1. Molecular mechanism of light-driven sodium pumping
- Author
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Kovalev, Kirill, Astashkin, Roman, Gushchin, Ivan, Orekhov, Philipp, Volkov, Dmytro, Zinovev, Egor, Marin, Egor, Rulev, Maksim, Alekseev, Alexey, Royant, Antoine, Carpentier, Philippe, Vaganova, Svetlana, Zabelskii, Dmitrii, Baeken, Christian, Sergeev, Ilya, Balandin, Taras, Bourenkov, Gleb, Carpena, Xavier, Boer, Roeland, Maliar, Nina, Borshchevskiy, Valentin, Büldt, Georg, Bamberg, Ernst, Gordeliy, Valentin, Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow, Moscow Institute of Physics and Technology [Moscow] (MIPT), Biocatalyse (BIOCAT), Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), European Synchrotron Radiation Facility (ESRF), Institute of Complex Systems (ICS), Forschungszentrum Jülich GmbH | Centre de recherche de Juliers, Helmholtz-Gemeinschaft = Helmholtz Association-Helmholtz-Gemeinschaft = Helmholtz Association, European Molecular Biology Laboratory [Hamburg] (EMBL), Max-Planck-Institut für Biophysik - Max Planck Institute of Biophysics (MPIBP), Max-Planck-Gesellschaft, and ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017)
- Subjects
Protein Folding ,Rhodopsin ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,Science ,Sodium ,Molecular Dynamics Simulation ,Crystallography, X-Ray ,Article ,Bacterial Proteins ,X-Ray Diffraction ,Escherichia coli ,lcsh:Q ,ddc:500 ,Sodium-Potassium-Exchanging ATPase ,lcsh:Science ,Flavobacteriaceae ,Ion transport ,X-ray crystallography - Abstract
Nature Communications 11(1), 2137 (2020). doi:10.1038/s41467-020-16032-y, The light-driven sodium-pumping rhodopsin KR2 from Krokinobacter eikastus is the only non-proton cation active transporter with demonstrated potential for optogenetics. However, the existing structural data on KR2 correspond exclusively to its ground state, and show no sodium inside the protein, which hampers the understanding of sodium-pumping mechanism. Here we present crystal structure of the O-intermediate of the physiologically relevant pentameric form of KR2 at the resolution of 2.1 Å, revealing a sodium ion near the retinal Schiff base, coordinated by N112 and D116 of the characteristic NDQ triad. We also obtained crystal structures of D116N and H30A variants, conducted metadynamics simulations and measured pumping activities of putative pathway mutants to demonstrate that sodium release likely proceeds alongside Q78 towards the structural sodium ion bound between KR2 protomers. Our findings highlight the importance of pentameric assembly for sodium pump function, and may be used for rational engineering of enhanced optogenetic tools., Published by Nature Publishing Group UK, [London]
- Published
- 2020
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