Computer modelling reveals new conformers of the ATP binding loop of Na<sup>+</sup>/K<sup>+</sup>-ATPase involved in the transphosphorylation process of the sodium pump

Tejral, Gracian; Sopko, B.; Nečas, Alois; Schoner, Wilhelm; Amler, Evžen

doi:10.7717/peerj.3087

Cited by 5 publications

(3 citation statements)

References 88 publications

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“…Moreover, it was also found that the NKA catalytic cycle is affected by Mg 2+ ions in the way that in the E 1 state, the Mg 2+ ions induce the cavity occlusion, followed by autophosphorylation and transition to the E 2 state [ 77 ]. These data are further confirmed by the computational simulations by [ 78 ], who used molecular docking and simulations of molecular dynamics to show that Mg 2+ facilitates NKA transition from the open to occluded conformation and subsequent autophosphorylation.…”

Section: Catalytic Cycle Of Na + /K + -Atpasesupporting

confidence: 59%

Na+/K+-ATPase Revisited: On Its Mechanism of Action, Role in Cancer, and Activity Modulation

et al. 2021

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Maintenance of Na+ and K+ gradients across the cell plasma membrane is an essential process for mammalian cell survival. An enzyme responsible for this process, sodium-potassium ATPase (NKA), has been currently extensively studied as a potential anticancer target, especially in lung cancer and glioblastoma. To date, many NKA inhibitors, mainly of natural origin from the family of cardiac steroids (CSs), have been reported and extensively studied. Interestingly, upon CS binding to NKA at nontoxic doses, the role of NKA as a receptor is activated and intracellular signaling is triggered, upon which cancer cell death occurs, which lies in the expression of different NKA isoforms than in healthy cells. Two major CSs, digoxin and digitoxin, originally used for the treatment of cardiac arrhythmias, are also being tested for another indication—cancer. Such drug repositioning has a big advantage in smoother approval processes. Besides this, novel CS derivatives with improved performance are being developed and evaluated in combination therapy. This article deals with the NKA structure, mechanism of action, activity modulation, and its most important inhibitors, some of which could serve not only as a powerful tool to combat cancer, but also help to decipher the so-far poorly understood NKA regulation.

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Section: Catalytic Cycle Of Na + /K + -Atpasesupporting

confidence: 59%

Na+/K+-ATPase Revisited: On Its Mechanism of Action, Role in Cancer, and Activity Modulation

et al. 2021

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“…In P-ATPases, ATP binding induces conformational changes in the N-domain structure [20,24,75,76], that may also be observed in the isolated N-domain [20,23,28,29]. In this study, ATP binding quenched the intrinsic uorescence of the NKA N-domain (Fig.…”

Section: Cation Interaction Mediated Nka N-domain Intrinsic Uorescenc...mentioning

confidence: 50%

Effect of cations on ATP binding to the N-domain of Na+, K+-ATPase

Ramírez-Alonso,

Sampedro

2024

Preprint

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The nucleotide-binding domain (N-domain) of the Na+, K+-ATPase (NKA) is physicochemically characterized by a high content of Glu and Asp residues, resulting in a low isoelectric point (pI = 5.0). Acidic proteins are known to interact with cations. The analysis in silico revealed potential cation interaction sites in the NKA N-domain structure. The interaction with cations was tested in vitro by using a recombinant NKA N-domain. The N-domain contains two Trp residues at the protein surface, as determined by acrylamide-mediated fluorescence quenching, that are useful for structural studies through fluorescence changes. Intrinsic fluorescence of the N-domain was quenched by the presence of cations (Na+, K+, Ca2+) indicating an effect on the protein structure. ATP binding also quenched the N-domain intrinsic fluorescence, which allowed nucleotide affinity determination and sigmoid kinetics for binding. In the presence of cations, the N-domain affinity for ATP was increased, as well as binding cooperativity. Molecular docking of fluorescein isothiocyanate (FITC) with the N-domain showed two binding modes with the isothiocyanate group located 5–6 Å close to Lys480 and Lys501 in the nucleotide-binding site. The presence of ATP prevented the FITC covalent labeling of the N-domain demonstrating the competitive behavior for the binding site. Finally, it was found that the presence of Na+ and K+, but not Ca2+, diminished the FITC labeling of the N-domain; i.e., by decreasing FITC affinity at the nucleotide-binding site. It is proposed that cations interact with the N-domain structure and thereby modulate nucleotide (ATP) affinity and possibly affecting NKA catalysis.

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“…The most similarity region among α isoforms is related to transmembrane hydrophobic regions, the cytoplasmic mid-region around the phosphorylation site (Asp369), and the C-terminus [7]. Numerous studies have been done to identify conserved motifs and amino acids in similar or different regions and their role in ion transport mechanism and other properties of the enzyme obtained during evolution [12][13][14][15][16].…”

Section: Introductionmentioning

confidence: 99%

Bioinformatics approaches for classification and investigation of the evolution of the Na/K-ATPase alpha-subunit

et al. 2022

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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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Computer modelling reveals new conformers of the ATP binding loop of Na⁺/K⁺-ATPase involved in the transphosphorylation process of the sodium pump

Cited by 5 publications

References 88 publications

Na+/K+-ATPase Revisited: On Its Mechanism of Action, Role in Cancer, and Activity Modulation

Na+/K+-ATPase Revisited: On Its Mechanism of Action, Role in Cancer, and Activity Modulation

Effect of cations on ATP binding to the N-domain of Na+, K+-ATPase

Bioinformatics approaches for classification and investigation of the evolution of the Na/K-ATPase alpha-subunit

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Computer modelling reveals new conformers of the ATP binding loop of Na+/K+-ATPase involved in the transphosphorylation process of the sodium pump

Cited by 5 publications

References 88 publications

Na+/K+-ATPase Revisited: On Its Mechanism of Action, Role in Cancer, and Activity Modulation

Na+/K+-ATPase Revisited: On Its Mechanism of Action, Role in Cancer, and Activity Modulation

Effect of cations on ATP binding to the N-domain of Na+, K+-ATPase

Bioinformatics approaches for classification and investigation of the evolution of the Na/K-ATPase alpha-subunit

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Computer modelling reveals new conformers of the ATP binding loop of Na⁺/K⁺-ATPase involved in the transphosphorylation process of the sodium pump