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Fagnen C, Bannwarth L, Oubella I, Zuniga D, Haouz A, Forest E, Scala R, Bendahhou S, De Zorzi R, Perahia D, Vénien-Bryan C. Integrative Study of the Structural and Dynamical Properties of a KirBac3.1 Mutant: Functional Implication of a Highly Conserved Tryptophan in the Transmembrane Domain. Int J Mol Sci 2021; 23:335. [PMID: 35008764 PMCID: PMC8745282 DOI: 10.3390/ijms23010335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/18/2021] [Accepted: 12/23/2021] [Indexed: 12/02/2022] Open
Abstract
ATP-sensitive potassium (K-ATP) channels are ubiquitously expressed on the plasma membrane of cells in several organs, including the heart, pancreas, and brain, and they govern a wide range of physiological processes. In pancreatic β-cells, K-ATP channels composed of Kir6.2 and SUR1 play a key role in coupling blood glucose and insulin secretion. A tryptophan residue located at the cytosolic end of the transmembrane helix is highly conserved in eukaryote and prokaryote Kir channels. Any mutation on this amino acid causes a gain of function and neonatal diabetes mellitus. In this study, we have investigated the effect of mutation on this highly conserved residue on a KirBac channel (prokaryotic homolog of mammalian Kir6.2). We provide the crystal structure of the mutant KirBac3.1 W46R (equivalent to W68R in Kir6.2) and its conformational flexibility properties using HDX-MS. In addition, the detailed dynamical view of the mutant during the gating was investigated using the in silico method. Finally, functional assays have been performed. A comparison of important structural determinants for the gating mechanism between the wild type KirBac and the mutant W46R suggests interesting structural and dynamical clues and a mechanism of action of the mutation that leads to the gain of function.
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Affiliation(s)
- Charline Fagnen
- IMPMC, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Sorbonne Université, 75005 Paris, France; (C.F.); (L.B.); (I.O.); (D.Z.)
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, 4 Ave. des Sciences, 91190 Gif-sur-Yvette, France;
| | - Ludovic Bannwarth
- IMPMC, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Sorbonne Université, 75005 Paris, France; (C.F.); (L.B.); (I.O.); (D.Z.)
| | - Iman Oubella
- IMPMC, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Sorbonne Université, 75005 Paris, France; (C.F.); (L.B.); (I.O.); (D.Z.)
| | - Dania Zuniga
- IMPMC, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Sorbonne Université, 75005 Paris, France; (C.F.); (L.B.); (I.O.); (D.Z.)
| | - Ahmed Haouz
- Institut Pasteur, C2RT-Plate-Forme de Cristallographie CNRS-UMR3528, 75724 Paris, France;
| | - Eric Forest
- CNRS, IBS, CEA, University Grenoble Alpes, 38044 Grenoble, France;
| | - Rosa Scala
- CNRS UMR7370, LP2M, Labex ICST, Faculté de Médecine, University Côte d’Azur, 06560 Nice, France; (R.S.); (S.B.)
| | - Saïd Bendahhou
- CNRS UMR7370, LP2M, Labex ICST, Faculté de Médecine, University Côte d’Azur, 06560 Nice, France; (R.S.); (S.B.)
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via Licio Giorgeri 1, 34127 Trieste, Italy;
| | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, 4 Ave. des Sciences, 91190 Gif-sur-Yvette, France;
| | - Catherine Vénien-Bryan
- IMPMC, UMR 7590, CNRS, Muséum National d’Histoire Naturelle, Sorbonne Université, 75005 Paris, France; (C.F.); (L.B.); (I.O.); (D.Z.)
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Fagnen C, Bannwarth L, Zuniga D, Oubella I, De Zorzi R, Forest E, Scala R, Guilbault S, Bendahhou S, Perahia D, Vénien-Bryan C. Unexpected Gating Behaviour of an Engineered Potassium Channel Kir. Front Mol Biosci 2021; 8:691901. [PMID: 34179097 PMCID: PMC8222812 DOI: 10.3389/fmolb.2021.691901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 05/26/2021] [Indexed: 11/24/2022] Open
Abstract
In this study, we investigated the dynamics and functional characteristics of the KirBac3.1 S129R, a mutated bacterial potassium channel for which the inner pore-lining helix (TM2) was engineered so that the bundle crossing is trapped in an open conformation. The structure of this channel has been previously determined at high atomic resolution. We explored the dynamical characteristics of this open state channel using an in silico method MDeNM that combines molecular dynamics simulations and normal modes. We captured the global and local motions at the mutation level and compared these data with HDX-MS experiments. MDeNM provided also an estimation of the probability of the different opening states that are in agreement with our electrophysiological experiments. In the S129R mutant, the Arg129 mutation releases the two constriction points in the channel that existed in the wild type but interestingly creates another restriction point.
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Affiliation(s)
- Charline Fagnen
- UMR 7590, CNRS, Muséum National d'Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, Sorbonne Université, Paris, France.,Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
| | - Ludovic Bannwarth
- UMR 7590, CNRS, Muséum National d'Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, Sorbonne Université, Paris, France
| | - Dania Zuniga
- UMR 7590, CNRS, Muséum National d'Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, Sorbonne Université, Paris, France
| | - Iman Oubella
- UMR 7590, CNRS, Muséum National d'Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, Sorbonne Université, Paris, France
| | - Rita De Zorzi
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Eric Forest
- IBS University Grenoble Alpes, CNRS, CEA, Grenoble, France
| | - Rosa Scala
- Faculté de Médecine, CNRS UMR7370, LP2M, Labex ICST, University Côte d'Azur, Nice, France
| | - Samuel Guilbault
- Faculté de Médecine, CNRS UMR7370, LP2M, Labex ICST, University Côte d'Azur, Nice, France
| | - Saïd Bendahhou
- Faculté de Médecine, CNRS UMR7370, LP2M, Labex ICST, University Côte d'Azur, Nice, France
| | - David Perahia
- Laboratoire de Biologie et de Pharmacologie Appliquée, Ecole Normale Supérieure Paris-Saclay, Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
| | - Catherine Vénien-Bryan
- UMR 7590, CNRS, Muséum National d'Histoire Naturelle, Institut de Minéralogie, Physique des Matériaux et Cosmochimie, IMPMC, Sorbonne Université, Paris, France
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New Structural insights into Kir channel gating from molecular simulations, HDX-MS and functional studies. Sci Rep 2020; 10:8392. [PMID: 32439887 PMCID: PMC7242327 DOI: 10.1038/s41598-020-65246-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/29/2020] [Indexed: 11/25/2022] Open
Abstract
Inward rectifier potassium (Kir) channels play diverse and important roles in shaping action potentials in biological membranes. An increasing number of diseases are now known to be directly associated with abnormal Kir function. However, the gating of Kir still remains unknown. To increase our understanding of its gating mechanism, a dynamical view of the entire channel is essential. Here the gating activation was studied using a recent developped in silico method, MDeNM, which combines normal mode analysis and molecular dynamics simulations that showed for the very first time the importance of interrelated collective and localized conformational movements. In particular, we highlighted the role played by concerted movements of the different regions throughout the entire protein, such as the cytoplasmic and transmembrane domains and the slide helices. In addition, the HDX-MS analysis achieved in these studies provided a comprehensive and detailed view of the dynamics associated with open/closed transition of the Kir channel in coherence with the theoretical results. MDeNM gives access to the probability of the different opening states that are in agreement with our electrophysiological experiments. The investigations presented in this article are important to remedy dysfunctional channels and are of interest for designing new pharmacological compounds.
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Altissimo M, Kiskinova M, Mincigrucci R, Vaccari L, Guarnaccia C, Masciovecchio C. Perspective: A toolbox for protein structure determination in physiological environment through oriented, 2D ordered, site specific immobilization. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:044017. [PMID: 28428974 PMCID: PMC5392127 DOI: 10.1063/1.4981224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 04/05/2017] [Indexed: 05/19/2023]
Abstract
Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based X-ray crystallography and cryo-electron microscopy have made major contributions in determining thousands of protein structures even from micro-sized crystals. They suffer from some limitations that have not been overcome, such as radiation damage, the natural inability to crystallize a number of proteins, and experimental conditions for structure determination that are incompatible with the physiological environment. Today, the ultra-short and ultra-bright pulses of X-ray free-electron lasers have made attainable the dream to determine protein structures before radiation damage starts to destroy the samples. However, the signal-to-noise ratio remains a great challenge to obtain usable diffraction patterns from a single protein molecule. With the perspective to overcome these challenges, we describe here a new methodology that has the potential to overcome the signal-to-noise-ratio and protein crystallization limits. Using a multidisciplinary approach, we propose to create ordered, two dimensional protein arrays with defined orientation attached on a self-assembled-monolayer. We develop a literature-based flexible toolbox capable of assembling different kinds of proteins on a functionalized surface and consider using a graphene cover layer that will allow performing experiments with proteins in physiological conditions.
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Affiliation(s)
- M Altissimo
- Elettra Sincrotrone Trieste, S. S. 14 km 163, 34149 Trieste, Basovizza, Italy
| | - M Kiskinova
- Elettra Sincrotrone Trieste, S. S. 14 km 163, 34149 Trieste, Basovizza, Italy
| | - R Mincigrucci
- Elettra Sincrotrone Trieste, S. S. 14 km 163, 34149 Trieste, Basovizza, Italy
| | - L Vaccari
- Elettra Sincrotrone Trieste, S. S. 14 km 163, 34149 Trieste, Basovizza, Italy
| | - C Guarnaccia
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34149 Trieste, Italy
| | - C Masciovecchio
- Elettra Sincrotrone Trieste, S. S. 14 km 163, 34149 Trieste, Basovizza, Italy
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Two-Dimensional Crystallization Procedure, from Protein Expression to Sample Preparation. BIOMED RESEARCH INTERNATIONAL 2015; 2015:693869. [PMID: 26413539 PMCID: PMC4564634 DOI: 10.1155/2015/693869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 07/02/2015] [Indexed: 11/18/2022]
Abstract
Membrane proteins play important roles for living cells. Structural studies of membrane proteins provide deeper understanding of their mechanisms and further aid in drug design. As compared to other methods, electron microscopy is uniquely suitable for analysis of a broad range of specimens, from small proteins to large complexes. Of various electron microscopic methods, electron crystallography is particularly well-suited to study membrane proteins which are reconstituted into two-dimensional crystals in lipid environments. In this review, we discuss the steps and parameters for obtaining large and well-ordered two-dimensional crystals. A general description of the principle in each step is provided since this information can also be applied to other biochemical and biophysical methods. The examples are taken from our own studies and published results with related proteins. Our purpose is to give readers a more general idea of electron crystallography and to share our experiences in obtaining suitable crystals for data collection.
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Lasala R, Coudray N, Abdine A, Zhang Z, Lopez-Redondo M, Kirshenbaum R, Alexopoulos J, Zolnai Z, Stokes DL, Ubarretxena-Belandia I. Sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. J Struct Biol 2014; 189:123-34. [PMID: 25478971 DOI: 10.1016/j.jsb.2014.11.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 11/18/2014] [Accepted: 11/24/2014] [Indexed: 01/09/2023]
Abstract
Electron crystallography is well suited for studying the structure of membrane proteins in their native lipid bilayer environment. This technique relies on electron cryomicroscopy of two-dimensional (2D) crystals, grown generally by reconstitution of purified membrane proteins into proteoliposomes under conditions favoring the formation of well-ordered lattices. Growing these crystals presents one of the major hurdles in the application of this technique. To identify conditions favoring crystallization a wide range of factors that can lead to a vast matrix of possible reagent combinations must be screened. However, in 2D crystallization these factors have traditionally been surveyed in a relatively limited fashion. To address this problem we carried out a detailed analysis of published 2D crystallization conditions for 12 β-barrel and 138 α-helical membrane proteins. From this analysis we identified the most successful conditions and applied them in the design of new sparse and incomplete factorial matrices to screen membrane protein 2D crystallization. Using these matrices we have run 19 crystallization screens for 16 different membrane proteins totaling over 1300 individual crystallization conditions. Six membrane proteins have yielded diffracting 2D crystals suitable for structure determination, indicating that these new matrices show promise to accelerate the success rate of membrane protein 2D crystallization.
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Affiliation(s)
- R Lasala
- New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA
| | - N Coudray
- New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA
| | - A Abdine
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Z Zhang
- New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA
| | - M Lopez-Redondo
- Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
| | - R Kirshenbaum
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - J Alexopoulos
- Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
| | - Z Zolnai
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706, USA
| | - D L Stokes
- New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA; Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
| | - I Ubarretxena-Belandia
- New York Structural Biology Center, 89 Convent Avenue, New York, NY 10027, USA; Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA.
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