title: Glutamate Water Gates in the Ion Binding Pocket of Na+Bound Na+, K+-ATPase.
abstract: The dynamically changing protonation states of the six acidic amino acid residues in the ion binding pocket of the Na+, K+-ATPase (NKA) during the ion transport cycle are proposed to drive ion binding, release and possibly determine Na+or K+selectivity. We use molecular dynamics (MD) and density functional theory (DFT) simulations to determine the protonation scheme of the Na+bound conformation of NKA. MD simulations of all possible protonation schemes show that the bound Na+ions are most stably bound when three or four protons reside in the binding sites, and that Glu954 in site III is always protonated. Glutamic acid residues in the three binding sites act as water gates, and their deprotonation triggers water entry to the binding sites. From DFT calculations of Na+binding energies, we conclude that three protons in the binding site are needed to effectively bind Na+from water and four are needed to release them in the next step. Protonation of Asp926 in site III will induce Na+release, and Glu327, Glu954 and Glu779 are all likely to be protonated in the Na+bound occluded conformation. Our data provides key insights into the role of protons in the Na+binding and release mechanism of NKA.
authors.affiliation: MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
authors.forename: Minwoo
authors.initials: M
authors.lastname: Han
authors.affiliation: MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
authors.forename: Wojciech
authors.initials: W
authors.lastname: Kopec
authors.affiliation: Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
authors.forename: Ilia A
authors.initials: IA
authors.lastname: Solov'yov
authors.affiliation: MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.
authors.forename: Himanshu
authors.initials: H
authors.lastname: Khandelia
mesh_terms: D000818:Animals; D001665:Binding Sites; D018698:Glutamic Acid / Q000737:chemistry*; D006801:Humans; D017136:Ion Transport; D056004:Molecular Dynamics Simulation; D011188:Potassium / Q000737:chemistry*; D011487:Protein Conformation; D000072417:Protein Domains / Q000235:genetics; D011522:Protons; D012964:Sodium / Q000737:chemistry*; D000254:Sodium-Potassium-Exchanging ATPase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D013379:Substrate Specificity; D014867:Water / Q000737:chemistry
chemical_list: D011522:Protons; D014867:Water; D018698:Glutamic Acid; D012964:Sodium; D000254:Sodium-Potassium-Exchanging ATPase; D011188:Potassium