title: Ion Pathways in the Na+/K+-ATPase.
abstract: Na+/K+-ATPase (NKA) is an essential cation pump protein responsible for the maintenance of the sodium and potassium gradients across the plasma membrane. Recently published high-resolution structures revealed amino acids forming the cation binding sites (CBS) in the transmembrane domain and variable position of the domains in the cytoplasmic headpiece. Here we report molecular dynamic simulations of the human NKA α1β1 isoform embedded into DOPC bilayer. We have analyzed the NKA conformational changes in the presence of Na+- or K+-cations in the CBS, for various combinations of the cytoplasmic ligands, and the two major enzyme conformations in the 100 ns runs (more than 2.5 μs of simulations in total). We identified two novel cytoplasmic pathways along the pairs of transmembrane helices TM3/TM7 or TM6/TM9 that allow hydration of the CBS or transport of cations from/to the bulk. These findings can provide a structural explanation for previous mutagenesis studies, where mutation of residues that are distal from the CBS resulted in the alteration of the enzyme affinity to the transported cations or change in the enzyme activity.
authors.affiliation: Department of Biophysics, Centre of the Region Hana for Biotechnological and Agricultural Research, Faculty of Science, Palacký University , Šlechtitelů 27, 783 71, Olomouc, Czech Republic.
authors.forename: Petra
authors.initials: P
authors.lastname: Čechová
authors.affiliation: Department of Physical Chemistry, Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University , 17. listopadu 12, 77146 Olomouc, Czech Republic.
authors.forename: Karel
authors.identifier: 0000-0001-9472-2589
authors.initials: K
authors.lastname: Berka
authors.affiliation: Department of Biophysics, Centre of the Region Hana for Biotechnological and Agricultural Research, Faculty of Science, Palacký University , Šlechtitelů 27, 783 71, Olomouc, Czech Republic.
authors.forename: Martin
authors.identifier: 0000-0002-3555-0016
authors.initials: M
authors.lastname: Kubala
mesh_terms: D000818:Animals; D002412:Cations / Q000378:metabolism; D006801:Humans; D008051:Lipid Bilayers / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D010713:Phosphatidylcholines / Q000378:metabolism*; D011188:Potassium / Q000378:metabolism*; D011487:Protein Conformation; D012964:Sodium / Q000378:metabolism*; D000254:Sodium-Potassium-Exchanging ATPase / Q000737:chemistry / Q000378:metabolism*
chemical_list: C503551:ATP1B1 protein, human; D002412:Cations; D008051:Lipid Bilayers; D010713:Phosphatidylcholines; D012964:Sodium; C499076:ATP1A1 protein, human; D000254:Sodium-Potassium-Exchanging ATPase; C017251:1,2-oleoylphosphatidylcholine; D011188:Potassium