title: A refined atomic scale model of the Saccharomyces cerevisiae K+-translocation protein Trk1p combined with experimental evidence confirms the role of selectivity filter glycines and other key residues.
abstract: Potassium ion (K+) uptake in yeast is mediated mainly by the Trk1/2 proteins that enable cells to survive on external K+ concentration as low as a few μM. Fungal Trks are related to prokaryotic TRK and Ktr and plant HKT K+ transport systems. Overall sequence similarity is very low, thus requiring experimental verification of homology models. Here a refined structural model of the Saccharomyces cerevisiae Trk1 is presented that was obtained by combining homology modeling, molecular dynamics simulation and experimental verification through functional analysis of mutants. Structural models and experimental results showed that glycines within the selectivity filter, conserved among the K-channel/transporter family, are not only important for protein function, but are also required for correct folding/membrane targeting. A conserved aspartic acid in the PA helix (D79) and a lysine in the M2D helix (K1147) were proposed earlier to interact. Our results suggested individual roles of these residues in folding, structural integrity and function. While mutations of D79 completely abolished protein folding, mutations at position 1147 were tolerated to some extent. Intriguingly, a secondary interaction of D79 with R76 could enhance folding/stability of Trk1 and enable a fraction of Trk1[K1147A] to fold. The part of the ion permeation path containing the selectivity filter is shaped similar to that of ion channels. However below the selectivity filter it is obstructed or regulated by a proline containing loop. The presented model could provide the structural basis for addressing the long standing question if Trk1 is a passive or active ion-translocation system.
authors: Institute of Nanobiology and Structural Biology, Global Change Research Center, Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic; Faculty of Sciences, University of South Bohemia, Nove Hrady, Czech Republic.
authors: Vasilina
authors: V
authors: Zayats
authors: Institute of Pharmacology, Medical University of Vienna, Vienna, Austria.
authors: Thomas
authors: T
authors: Stockner
authors: Institute of Nanobiology and Structural Biology, Global Change Research Center, Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic; Faculty of Sciences, University of South Bohemia, Nove Hrady, Czech Republic.
authors: Saurabh Kumar
authors: SK
authors: Pandey
authors: Molecular Bioenergetics, Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany.
authors: Katharina
authors: K
authors: Wörz
authors: Institute of Nanobiology and Structural Biology, Global Change Research Center, Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic; Faculty of Sciences, University of South Bohemia, Nove Hrady, Czech Republic. Electronic address: ettrich@nh.cas.cz.
authors: Rüdiger
authors: R
authors: Ettrich
authors: Institute of Nanobiology and Structural Biology, Global Change Research Center, Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic; Molecular Bioenergetics, Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany. Electronic address: jost.ludwig@uni-bonn.de.
authors: Jost
authors: J
authors: Ludwig
mesh_terms: D000595:Amino Acid Sequence; D001224:Aspartic Acid; D027682:Cation Transport Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D002462:Cell Membrane / Q000737:chemistry / Q000378:metabolism*; D002463:Cell Membrane Permeability; D019295:Computational Biology; D017124:Conserved Sequence; D005998:Glycine; D015640:Ion Channel Gating; D007700:Kinetics; D008239:Lysine; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009154:Mutation; D011188:Potassium / Q000378:metabolism*; D011487:Protein Conformation; D017510:Protein Folding; D055550:Protein Stability; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D013329:Structure-Activity Relationship
chemical_list: D027682:Cation Transport Proteins; D029701:Saccharomyces cerevisiae Proteins; C068664:TRK1 protein, S cerevisiae; D001224:Aspartic Acid; D008239:Lysine; D011188:Potassium; D005998:Glycine
keywords: Eukaryotic Trk; Homology modeling; K(+)-translocation; Molecular dynamics; Saccharomyces cerevisiae; Selectivity filter