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

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

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.

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

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.

Biochemical Characterization and Allosteric Modulation by Magnesium of (Na+, K+)-ATPase Activity in the Gills of the Red Mangrove Crab Goniopsis cruentata (Brachyura, Grapsidae)

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 M_r of ≈ 10 kDa and hydrolyzes ATP obeying cooperative kinetics. Low (V_M = 186.0 ± 9.3 nmol Pi min^-1 mg^-1 protein and K_0.5 = 0.085 ± 0.004 mmol L^-1) and high (V_M = 153.4 ± 7.7 nmol Pi min^-1 mg^-1 protein and K_0.5 = 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⁺ (V_M = 425.9 ± 25.5 nmol Pi min^-1 mg^-1 protein, K_0.5 = 0.16 ± 0.01 mmol L^-1), K⁺ (V_M = 485.3 ± 24.3 nmol Pi min^-1 mg^-1 protein, K_0.5 = 0.9 ± 0.05 mmol L^-1), Na⁺ (V_M = 425.0 ± 23.4 nmol Pi min^-1 mg^-1 protein, K_0.5 = 5.1 ± 0.3 mmol L^-1) and NH₄⁺ (V_M = 497.9 ± 24.9 nmol Pi min^-1 mg^-1 protein, K_0.5 = 9.7 ± 0.5 mmol L^-1) obeys cooperative kinetics. Ouabain inhibits up to 95% of ATPase activity with K_I = 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.