | | - Marcelo R Pinto
- Laboratório de Biopatologia e Biologia Molecular Universidade Uberaba, Uberaba, MG, Brazil
| | - Leonardo M Fabri
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes 3900, Ribeirão Preto, SP, 14040-901, Brazil
| | - Rogério O Faleiros
- Departamento de Ciências Agrárias e Biológicas, Universidade Federal do Espírito Santo, São Mateus, ES, Brazil
| | - Carlos F L Fontes
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - John C McNamara
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
- Centro de Biologia Marinha, Universidade de São Paulo, São Sebastião, SP, Brazil
| | - Francisco A Leone
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes 3900, Ribeirão Preto, SP, 14040-901, Brazil.
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Šeflová J, Čechová P, Štenclová T, Šebela M, Kubala M. Identification of cisplatin-binding sites on the large cytoplasmic loop of the Na +/K +-ATPase. J Enzyme Inhib Med Chem 2018; 33:701-706. [PMID: 29577756 PMCID: PMC6009960 DOI: 10.1080/14756366.2018.1445735] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Cisplatin is the most widely used chemotherapeutic drug for the treatment of various types of cancer; however, its administration brings also numerous side effects. It was demonstrated that cisplatin can inhibit the Na+/K+-ATPase (NKA), which can explain a large part of the adverse effects. In this study, we have identified five cysteinyl residues (C452, C456, C457, C577, and C656) as the cisplatin binding sites on the cytoplasmic loop connecting transmembrane helices 4 and 5 (C45), using site-directed mutagenesis and mass spectrometry experiments. The identified residues are known to be susceptible to glutathionylation indicating their involvement in a common regulatory mechanism.
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Affiliation(s)
- Jaroslava Šeflová
- a Department of Biophysics, Faculty of Science , Centre of Region Haná for Biotechnological and Agricultural Research, Palacký University , Olomouc , Czech Republic
| | - Petra Čechová
- a Department of Biophysics, Faculty of Science , Centre of Region Haná for Biotechnological and Agricultural Research, Palacký University , Olomouc , Czech Republic
| | - Tereza Štenclová
- a Department of Biophysics, Faculty of Science , Centre of Region Haná for Biotechnological and Agricultural Research, Palacký University , Olomouc , Czech Republic
| | - Marek Šebela
- b Department of Protein Biochemistry and Proteomics, Faculty of Science , Centre of Region Haná for Biotechnological and Agricultural Research, Palacký University , Olomouc , Czech Republic
| | - Martin Kubala
- a Department of Biophysics, Faculty of Science , Centre of Region Haná for Biotechnological and Agricultural Research, Palacký University , Olomouc , Czech Republic
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RH421 binds into the ATP-binding site on the Na +/K +-ATPase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2113-2122. [PMID: 28774819 DOI: 10.1016/j.bbamem.2017.07.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 07/28/2017] [Accepted: 07/30/2017] [Indexed: 11/22/2022]
Abstract
The Na+/K+-ATPase plays a key role in ion transport across the plasma membrane of all animal cells. The voltage-sensitive styrylpyrimidium dye RH421 has been used in several laboratories for monitoring of Na+/K+-ATPase kinetics. It is known, that RH421 can interact with the enzyme and it can influence its activity at micromolar concentrations, but structural details of this interaction are only poorly understood. Experiments with isolated large cytoplasmic loop (C45) of Na+/K+-ATPase revealed that RH421 can interact with this part of the protein with dissociation constant 1μM. The Trp-to-RH421 FRET performed on six single-tryptophan mutants revealed that RH421 binds directly into the ATP-binding site. This conclusion was further supported by results from molecular docking, site-directed mutagenesis and by competitive experiments using ATP. Experiments with C45/DPPC mixture revealed that RH421 can bind to both C45 and lipids, but only the former interaction was influenced by the presence of ATP.
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Tejral G, Sopko B, Necas A, Schoner W, Amler E. Computer modelling reveals new conformers of the ATP binding loop of Na +/K +-ATPase involved in the transphosphorylation process of the sodium pump. PeerJ 2017; 5:e3087. [PMID: 28316890 PMCID: PMC5354106 DOI: 10.7717/peerj.3087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 02/14/2017] [Indexed: 01/02/2023] Open
Abstract
Hydrolysis of ATP by Na+/K+-ATPase, a P-Type ATPase, catalyzing active Na+ and K+ transport through cellular membranes leads transiently to a phosphorylation of its catalytical α-subunit. Surprisingly, three-dimensional molecular structure analysis of P-type ATPases reveals that binding of ATP to the N-domain connected by a hinge to the P-domain is much too far away from the Asp369 to allow the transfer of ATP’s terminal phosphate to its aspartyl-phosphorylation site. In order to get information for how the transfer of the γ-phosphate group of ATP to the Asp369 is achieved, analogous molecular modeling of the M4–M5 loop of ATPase was performed using the crystal data of Na+/K+-ATPase of different species. Analogous molecular modeling of the cytoplasmic loop between Thr338 and Ile760 of the α2-subunit of Na+/K+-ATPase and the analysis of distances between the ATP binding site and phosphorylation site revealed the existence of two ATP binding sites in the open conformation; the first one close to Phe475 in the N-domain, the other one close to Asp369 in the P-domain. However, binding of Mg2+•ATP to any of these sites in the “open conformation” may not lead to phosphorylation of Asp369. Additional conformations of the cytoplasmic loop were found wobbling between “open conformation” <==> “semi-open conformation <==> “closed conformation” in the absence of 2Mg2+•ATP. The cytoplasmic loop’s conformational change to the “semi-open conformation”—characterized by a hydrogen bond between Arg543 and Asp611—triggers by binding of 2Mg2+•ATP to a single ATP site and conversion to the “closed conformation” the phosphorylation of Asp369 in the P-domain, and hence the start of Na+/K+-activated ATP hydrolysis.
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Affiliation(s)
- Gracian Tejral
- Department of Biophysics, 2nd Faculty of Medicine, Charles University Prague, Prague, Czech Republic; Laboratory of Tissue Engineering, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Bruno Sopko
- Department of Medical Chemistry and Clinical Biochemistry, 2nd Faculty of Medicine, Charles University Prague , Prague , Czech Republic
| | - Alois Necas
- Small Animal Clinic, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Science , Brno , Czech Republic
| | - Wilhelm Schoner
- Institute of Biochemistry and Endocrinology, University of Giessen , Giessen , Germany
| | - Evzen Amler
- Department of Biophysics, 2nd Faculty of Medicine, Charles University Prague, Prague, Czech Republic; Laboratory of Tissue Engineering, Institute of Experimental Medicine, Academy of Sciences of the Czech Republic, Prague, Czech Republic
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Kubala M, Čechová P, Geletičová J, Biler M, Štenclová T, Trouillas P, Biedermann D. Flavonolignans As a Novel Class of Sodium Pump Inhibitors. Front Physiol 2016; 7:115. [PMID: 27065883 PMCID: PMC4812144 DOI: 10.3389/fphys.2016.00115] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 03/14/2016] [Indexed: 11/13/2022] Open
Abstract
We examined the inhibitory effects of three flavonolignans and their dehydro- derivatives, taxifolin and quercetin on the activity of the Na+/K+-ATPase (NKA). The flavonolignans silychristin, dehydrosilychristin and dehydrosilydianin inhibited NKA with IC50 of 110 ± 40 μM, 38 ± 8 μM, and 36 ± 14 μM, respectively. Using the methods of molecular modeling, we identified several possible binding sites for these species on NKA and proposed the possible mechanisms of inhibition. The binding to the extracellular- or cytoplasmic C-terminal sites can block the transport of cations through the plasma membrane, while the binding on the interface of cytoplasmic domains can inhibit the enzyme allosterically. Fluorescence spectroscopy experiments confirmed the interaction of these three species with the large cytoplasmic segment connecting transmembrane helices 4 and 5 (C45). The flavonolignans are distinct from the cardiac glycosides that are currently used in NKA treatment. Because their binding sites are different, the mechanism of inhibition is different as well as the range of active concentrations, one can expect that these new NKA inhibitors would exhibit also a different biomedical actions than cardiac glycosides.
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Affiliation(s)
- Martin Kubala
- Department of Biophysics, Faculty of Science, Centre of Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Czech Republic
| | - Petra Čechová
- Department of Biophysics, Faculty of Science, Centre of Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Czech Republic
| | - Jaroslava Geletičová
- Department of Biophysics, Faculty of Science, Centre of Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Czech Republic
| | - Michal Biler
- Department of Biophysics, Faculty of Science, Centre of Region Haná for Biotechnological and Agricultural Research, Palacký UniversityOlomouc, Czech Republic; INSERM UMR 850, School of Pharmacy, University LimogesLimoges, France
| | - Tereza Štenclová
- Department of Biophysics, Faculty of Science, Centre of Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Czech Republic
| | - Patrick Trouillas
- INSERM UMR 850, School of Pharmacy, University LimogesLimoges, France; Department of Physical Chemistry, Faculty of Science, Regional Centre of Advanced Technologies and Materials, Palacký UniversityOlomouc, Czech Republic
| | - David Biedermann
- Laboratory of Biotransformation, Institute of Microbiology, Czech Academy of Sciences Prague, Czech Republic
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Kubala M, Geleticova J, Huliciak M, Zatloukalova M, Vacek J, Sebela M. Na(+)/K(+)-ATPase inhibition by cisplatin and consequences for cisplatin nephrotoxicity. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2014; 158:194-200. [PMID: 24781046 DOI: 10.5507/bp.2014.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Accepted: 04/02/2014] [Indexed: 01/30/2023] Open
Abstract
AIMS Cisplatin is a widely used chemotherapeutic. However, it is associated with numerous adverse effects. The aim of our study was examination of cisplatin interaction with Na(+)/K(+)-ATPase (NKA, the sodium pump). This enzyme is of crucial importance for all animal cells and particularly for the kidney, which is frequently damaged during chemotherapy. METHODS The entire NKA was isolated from porcine kidney. Its large cytoplasmic segment connecting transmembrane helices 4 and 5 (C45), was heterologously expressed in E.coli (wild-type or C367S mutant). The ATPase activity was evaluated according to the inorganic phosphate production and the interaction of isolated C45 with cisplatin was studied using chronopotentiometry and mass spectrometry. RESULTS Our experiments revealed that cisplatin can inhibit NKA. The finding that other platinum-based drugs with a low nephrotoxicity, carboplatin and oxaliplatin, did not inhibit NKA, suggested that NKA/cisplatin interaction is an important factor in cisplatin adverse effects. The inhibitory effect of cisplatin could be prevented by preincubation of the enzyme with reduced glutathione or DTT. Using chronopotentiometry and mass spectrometry, we found that cisplatin is bound to C45. However, our mutagenesis experiment did not confirm that the suggested Cys367 could be the binding site for cisplatin. CONCLUSION Unintended interactions of drugs present serious limitations to treatment success. Although a large number of membrane pumps have been identified as potential targets of cisplatin, vis-a-vis nephrotoxicity, NKA inhibition seems to be of crucial importance. Experiments with isolated large cytoplasmic segment C45 revealed that it is the main target of cisplatin on NKA and that the reaction with cysteine residues plays an important role in cisplatin/NKA interactions. However, further experiments must be performed to identify the interacting amino acid residues more precisely.
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Affiliation(s)
- Martin Kubala
- Department of Biophysics, Centre of the Region Hana for Biotechnological and Agricultural Research, Palacky University Olomouc, Czech Republic
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Havlíková M, Huličiak M, Bazgier V, Berka K, Kubala M. Fluorone dyes have binding sites on both cytoplasmic and extracellular domains of Na,K-ATPase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1828:568-76. [PMID: 23142565 DOI: 10.1016/j.bbamem.2012.10.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Revised: 10/24/2012] [Accepted: 10/31/2012] [Indexed: 11/30/2022]
Abstract
Combination of fluorescence techniques and molecular docking was used to monitor interaction of Na,K-ATPase and its large cytoplasmic loop connecting fourth and fifth transmembrane helices (C45) with fluorone dyes (i.e. eosin Y, 5(6)-carboxyeosin, rose bengal, fluorescein, and erythrosine B). Our data suggested that there are at least two binding sites for all used fluorone dyes, except of 5(6)-carboxyeosin. The first binding site is located on C45 loop, and it is sensitive to the presence of nucleotide. The other site is located on the extracellular part of the enzyme, and it is sensitive to the presence of Na(+) or K(+) ions. The molecular docking revealed that in the open conformation of C45 loop (which is obtained in the presence of ATP) all used fluorone dyes occupy position directly inside the ATP-binding pocket, while in the closed conformation (i.e. in the absence of any ligand) they are located only near the ATP-binding site depending on their different sizes. On the extracellular part of the protein, the molecular docking predicts two possible binding sites with similar binding energy near Asp897(α) or Gln69(β). The former was identified as a part of interaction site between α- and β-subunits, the latter is in contact with conserved FXYD sequence of the γ-subunit. Our findings provide structural explanation for numerous older studies, which were performed with fluorone dyes before the high-resolution structures were known. Further, fluorone dyes seem to be good probes for monitoring of intersubunit interactions influenced by Na(+) and K(+) binding.
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Affiliation(s)
- Marika Havlíková
- Department of Biophysics, Faculty of Science, Palacký University in Olomouc, tř. 17. listopadu 12, 771 46 Olomouc, Czech Republic.
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Huličiak M, Vacek J, Sebela M, Orolinová E, Znaleziona J, Havlíková M, Kubala M. Covalent binding of cisplatin impairs the function of Na(+)/K(+)-ATPase by binding to its cytoplasmic part. Biochem Pharmacol 2012; 83:1507-13. [PMID: 22394404 DOI: 10.1016/j.bcp.2012.02.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 02/17/2012] [Accepted: 02/20/2012] [Indexed: 01/26/2023]
Abstract
This study was aimed at verifying the hypothesis that acute kidney failure accompanying cisplatin administration in the cancer therapy could be due to cisplatin interaction with the cytoplasmic part of Na(+)/K(+)-ATPase. Our results demonstrated that cisplatin-binding caused inhibition of Na(+)/K(+)-ATPase, in contrast to other platinated chemotherapeutics such as carboplatin and oxaliplatin, which are known to be much less nephrotoxic. To acquire more detailed structural information, we performed a series of experiments with the isolated large cytoplasmic segment connecting transmembrane helices 4 and 5 (C45 loop) of Na(+)/K(+)-ATPase. Electrochemistry showed that cisplatin is bound to the cysteine residues of the C45 loop, mass spectrometry revealed a modification of the C45 peptide fragment GSHMASLEAVETLGSTSTICSDK, which contains the conserved phosphorylated residue Asp369. Hence, we hypothesize that binding of cisplatin to Cys367 can cause sterical obstruction during the phosphorylation or dephosphorylation step of the Na(+)/K(+)-ATPase catalytic cycle.
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Affiliation(s)
- Miroslav Huličiak
- Department of Biophysics, Palacký University in Olomouc, Olomouc, Czech Republic
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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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Mi L, Di Pasqua AJ, Chung FL. Proteins as binding targets of isothiocyanates in cancer prevention. Carcinogenesis 2011; 32:1405-13. [PMID: 21665889 PMCID: PMC3179418 DOI: 10.1093/carcin/bgr111] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 06/01/2011] [Accepted: 06/05/2011] [Indexed: 01/18/2023] Open
Abstract
Isothiocyanates are versatile cancer-preventive compounds. Evidence from animal studies indicates that the anticarcinogenic activities of ITCs involve all the major stages of tumor growth: initiation, promotion and progression. Epidemiological studies have also shown that dietary intake of ITCs is associated with reduced risk of certain human cancers. A number of mechanisms have been proposed for the chemopreventive activities of ITCs. To identify the molecular targets of ITCs is a first step to understand the molecular mechanisms of ITCs. Studies in recent years have shown that the covalent binding to certain protein targets by ITCs seems to play an important role in ITC-induced apoptosis and cell growth inhibition and other cellular effects. The knowledge gained from these studies may be used to guide future design and screen of better and more efficacious compounds. In this review, we intend to cover all potential protein targets of ITCs so far studied and summarize what are known about their binding sites and the potential biological consequences. In the end, we also offer discussions to shed light onto the relationship between protein binding and reactive oxygen species generation by ITCs.
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Affiliation(s)
- Lixin Mi
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA.
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Zhou J, Lu G. Spectroscopy study on the noncovalent interactions in the binary and ternary systems of L-lysine, adenosine 5'-triphosphate and magnesium ions. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2011; 78:1305-1309. [PMID: 21292544 DOI: 10.1016/j.saa.2011.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2010] [Revised: 12/28/2010] [Accepted: 01/06/2011] [Indexed: 05/30/2023]
Abstract
Intermolecular interactions of adenosine 5'-triphosphate (ATP) with Lysine (Lys) and Mg(2+) were studied in aqueous solution by (1)H and (31)P NMR spectra. In the metal-free system, the N-1 atom of the purine ring of ATP and carboxyl group of Lys are the interaction sites at low pH conditions. With increasing pH, the interaction efficiency between the phosphate group of ATP and the protonated ammonium group of Lys increased significantly, while that with carboxyl group in Lys decreased. In the Mg(2+)-Lys-ATP system, multi-interactions, such as coordination, cations (Mg(2+), NH(3)(+))-π, hydrogen bonding, ion-pairing interactions and electrostatic interactions co-existed. In addition, the recognition of ATP by the amino acid cation (Lys) was significantly promoted by the addition of magnesium ion, which led to the coordination competition between Lys and ATP.
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Affiliation(s)
- Jinying Zhou
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou, Gansu, China
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Kubala M, Grycova L, Lansky Z, Sklenovsky P, Janovska M, Otyepka M, Teisinger J. Changes in electrostatic surface potential of Na+/K+-ATPase cytoplasmic headpiece induced by cytoplasmic ligand(s) binding. Biophys J 2009; 97:1756-64. [PMID: 19751681 DOI: 10.1016/j.bpj.2009.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2009] [Revised: 06/23/2009] [Accepted: 07/07/2009] [Indexed: 10/20/2022] Open
Abstract
A set of single-tryptophan mutants of the Na(+)/K(+)-ATPase isolated, large cytoplasmic loop connecting transmembrane helices M4 and M5 (C45) was prepared to monitor effects of the natural cytoplasmic ligands (i.e., Mg(2+) and/or ATP) binding. We introduced a novel method for the monitoring of the changes in the electrostatic surface potential (ESP) induced by ligand binding, using the quenching of the intrinsic tryptophan fluorescence by acrylamide or iodide. This approach opens a new way to understanding the interactions within the proteins. Our experiments revealed that the C45 conformation in the presence of the ATP (without magnesium) substantially differed from the conformation in the presence of Mg(2+) or MgATP or in the absence of any ligand not only in the sense of geometry but also in the sense of the ESP. Notably, the set of ESP-sensitive residues was different from the set of geometry-sensitive residues. Moreover, our data indicate that the effect of the ligand binding is not restricted only to the close environment of the binding site and that the information is in fact transmitted also to the distal parts of the molecule. This property could be important for the communication between the cytoplasmic headpiece and the cation binding sites located within the transmembrane domain.
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Affiliation(s)
- Martin Kubala
- Laboratory of Biophysics, Faculty of Science, Palacký University, Olomouc, Czech Republic.
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Grycova L, Sklenovsky P, Lansky Z, Janovska M, Otyepka M, Amler E, Teisinger J, Kubala M. ATP and magnesium drive conformational changes of the Na+/K+-ATPase cytoplasmic headpiece. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:1081-91. [PMID: 19232513 DOI: 10.1016/j.bbamem.2009.02.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Revised: 01/16/2009] [Accepted: 02/03/2009] [Indexed: 10/21/2022]
Abstract
Conformational changes of the Na(+)/K(+)-ATPase isolated large cytoplasmic segment connecting transmembrane helices M4 and M5 (C45) induced by the interaction with enzyme ligands (i.e. Mg(2+) and/or ATP) were investigated by means of the intrinsic tryptophan fluorescence measurement and molecular dynamic simulations. Our data revealed that this model system consisting of only two domains retained the ability to adopt open or closed conformation, i.e. behavior, which is expected from the crystal structures of relative Ca(2+)-ATPase from sarco(endo)plasmic reticulum for the corresponding part of the entire enzyme. Our data revealed that the C45 is found in the closed conformation in the absence of any ligand, in the presence of Mg(2+) only, or in the simultaneous presence of Mg(2+) and ATP. Binding of the ATP alone (i.e. in the absence of Mg(2+)) induced open conformation of the C45. The fact that the transmembrane part of the enzyme was absent in our experiments suggested that the observed conformational changes are consequences only of the interaction with ATP or Mg(2+) and may not be related to the transported cations binding/release, as generally believed. Our data are consistent with the model, where ATP binding to the low-affinity site induces conformational change of the cytoplasmic part of the enzyme, traditionally attributed to E2-->E1 transition, and subsequent Mg(2+) binding to the enzyme-ATP complex induces in turn conformational change traditionally attributed to E1-->E2 transition.
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Affiliation(s)
- Lenka Grycova
- Institute of Physiology, Academy of Sciences of the Czech Republic, Vídenská 1083, 14220 Prague 4, Czech Republic
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Grycova L, Lansky Z, Friedlova E, Vlachova V, Kubala M, Obsilova V, Obsil T, Teisinger J. ATP binding site on the C-terminus of the vanilloid receptor. Arch Biochem Biophys 2007; 465:389-98. [PMID: 17706589 DOI: 10.1016/j.abb.2007.06.035] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2007] [Revised: 06/29/2007] [Accepted: 06/30/2007] [Indexed: 10/23/2022]
Abstract
Transient receptor potential channel vanilloid receptor subunit 1 (TRPV1) is a thermosensitive cation channel activated by noxious heat as well as a wide range of chemical stimuli. Although ATP by itself does not directly activate TRPV1, it was shown that intracellular ATP increases its activity by directly interacting with the Walker A motif residing on the C-terminus of TRPV1. In order to identify the amino acid residues that are essential for the binding of ATP to the TRPV1 channel, we performed the following point mutations of the Walker A motif: P732A, D733A, G734A, K735A, D736A, and D737A. Employing bulk fluorescence measurements, namely a TNP-ATP competition assay and FITC labelling and quenching experiments, we identified the key role of the K735 residue in the binding of the nucleotide. Experimental data was interpreted according to our molecular modelling simulations.
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Affiliation(s)
- Lenka Grycova
- Institute of Physiology, Academy of Sciences of the Czech Republic, Vídenská 1083, 14220 Prague, Czech Republic
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Kubala M. ATP-binding to P-type ATPases as revealed by biochemical, spectroscopic, and crystallographic experiments. Proteins 2006; 64:1-12. [PMID: 16649212 DOI: 10.1002/prot.20969] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
P-type ATPases form a large family of cation translocating ATPases. Recent progress in crystallography yielded several high-resolution structures of Ca(2+)-ATPase from sarco(endo)plasmic reticulum (SERCA) in various conformations. They could elucidate the conformational changes of the enzyme, which are necessary for the translocation of cations, or the mechanism that explains how the nucleotide binding is coupled to the cation transport. However, crystals of proteins are usually obtained only under conditions that significantly differ from the physiological ones and with ligands that are incompatible with the enzyme function, and both of these factors can inevitably influence the enzyme structure. Biochemical (such as mutagenesis, cleavage, and labeling) or spectroscopic experiments can yield only limited structural information, but this information could be considered relevant, because measurement can be performed under physiological conditions and with true ligands. However, interpretation of some biochemical or spectroscopic data could be difficult without precise knowledge of the structure. Thus, only a combination of both these approaches can extract the relevant information and identify artifacts. Briefly, there is good agreement between crystallographic and other experimental data concerning the overall shape of the molecule and the movement of cytoplasmic domains. On the contrary, the E1-AMPPCP crystallographic structure is, in details, in severe conflict with numerous spectroscopic experiments and probably does not represent the physiological state. Notably, the E1-ADP-AlF(4) structure is almost identical to the E1-AMPPCP, again suggesting that the structure is primarily determined by the crystal-growth conditions. The physiological relevance of the E2 and E2-P structures is also questionable, because the crystals were prepared in the presence of thapsigargin, which is known to be a very efficient inhibitor of SERCA. Thus, probably only crystals of E1-2Ca conformation could reflect some physiological state. Combination of biochemical, spectroscopic, and crystallographic data revealed amino acids that are responsible for the interaction with the nucleotide. High sequence homology of the P-type ATPases in the cytoplasmic domains enables prediction of the ATP-interacting amino acids also for other P-type ATPases.
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Affiliation(s)
- Martin Kubala
- Department of Biophysics, Faculty of Sciences, Palacky University, Olomouc, Czech Republic.
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Krumscheid R, Ettrich R, Sovová Z, Susánková K, Lánský Z, Hofbauerová K, Linnertz H, Teisinger J, Amler E, Schoner W. The phosphatase activity of the isolated H4-H5 loop of Na+/K+ ATPase resides outside its ATP binding site. ACTA ACUST UNITED AC 2004; 271:3923-36. [PMID: 15373838 DOI: 10.1111/j.1432-1033.2004.04330.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structural stability of the large cytoplasmic domain (H(4)-H(5) loop) of mouse alpha(1) subunit of Na(+)/K(+) ATPase (L354-I777), the number and the location of its binding sites for 2'-3'-O-(trinitrophenyl) adenosine 5'-triphosphate (TNP-ATP) and p-nitrophenylphosphate (pNPP) were investigated. C- and N-terminal shortening revealed that neither part of the phosphorylation (P)-domain are necessary for TNP-ATP binding. There is no indication of a second ATP site on the P-domain of the isolated loop, even though others reported previously of its existence by TNP-N(3)ADP affinity labeling of the full enzyme. Fluorescein isothiocyanate (FITC)-anisotropy measurements reveal a considerable stability of the nucleotide (N)-domain suggesting that it may not undergo a substantial conformational change upon ATP binding. The FITC modified loop showed only slightly diminished phosphatase activity, most likely due to a pNPP site on the N-domain around N398 whose mutation to D reduced the phosphatase activity by 50%. The amino acids forming this pNPP site (M384, L414, W411, S400, S408) are conserved in the alpha(1-4) isoforms of Na(+)/K(+) ATPase, whereas N398 is only conserved in the vertebrates' alpha(1) subunit. The phosphatase activity of the isolated H(4)-H(5) loop was neither inhibited by ATP, nor affected by mutation of D369, which is phosphorylated in native Na(+)/K(+) ATPase.
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Affiliation(s)
- Rita Krumscheid
- Institute of Biochemistry and Endocrinology, Justus-Liebig-University Giessen, D-35392 Giessen, Germany
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