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      Structural basis of proton-coupled potassium transport in the KUP family

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          Abstract

          Potassium homeostasis is vital for all organisms, but is challenging in single-celled organisms like bacteria and yeast and immobile organisms like plants that constantly need to adapt to changing external conditions. KUP transporters facilitate potassium uptake by the co-transport of protons. Here, we uncover the molecular basis for transport in this widely distributed family. We identify the potassium importer KimA from Bacillus subtilis as a member of the KUP family, demonstrate that it functions as a K +/H + symporter and report a 3.7 Å cryo-EM structure of the KimA homodimer in an inward-occluded, trans-inhibited conformation. By introducing point mutations, we identify key residues for potassium and proton binding, which are conserved among other KUP proteins.

          Abstract

          KUP transporters facilitate potassium uptake by the co-transport of protons and are key players in potassium homeostasis. Here authors identify the potassium importer KimA from Bacillus subtilis as a new member of the KUP transporter family and show the cryo-EM structure of KimA in an inward-occluded, trans-inhibited conformation.

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          Most cited references37

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          MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes

          Summary There has been exponential growth in the number of membrane protein structures determined. Nevertheless, these structures are usually resolved in the absence of their lipid environment. Coarse-grained molecular dynamics (CGMD) simulations enable insertion of membrane proteins into explicit models of lipid bilayers. We have automated the CGMD methodology, enabling membrane protein structures to be identified upon their release into the PDB and embedded into a membrane. The simulations are analyzed for protein-lipid interactions, identifying lipid binding sites, and revealing local bilayer deformations plus molecular access pathways within the membrane. The coarse-grained models of membrane protein/bilayer complexes are transformed to atomistic resolution for further analysis and simulation. Using this automated simulation pipeline, we have analyzed a number of recently determined membrane protein structures to predict their locations within a membrane, their lipid/protein interactions, and the functional implications of an enhanced understanding of the local membrane environment of each protein.
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            Common folds and transport mechanisms of secondary active transporters.

            Yigong Shi (2013)
            Secondary active transporters exploit the electrochemical potential of solutes to shuttle specific substrate molecules across biological membranes, usually against their concentration gradient. Transporters of different functional families with little sequence similarity have repeatedly been found to exhibit similar folds, exemplified by the MFS, LeuT, and NhaA folds. Observations of multiple conformational states of the same transporter, represented by the LeuT superfamily members Mhp1, AdiC, vSGLT, and LeuT, led to proposals that structural changes are associated with substrate binding and transport. Despite recent biochemical and structural advances, our understanding of substrate recognition and energy coupling is rather preliminary. This review focuses on the common folds and shared transport mechanisms of secondary active transporters. Available structural information generally supports the alternating access model for substrate transport, with variations and extensions made by emerging structural, biochemical, and computational evidence.
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              Membrane reconstitution of ABC transporters and assays of translocator function.

              In this protocol, we describe a procedure for incorporating ATP-binding cassette (ABC) transporters into large unilamellar vesicles (LUVs) and assays to determine ligand binding and solute translocation by these membrane-reconstituted systems. The reconstitution technique as described has been optimized for ABC transporters but can be readily adapted for other types of transport systems. Purified transporters are inserted into detergent-destabilized preformed liposomes and detergent is subsequently removed by adsorption onto polystyrene beads. Next, Mg-ATP or an ATP-regenerating system is incorporated into the vesicle lumen by one or more cycles of freezing-thawing, followed by extrusion through polycarbonate filters to obtain unilamellar vesicles. Binding and translocation of substrates are measured using isotope-labeled ligands and rapid filtration to separate the proteoliposomes from the surrounding medium. Quantitative information is obtained about dissociation constants (K(d)) for ligand binding, number of binding-sites, transport affinities (K(m)), rates of transport, and the activities of transporter molecules with opposite orientations in the membrane. The full protocol can be completed within 4-5 d.
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                Author and article information

                Contributors
                janet.vonck@biophys.mpg.de
                Haenelt@biochem.uni-frankfurt.de
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                31 January 2020
                31 January 2020
                2020
                : 11
                : 626
                Affiliations
                [1 ]ISNI 0000 0004 1936 9721, GRID grid.7839.5, Institute of Biochemistry, , Goethe University Frankfurt, ; Frankfurt am Main, Germany
                [2 ]ISNI 0000 0001 1018 9466, GRID grid.419494.5, Department of Structural Biology, , Max Planck Institute of Biophysics, ; Frankfurt am Main, Germany
                [3 ]ISNI 0000 0004 1936 8948, GRID grid.4991.5, Department of Biochemistry, , University of Oxford, ; Oxford, UK
                [4 ]ISNI 0000 0000 8809 1613, GRID grid.7372.1, School of Life Sciences & Department of Chemistry, , University of Warwick, ; Coventry, CV4 7AL UK
                Author information
                http://orcid.org/0000-0003-2526-6238
                http://orcid.org/0000-0002-3564-897X
                http://orcid.org/0000-0001-8800-7669
                http://orcid.org/0000-0003-1495-3163
                Article
                14441
                10.1038/s41467-020-14441-7
                6994465
                32005818
                ecafc316-de08-49db-8a9a-648b9482d209
                © The Author(s) 2020

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 22 August 2019
                : 10 January 2020
                Funding
                Funded by: FundRef https://doi.org/10.13039/501100004189, Max-Planck-Gesellschaft (Max Planck Society);
                Funded by: FundRef https://doi.org/10.13039/501100000266, RCUK | Engineering and Physical Sciences Research Council (EPSRC);
                Award ID: EP/R029407/1
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100000265, RCUK | Medical Research Council (MRC);
                Award ID: MR/S009213/1
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100000268, RCUK | Biotechnology and Biological Sciences Research Council (BBSRC);
                Award ID: BB/P01948X/1, BB/R002517/1 BB/S003339/1
                Award Recipient :
                Funded by: FundRef https://doi.org/10.13039/501100001659, Deutsche Forschungsgemeinschaft (German Research Foundation);
                Award ID: HA 6322/4-1, VO 1449/1-1
                Award Recipient :
                Funded by: Cluster of Excellence Macromolecular Complexes, Frankfurt
                Categories
                Article
                Custom metadata
                © The Author(s) 2020

                Uncategorized
                cryoelectron microscopy,ion transport,permeation and transport,bacterial structural biology

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