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

Vasilina Zayats1,2, Thomas Stockner3, Saurabh Kumar Pandey1,2, Katharina Wörz4, Rüdiger Ettrich1,2, Jost Ludwig1,4

1Institute of Nanobiology and Structural Biology, Global Change Research Center, Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic

2Faculty of Sciences, University of South Bohemia, Nove Hrady, Czech Republic

3Institute of Pharmacology, Medical University of Vienna, Vienna, Austria

4Molecular Bioenergetics, Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany

e-mail: ludwig@nh.cas.cz


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 (the SKT protein family). 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 amongst 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.