1
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Coyote-Maestas W, Nedrud D, Suma A, He Y, Matreyek KA, Fowler DM, Carnevale V, Myers CL, Schmidt D. Probing ion channel functional architecture and domain recombination compatibility by massively parallel domain insertion profiling. Nat Commun 2021; 12:7114. [PMID: 34880224 PMCID: PMC8654947 DOI: 10.1038/s41467-021-27342-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/16/2021] [Indexed: 11/10/2022] Open
Abstract
Protein domains are the basic units of protein structure and function. Comparative analysis of genomes and proteomes showed that domain recombination is a main driver of multidomain protein functional diversification and some of the constraining genomic mechanisms are known. Much less is known about biophysical mechanisms that determine whether protein domains can be combined into viable protein folds. Here, we use massively parallel insertional mutagenesis to determine compatibility of over 300,000 domain recombination variants of the Inward Rectifier K+ channel Kir2.1 with channel surface expression. Our data suggest that genomic and biophysical mechanisms acted in concert to favor gain of large, structured domain at protein termini during ion channel evolution. We use machine learning to build a quantitative biophysical model of domain compatibility in Kir2.1 that allows us to derive rudimentary rules for designing domain insertion variants that fold and traffic to the cell surface. Positional Kir2.1 responses to motif insertion clusters into distinct groups that correspond to contiguous structural regions of the channel with distinct biophysical properties tuned towards providing either folding stability or gating transitions. This suggests that insertional profiling is a high-throughput method to annotate function of ion channel structural regions.
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Affiliation(s)
- Willow Coyote-Maestas
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455 USA
| | - David Nedrud
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, MN 55455 USA
| | - Antonio Suma
- grid.264727.20000 0001 2248 3398Department of Chemistry, Temple University, Philadelphia, PA 19122 USA
| | - Yungui He
- grid.17635.360000000419368657Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN 55455 USA
| | - Kenneth A. Matreyek
- grid.67105.350000 0001 2164 3847Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
| | - Douglas M. Fowler
- grid.34477.330000000122986657Department of Genome Sciences, University of Washington, Seattle, WA 98115 USA ,grid.34477.330000000122986657Department of Bioengineering, University of Washington, Seattle, WA 98115 USA
| | - Vincenzo Carnevale
- grid.264727.20000 0001 2248 3398Department of Chemistry, Temple University, Philadelphia, PA 19122 USA
| | - Chad L. Myers
- grid.17635.360000000419368657Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455 USA
| | - Daniel Schmidt
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, MN, 55455, USA.
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2
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Suzumoto Y, Columbano V, Gervasi L, Giunta R, Mattina T, Trimarchi G, Capolongo G, Simeoni M, Perna AF, Zacchia M, Toriello G, Pollastro RM, Rapisarda F, Capasso G, Trepiccione F. A case series of adult patients affected by EAST/SeSAME syndrome suggests more severe disease in subjects bearing KCNJ10 truncating mutations. Intractable Rare Dis Res 2021; 10:95-101. [PMID: 33996354 PMCID: PMC8122315 DOI: 10.5582/irdr.2020.03158] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
EAST/SeSAME syndrome is a rare disease affecting the Central Nervous System (CNS), inner ear, and kidney. The syndrome is due to loss-of-function mutations in the KCNJ10 gene encoding the inward-rectifying potassium channel Kir4.1. EAST/SeSAME syndrome is mainly diagnosed during childhood with a tonic-clonic seizure being the usual first symptom. Due to a limited number of patients and recent identification of the disease, few data are available on the clinical progress of this disease in adulthood. In particular, neurologic and nephrological outcomes have not been reported. We present a case series of 4 adult patients harbouring homozygous missense mutation p.Ala167Val and homozygous frameshift mutations p.Asn232Glnfs*14 and p.Gly275Valfs*7. Effects of these mutations were predicted by in silico modelling and bioinformatic tools. Patients with truncating mutations were associated with more severe outcomes, both in tubulopathy severity and neurological symptomatology. Conversely, either missense or truncating mutations were correlated with similar severity of epilepsy, with a long free-of-event period up to 20 years old. No eGFR decline was documented. Modelling predicted that truncating mutations lead to complete Kir4.1 dysfunction. Finally, all patients had a mild increase in urinary protein excretion. Our study indicates that the prognosis of patients suffering from EAST/SeSAME syndrome is related to the severity of the mutation causing the disease. As predicted by in silico modelling, truncating mutations of KCNJ10 are associated with more severe disease, with recurrence of symptomatic hypokalemia and more severe neurological phenotype. The type of mutation should be considered for the therapy tailored to patients' phenotype.
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Affiliation(s)
| | - Valeria Columbano
- Department of Translational Medical Sciences, University of Campania "L. Vanvitelli", Naples, Italy
| | - Luciano Gervasi
- School of Nephrology, Department of Clinical and Experimental Medicine, University of Catania, Italy
| | - Rosa Giunta
- School of Nephrology, Department of Clinical and Experimental Medicine, University of Catania, Italy
| | - Teresa Mattina
- Department of Biomedical and Biotechnological Sciences, University of Catania, Italy
| | - Gabriele Trimarchi
- Department of Biomedical and Biotechnological Sciences, University of Catania, Italy
| | - Giovanna Capolongo
- Department of Translational Medical Sciences, University of Campania "L. Vanvitelli", Naples, Italy
| | - Mariadelina Simeoni
- Department of Translational Medical Sciences, University of Campania "L. Vanvitelli", Naples, Italy
| | - Alessandra F. Perna
- Department of Translational Medical Sciences, University of Campania "L. Vanvitelli", Naples, Italy
| | - Miriam Zacchia
- Department of Translational Medical Sciences, University of Campania "L. Vanvitelli", Naples, Italy
| | | | - Rosa M. Pollastro
- Department of Translational Medical Sciences, University of Campania "L. Vanvitelli", Naples, Italy
| | - Francesco Rapisarda
- School of Nephrology, Department of Clinical and Experimental Medicine, University of Catania, Italy
| | - Giovambattista Capasso
- Biogem Research Institute, Ariano Irpino, Italy
- Department of Translational Medical Sciences, University of Campania "L. Vanvitelli", Naples, Italy
| | - Francesco Trepiccione
- Biogem Research Institute, Ariano Irpino, Italy
- Department of Translational Medical Sciences, University of Campania "L. Vanvitelli", Naples, Italy
- Address correspondence to:Francesco Trepiccione, Department of Translational Medical Sciences University of Campania "L.Vanvitelli", Via Pansini n5, 80131 Naples, Italy. E-mail:
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3
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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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4
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Wang S, Borschel WF, Heyman S, Hsu P, Nichols CG. Conformational changes at cytoplasmic intersubunit interactions control Kir channel gating. J Biol Chem 2017; 292:10087-10096. [PMID: 28446610 DOI: 10.1074/jbc.m117.785154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/17/2017] [Indexed: 02/02/2023] Open
Abstract
The defining structural feature of inward-rectifier potassium (Kir) channels is the unique Kir cytoplasmic domain. Recently we showed that salt bridges located at the cytoplasmic domain subunit interfaces (CD-Is) of eukaryotic Kir channels control channel gating via stability of a novel inactivated closed state. The cytoplasmic domains of prokaryotic and eukaryotic Kir channels show similar conformational rearrangements to the common gating ligand, phosphatidylinositol bisphosphate (PIP2), although these exhibit opposite coupling to opening and closing transitions. In Kir2.1, mutation of one of these CD-I salt bridge residues (R204A) reduces apparent PIP2 sensitivity of channel activity, and here we show that Ala or Cys substitutions of the functionally equivalent residue (Arg-165) in the prokaryotic Kir channel KirBac1.1 also significantly decrease sensitivity of the channel to PIP2 (by 5-30-fold). To further understand the structural basis of CD-I control of Kir channel gating, we examined the effect of the R165A mutation on PIP2-induced changes in channel function and conformation. Single-channel analyses indicated that the R165A mutation disrupts the characteristic long interburst closed state of reconstituted KirBac1.1 in giant liposomes, resulting in a higher open probability due to more frequent opening bursts. Intramolecular FRET measurements indicate that, relative to wild-type channels, the R165A mutation results in splaying of the cytoplasmic domains away from the central axis and that PIP2 essentially induces opposite motions of the major β-sheet in this channel mutant. We conclude that the removal of stabilizing CD-I salt bridges results in a collapsed state of the Kir domain.
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Affiliation(s)
- Shizhen Wang
- From the Department of Cell Biology and Physiology and the Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri 63110
| | - William F Borschel
- From the Department of Cell Biology and Physiology and the Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Sarah Heyman
- From the Department of Cell Biology and Physiology and the Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Phillip Hsu
- From the Department of Cell Biology and Physiology and the Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Colin G Nichols
- From the Department of Cell Biology and Physiology and the Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri 63110
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5
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Lee SJ, Ren F, Zangerl-Plessl EM, Heyman S, Stary-Weinzinger A, Yuan P, Nichols CG. Structural basis of control of inward rectifier Kir2 channel gating by bulk anionic phospholipids. J Gen Physiol 2016; 148:227-37. [PMID: 27527100 PMCID: PMC5004336 DOI: 10.1085/jgp.201611616] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/12/2016] [Indexed: 01/11/2023] Open
Abstract
Phospholipids are required to bind to two distinct sites on the inward rectifier potassium channel for maximal efficacy. Lee et al. show that a membrane-associating tryptophan residue in the second site can mimic the effect of phospholipid binding and cause a conformational change to reveal the primary binding site. Inward rectifier potassium (Kir) channel activity is controlled by plasma membrane lipids. Phosphatidylinositol-4,5-bisphosphate (PIP2) binding to a primary site is required for opening of classic inward rectifier Kir2.1 and Kir2.2 channels, but interaction of bulk anionic phospholipid (PL−) with a distinct second site is required for high PIP2 sensitivity. Here we show that introduction of a lipid-partitioning tryptophan at the second site (K62W) generates high PIP2 sensitivity, even in the absence of PL−. Furthermore, high-resolution x-ray crystal structures of Kir2.2[K62W], with or without added PIP2 (2.8- and 2.0-Å resolution, respectively), reveal tight tethering of the C-terminal domain (CTD) to the transmembrane domain (TMD) in each condition. Our results suggest a refined model for phospholipid gating in which PL− binding at the second site pulls the CTD toward the membrane, inducing the formation of the high-affinity primary PIP2 site and explaining the positive allostery between PL− binding and PIP2 sensitivity.
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Affiliation(s)
- Sun-Joo Lee
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110 Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110
| | - Feifei Ren
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110 Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110
| | | | - Sarah Heyman
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110 Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110
| | - Anna Stary-Weinzinger
- Department of Pharmacology and Toxicology, University of Vienna, A-1090 Vienna, Austria
| | - Peng Yuan
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110 Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110
| | - Colin G Nichols
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110 Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110
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6
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Zubcevic L, Wang S, Bavro VN, Lee SJ, Nichols CG, Tucker SJ. Modular Design of the Selectivity Filter Pore Loop in a Novel Family of Prokaryotic 'Inward Rectifier' (NirBac) channels. Sci Rep 2015; 5:15305. [PMID: 26470642 PMCID: PMC4607889 DOI: 10.1038/srep15305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 09/11/2015] [Indexed: 11/09/2022] Open
Abstract
Potassium channels exhibit a modular design with distinct structural and functional domains; in particular, a highly conserved pore-loop sequence that determines their ionic selectivity. We now report the functional characterisation of a novel group of functionally non-selective members of the prokaryotic 'inward rectifier' subfamily of K(+) channels. These channels share all the key structural domains of eukaryotic and prokaryotic Kir/KirBac channels, but instead possess unique pore-loop selectivity filter sequences unrelated to any other known ionic selectivity filter. The strikingly unusual architecture of these 'NirBac' channels defines a new family of functionally non-selective ion channels, and also provides important insights into the modular design of ion channels, as well as the evolution of ionic selectivity within this superfamily of tetrameric cation channels.
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Affiliation(s)
- Lejla Zubcevic
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Shizhen Wang
- Washington University St. Louis, School Of Medicine, Centre for the Investigation of Membrane Excitability Diseases (CIMED), St. Louis, MO, USA
| | - Vassiliy N. Bavro
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Sun-Joo Lee
- Washington University St. Louis, School Of Medicine, Centre for the Investigation of Membrane Excitability Diseases (CIMED), St. Louis, MO, USA
| | - Colin G. Nichols
- Washington University St. Louis, School Of Medicine, Centre for the Investigation of Membrane Excitability Diseases (CIMED), St. Louis, MO, USA
| | - Stephen J. Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
- OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford, United Kingdom
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7
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Kuang Q, Purhonen P, Hebert H. Structure of potassium channels. Cell Mol Life Sci 2015; 72:3677-93. [PMID: 26070303 PMCID: PMC4565861 DOI: 10.1007/s00018-015-1948-5] [Citation(s) in RCA: 167] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 05/09/2015] [Accepted: 06/03/2015] [Indexed: 12/25/2022]
Abstract
Potassium channels ubiquitously exist in nearly all kingdoms of life and perform diverse but important functions. Since the first atomic structure of a prokaryotic potassium channel (KcsA, a channel from Streptomyces lividans) was determined, tremendous progress has been made in understanding the mechanism of potassium channels and channels conducting other ions. In this review, we discuss the structure of various kinds of potassium channels, including the potassium channel with the pore-forming domain only (KcsA), voltage-gated, inwardly rectifying, tandem pore domain, and ligand-gated ones. The general properties shared by all potassium channels are introduced first, followed by specific features in each class. Our purpose is to help readers to grasp the basic concepts, to be familiar with the property of the different domains, and to understand the structure and function of the potassium channels better.
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Affiliation(s)
- Qie Kuang
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 14183, Huddinge, Sweden.
- School of Technology and Health, KTH Royal Institute of Technology, Novum, 14183, Huddinge, Sweden.
| | - Pasi Purhonen
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 14183, Huddinge, Sweden
| | - Hans Hebert
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 14183, Huddinge, Sweden
- School of Technology and Health, KTH Royal Institute of Technology, Novum, 14183, Huddinge, Sweden
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8
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Identification of the Conformational transition pathway in PIP2 Opening Kir Channels. Sci Rep 2015; 5:11289. [PMID: 26063437 PMCID: PMC4462750 DOI: 10.1038/srep11289] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 04/29/2015] [Indexed: 11/08/2022] Open
Abstract
The gating of Kir channels depends critically on phosphatidylinositol 4,5-bisphosphate (PIP2), but the detailed mechanism by which PIP2 regulates Kir channels remains obscure. Here, we performed a series of Targeted molecular dynamics simulations on the full-length Kir2.1 channel and, for the first time, were able to achieve the transition from the closed to the open state. Our data show that with the upward motion of the cytoplasmic domain (CTD) the structure of the C-Linker changes from a loop to a helix. The twisting of the C-linker triggers the rotation of the CTD, which induces a small downward movement of the CTD and an upward motion of the slide helix toward the membrane that pulls the inner helix gate open. At the same time, the rotation of the CTD breaks the interaction between the CD- and G-loops thus releasing the G-loop. The G-loop then bounces away from the CD-loop, which leads to the opening of the G-loop gate and the full opening of the pore. We identified a series of interaction networks, between the N-terminus, CD loop, C linker and G loop one by one, which exquisitely regulates the global conformational changes during the opening of Kir channels by PIP2.
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9
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Tang QY, Larry T, Hendra K, Yamamoto E, Bell J, Cui M, Logothetis DE, Boland LM. Mutations in Nature Conferred a High Affinity Phosphatidylinositol 4,5-Bisphosphate-binding Site in Vertebrate Inwardly Rectifying Potassium Channels. J Biol Chem 2015; 290:16517-29. [PMID: 25957411 DOI: 10.1074/jbc.m115.640409] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Indexed: 11/06/2022] Open
Abstract
All vertebrate inwardly rectifying potassium (Kir) channels are activated by phosphatidylinositol 4,5-bisphosphate (PIP2) (Logothetis, D. E., Petrou, V. I., Zhang, M., Mahajan, R., Meng, X. Y., Adney, S. K., Cui, M., and Baki, L. (2015) Annu. Rev. Physiol. 77, 81-104; Fürst, O., Mondou, B., and D'Avanzo, N. (2014) Front. Physiol. 4, 404-404). Structural components of a PIP2-binding site are conserved in vertebrate Kir channels but not in distantly related animals such as sponges and sea anemones. To expand our understanding of the structure-function relationships of PIP2 regulation of Kir channels, we studied AqKir, which was cloned from the marine sponge Amphimedon queenslandica, an animal that represents the phylogenetically oldest metazoans. A requirement for PIP2 in the maintenance of AqKir activity was examined in intact oocytes by activation of a co-expressed voltage-sensing phosphatase, application of wortmannin (at micromolar concentrations), and activation of a co-expressed muscarinic acetylcholine receptor. All three mechanisms to reduce the availability of PIP2 resulted in inhibition of AqKir current. However, time-dependent rundown of AqKir currents in inside-out patches could not be re-activated by direct application to the inside membrane surface of water-soluble dioctanoyl PIP2, and the current was incompletely re-activated by the more hydrophobic arachidonyl stearyl PIP2. When we introduced mutations to AqKir to restore two positive charges within the vertebrate PIP2-binding site, both forms of PIP2 strongly re-activated the mutant sponge channels in inside-out patches. Molecular dynamics simulations validate the additional hydrogen bonding potential of the sponge channel mutants. Thus, nature's mutations conferred a high affinity activation of vertebrate Kir channels by PIP2, and this is a more recent evolutionary development than the structures that explain ion channel selectivity and inward rectification.
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Affiliation(s)
- Qiong-Yao Tang
- From the Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298, the Jiangsu Province Key Laboratory of Anesthesiology and Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, XuZhou Medical College, Xuzhou, 221004 Jiangsu Province, China
| | - Trevor Larry
- the Department of Biology, University of Richmond, Richmond, Virginia 23173
| | - Kalen Hendra
- the Department of Biology, University of Richmond, Richmond, Virginia 23173
| | - Erica Yamamoto
- the Department of Biology, University of Richmond, Richmond, Virginia 23173
| | - Jessica Bell
- the Department of Chemistry and Biochemistry, University of San Diego, San Diego, California 92110, and
| | - Meng Cui
- From the Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298
| | - Diomedes E Logothetis
- From the Department of Physiology and Biophysics, Virginia Commonwealth University School of Medicine, Richmond, Virginia 23298
| | - Linda M Boland
- the Department of Biology, University of Richmond, Richmond, Virginia 23173
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10
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Linder T, Wang S, Zangerl-Plessl EM, Nichols CG, Stary-Weinzinger A. Molecular Dynamics Simulations of KirBac1.1 Mutants Reveal Global Gating Changes of Kir Channels. J Chem Inf Model 2015; 55:814-22. [PMID: 25794351 PMCID: PMC4415035 DOI: 10.1021/acs.jcim.5b00010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Indexed: 12/12/2022]
Abstract
Prokaryotic inwardly rectifying (KirBac) potassium channels are homologous to mammalian Kir channels. Their activity is controlled by dynamical conformational changes that regulate ion flow through a central pore. Understanding the dynamical rearrangements of Kir channels during gating requires high-resolution structure information from channels crystallized in different conformations and insight into the transition steps, which are difficult to access experimentally. In this study, we use MD simulations on wild type KirBac1.1 and an activatory mutant to investigate activation gating of KirBac channels. Full atomistic MD simulations revealed that introducing glutamate in position 143 causes significant widening at the helix bundle crossing gate, enabling water flux into the cavity. Further, global rearrangements including a twisting motion as well as local rearrangements at the subunit interface in the cytoplasmic domain were observed. These structural rearrangements are similar to recently reported KirBac3.1 crystal structures in closed and open conformation, suggesting that our simulations capture major conformational changes during KirBac1.1 opening. In addition, an important role of protein-lipid interactions during gating was observed. Slide-helix and C-linker interactions with lipids were strengthened during activation gating.
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Affiliation(s)
- Tobias Linder
- Department
of Pharmacology and Toxicology, University
of Vienna, 1090 Vienna, Austria
| | - Shizhen Wang
- Center
for Investigation of Membrane Excitability Diseases, Department of
Cell Biology and Physiology, Washington
University School of Medicine, St. Louis, Missouri 63110, United States
| | | | - Colin G. Nichols
- Center
for Investigation of Membrane Excitability Diseases, Department of
Cell Biology and Physiology, Washington
University School of Medicine, St. Louis, Missouri 63110, United States
| | - Anna Stary-Weinzinger
- Department
of Pharmacology and Toxicology, University
of Vienna, 1090 Vienna, Austria
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11
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Fürst O, Mondou B, D'Avanzo N. Phosphoinositide regulation of inward rectifier potassium (Kir) channels. Front Physiol 2014; 4:404. [PMID: 24409153 PMCID: PMC3884141 DOI: 10.3389/fphys.2013.00404] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 12/23/2013] [Indexed: 12/12/2022] Open
Abstract
Inward rectifier potassium (Kir) channels are integral membrane proteins charged with a key role in establishing the resting membrane potential of excitable cells through selective control of the permeation of K+ ions across cell membranes. In conjunction with secondary anionic phospholipids, members of this family are directly regulated by phosphoinositides (PIPs) in the absence of other proteins or downstream signaling pathways. Different Kir isoforms display distinct specificities for the activating PIPs but all eukaryotic Kir channels are activated by PI(4,5)P2. On the other hand, the bacterial KirBac1.1 channel is inhibited by PIPs. Recent crystal structures of eukaryotic Kir channels in apo and lipid bound forms reveal one specific binding site per subunit, formed at the interface of N- and C-terminal domains, just beyond the transmembrane segments and clearly involving some of the key residues previously identified as controlling PI(4,5)P2 sensitivity. Computational, biochemical, and biophysical approaches have attempted to address the energetic determinants of PIP binding and selectivity among Kir channel isoforms, as well as the conformational changes that trigger channel gating. Here we review our current understanding of the molecular determinants of PIP regulation of Kir channel activity, including in context with other lipid modulators, and provide further discussion on the key questions that remain to be answered.
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Affiliation(s)
- Oliver Fürst
- Groupe d'étude des Protéines Membranaires (GÉPROM), Physiologie, Université de Montréal Montréal, QC, Canada
| | - Benoit Mondou
- Groupe d'étude des Protéines Membranaires (GÉPROM), Physiologie, Université de Montréal Montréal, QC, Canada
| | - Nazzareno D'Avanzo
- Groupe d'étude des Protéines Membranaires (GÉPROM), Physiologie, Université de Montréal Montréal, QC, Canada
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12
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Lee SJ, Wang S, Borschel W, Heyman S, Gyore J, Nichols CG. Secondary anionic phospholipid binding site and gating mechanism in Kir2.1 inward rectifier channels. Nat Commun 2013; 4:2786. [PMID: 24270915 PMCID: PMC3868208 DOI: 10.1038/ncomms3786] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 10/16/2013] [Indexed: 12/03/2022] Open
Abstract
Inwardly rectifying potassium (Kir) channels regulate multiple tissues. All Kir channels require interaction of phosphatidyl-4,5-bisphosphate (PIP2) at a crystallographically identified binding site, but an additional nonspecific secondary anionic phospholipid (PL(-)) is required to generate high PIP2 sensitivity of Kir2 channel gating. The PL(-)-binding site and mechanism are yet to be elucidated. Here we report docking simulations that identify a putative PL(-)-binding site, adjacent to the PIP2-binding site, generated by two lysine residues from neighbouring subunits. When either lysine is mutated to cysteine (K64C and K219C), channel activity is significantly decreased in cells and in reconstituted liposomes. Directly tethering K64C to the membrane by modification with decyl-MTS generates high PIP2 sensitivity in liposomes, even in the complete absence of PL(-)s. The results provide a coherent molecular mechanism whereby PL(-) interaction with a discrete binding site results in a conformational change that stabilizes the high-affinity PIP2 activatory site.
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Affiliation(s)
- Sun-Joo Lee
- Department of Cell Biology and Physiology and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Shizhen Wang
- Department of Cell Biology and Physiology and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - William Borschel
- Department of Cell Biology and Physiology and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Sarah Heyman
- Department of Cell Biology and Physiology and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Jacob Gyore
- Department of Cell Biology and Physiology and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Colin G. Nichols
- Department of Cell Biology and Physiology and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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13
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Bavro VN, De Zorzi R, Schmidt MR, Muniz JRC, Zubcevic L, Sansom MSP, Vénien-Bryan C, Tucker SJ. Structure of a KirBac potassium channel with an open bundle crossing indicates a mechanism of channel gating. Nat Struct Mol Biol 2012; 19:158-63. [PMID: 22231399 PMCID: PMC3272479 DOI: 10.1038/nsmb.2208] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Accepted: 11/14/2011] [Indexed: 02/04/2023]
Abstract
KirBac channels are prokaryotic homologs of mammalian inwardly rectifying (Kir) potassium channels, and recent crystal structures of both Kir and KirBac channels have provided major insight into their unique structural architecture. However, all of the available structures are closed at the helix bundle crossing, and therefore the structural mechanisms that control opening of their primary activation gate remain unknown. In this study, we engineered the inner pore-lining helix (TM2) of KirBac3.1 to trap the bundle crossing in an apparently open conformation and determined the crystal structure of this mutant channel to 3.05 Å resolution. Contrary to previous speculation, this new structure suggests a mechanistic model in which rotational 'twist' of the cytoplasmic domain is coupled to opening of the bundle-crossing gate through a network of inter- and intrasubunit interactions that involve the TM2 C-linker, slide helix, G-loop and the CD loop.
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Affiliation(s)
- Vassiliy N Bavro
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, UK
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14
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Cheng WWL, D'Avanzo N, Doyle DA, Nichols CG. Dual-mode phospholipid regulation of human inward rectifying potassium channels. Biophys J 2011; 100:620-628. [PMID: 21281576 DOI: 10.1016/j.bpj.2010.12.3724] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 12/16/2010] [Accepted: 12/17/2010] [Indexed: 12/29/2022] Open
Abstract
The lipid bilayer is a critical determinant of ion channel activity; however, efforts to define the lipid dependence of channel function have generally been limited to cellular expression systems in which the membrane composition cannot be fully controlled. We reconstituted purified human Kir2.1 and Kir2.2 channels into liposomes of defined composition to study their phospholipid dependence of activity using (86)Rb(+) flux and patch-clamp assays. Our results demonstrate that Kir2.1 and Kir2.2 have two distinct lipid requirements for activity: a specific requirement for phosphatidylinositol 4,5-bisphosphate (PIP(2)) and a nonspecific requirement for anionic phospholipids. Whereas we previously showed that PIP(2) increases the channel open probability, in this work we find that activation by POPG increases both the open probability and unitary conductance. Oleoyl CoA potently inhibits Kir2.1 by antagonizing the specific requirement for PIP(2), and EPC appears to antagonize activation by the nonspecific anionic requirement. Phosphatidylinositol phosphates can act on both lipid requirements, yielding variable and even opposite effects on Kir2.1 activity depending on the lipid background. Mutagenesis experiments point to the role of intracellular residues in activation by both PIP(2) and anionic phospholipids. In conclusion, we utilized purified proteins in defined lipid membranes to quantitatively determine the phospholipid requirements for human Kir channel activity.
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Affiliation(s)
- Wayland W L Cheng
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri; Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri
| | - Nazzareno D'Avanzo
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri; Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri
| | - Declan A Doyle
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - Colin G Nichols
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, Missouri; Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri.
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15
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D'Avanzo N, Hyrc K, Enkvetchakul D, Covey DF, Nichols CG. Enantioselective protein-sterol interactions mediate regulation of both prokaryotic and eukaryotic inward rectifier K+ channels by cholesterol. PLoS One 2011; 6:e19393. [PMID: 21559361 PMCID: PMC3084843 DOI: 10.1371/journal.pone.0019393] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 03/29/2011] [Indexed: 02/06/2023] Open
Abstract
Cholesterol is the major sterol component of all mammalian cell plasma membranes and plays a critical role in cell function and growth. Previous studies have shown that cholesterol inhibits inward rectifier K+ (Kir) channels, but have not distinguished whether this is due directly to protein-sterol interactions or indirectly to changes in the physical properties of the lipid bilayer. Using purified bacterial and eukaryotic Kir channels reconstituted into liposomes of controlled lipid composition, we demonstrate by 86Rb+ influx assays that bacterial Kir channels (KirBac1.1 and KirBac3.1) and human Kir2.1 are all inhibited by cholesterol, most likely by locking the channels into prolonged closed states, whereas the enantiomer, ent-cholesterol, does not inhibit these channels. These data indicate that cholesterol regulates Kir channels through direct protein-sterol interactions likely taking advantage of an evolutionarily conserved binding pocket.
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Affiliation(s)
- Nazzareno D'Avanzo
- Department of Cell Biology and Physiology, and Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Krzysztof Hyrc
- Department of Cell Biology and Physiology, and Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Decha Enkvetchakul
- Department of Pharmacological and Physiological Science, Saint Louis University School of Medicine, St. Louis, Missouri, United States of America
| | - Douglas F. Covey
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Colin G. Nichols
- Department of Cell Biology and Physiology, and Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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16
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D'Avanzo N, Cheng WWL, Doyle DA, Nichols CG. Direct and specific activation of human inward rectifier K+ channels by membrane phosphatidylinositol 4,5-bisphosphate. J Biol Chem 2010; 285:37129-32. [PMID: 20921230 DOI: 10.1074/jbc.c110.186692] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many ion channels are modulated by phosphatidylinositol 4,5-bisphosphate (PIP(2)), but studies examining the PIP(2) dependence of channel activity have been limited to cell expression systems, which present difficulties for controlling membrane composition. We have characterized the PIP(2) dependence of purified human Kir2.1 and Kir2.2 activity using (86)Rb(+) flux and patch clamp assays in liposomes of defined composition. We definitively show that these channels are directly activated by PIP(2) and that PIP(2) is absolutely required in the membrane for channel activity. The results provide the first quantitative description of the dependence of eukaryotic Kir channel function on PIP(2) levels in the membrane; Kir2.1 shows measureable activity in as little as 0.01% PIP(2), and open probability increases to ∼0.4 at 1% PIP(2). Activation of Kir2.1 by phosphatidylinositol phosphates is also highly selective for PIP(2); PI, PI(4)P, and PI(5)P do not activate channels, and PI(3,4,5)P(3) causes minimal activity. The PIP(2) dependence of eukaryotic Kir activity is almost exactly opposite that of KirBac1.1, which shows marked inhibition by PIP(2). This raises the interesting hypothesis that PIP(2) activation of eukaryotic channels reflects an evolutionary adaptation of the channel to the appearance of PIP(2) in the eukaryotic cell membrane.
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Affiliation(s)
- Nazzareno D'Avanzo
- Department of Cell Biology and Physiology and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St Louis, Missouri 63110, USA
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