1
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Prignano LA, Stevens MJ, Vanegas JM, Rempe SB, Dempski RE. Metadynamics simulations reveal mechanisms of Na+ and Ca2+ transport in two open states of the channelrhodopsin chimera, C1C2. PLoS One 2024; 19:e0309553. [PMID: 39241014 PMCID: PMC11379304 DOI: 10.1371/journal.pone.0309553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 07/30/2024] [Indexed: 09/08/2024] Open
Abstract
Cation conducting channelrhodopsins (ChRs) are a popular tool used in optogenetics to control the activity of excitable cells and tissues using light. ChRs with altered ion selectivity are in high demand for use in different cell types and for other specialized applications. However, a detailed mechanism of ion permeation in ChRs is not fully resolved. Here, we use complementary experimental and computational methods to uncover the mechanisms of cation transport and valence selectivity through the channelrhodopsin chimera, C1C2, in the high- and low-conducting open states. Electrophysiology measurements identified a single-residue substitution within the central gate, N297D, that increased Ca2+ permeability vs. Na+ by nearly two-fold at peak current, but less so at stationary current. We then developed molecular models of dimeric wild-type C1C2 and N297D mutant channels in both open states and calculated the PMF profiles for Na+ and Ca2+ permeation through each protein using well-tempered/multiple-walker metadynamics. Results of these studies agree well with experimental measurements and demonstrate that the pore entrance on the extracellular side differs from original predictions and is actually located in a gap between helices I and II. Cation transport occurs via a relay mechanism where cations are passed between flexible carboxylate sidechains lining the full length of the pore by sidechain swinging, like a monkey swinging on vines. In the mutant channel, residue D297 enhances Ca2+ permeability by mediating the handoff between the central and cytosolic binding sites via direct coordination and sidechain swinging. We also found that altered cation binding affinities at both the extracellular entrance and central binding sites underly the distinct transport properties of the low-conducting open state. This work significantly advances our understanding of ion selectivity and permeation in cation channelrhodopsins and provides the insights needed for successful development of new ion-selective optogenetic tools.
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Affiliation(s)
- Lindsey A Prignano
- Department of Chemistry & Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Mark J Stevens
- Sandia National Laboratories, Albuquerque, New Mexico, United States of America
| | - Juan M Vanegas
- Department of Biochemistry & Biophysics, Oregon State University, Corvallis, Oregon, United States of America
| | - Susan B Rempe
- Sandia National Laboratories, Albuquerque, New Mexico, United States of America
| | - Robert E Dempski
- Department of Chemistry & Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
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2
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Wu Y, Yan Y, Yang Y, Bian S, Rivetta A, Allen K, Sigworth FJ. Cryo-EM structures of Kv1.2 potassium channels, conducting and non-conducting. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.02.543446. [PMID: 37398110 PMCID: PMC10312591 DOI: 10.1101/2023.06.02.543446] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
We present near-atomic-resolution cryo-EM structures of the mammalian voltage-gated potassium channel Kv1.2 in open, C-type inactivated, toxin-blocked and sodium-bound states at 3.2 Å, 2.5 Å, 3.2 Å, and 2.9Å. These structures, all obtained at nominally zero membrane potential in detergent micelles, reveal distinct ion-occupancy patterns in the selectivity filter. The first two structures are very similar to those reported in the related Shaker channel and the much-studied Kv1.2-2.1 chimeric channel. On the other hand, two new structures show unexpected patterns of ion occupancy. First, the toxin α-Dendrotoxin, like Charybdotoxin, is seen to attach to the negatively-charged channel outer mouth, and a lysine residue penetrates into the selectivity filter, with the terminal amine coordinated by carbonyls, partially disrupting the outermost ion-binding site. In the remainder of the filter two densities of bound ions are observed, rather than three as observed with other toxin-blocked Kv channels. Second, a structure of Kv1.2 in Na+ solution does not show collapse or destabilization of the selectivity filter, but instead shows an intact selectivity filter with ion density in each binding site. We also attempted to image the C-type inactivated Kv1.2 W366F channel in Na+ solution, but the protein conformation was seen to be highly variable and only a low-resolution structure could be obtained. These findings present new insights into the stability of the selectivity filter and the mechanism of toxin block of this intensively studied, voltage-gated potassium channel.
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Affiliation(s)
- Yangyu Wu
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut USA
| | - Yangyang Yan
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut USA
| | - Youshan Yang
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut USA
| | - Shumin Bian
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut USA
| | - Alberto Rivetta
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut USA
| | - Ken Allen
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut USA
| | - Fred J Sigworth
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut USA
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3
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Si F, Song S, Yu R, Li Z, Wei W, Wu C. Coronavirus accessory protein ORF3 biology and its contribution to viral behavior and pathogenesis. iScience 2023; 26:106280. [PMID: 36945252 PMCID: PMC9972675 DOI: 10.1016/j.isci.2023.106280] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
Coronavirus porcine epidemic diarrhea virus (PEDV) is classified in the genus Alphacoronavirus, family Coronaviridae that encodes the only accessory protein, ORF3 protein. However, how ORF3 contributes to viral pathogenicity, adaptability, and replication is obscure. In this review, we summarize current knowledge and identify gaps in many aspects of ORF3 protein in PEDV, with emphasis on its unique biological features, including membrane topology, Golgi retention mechanism, potential intrinsic disordered property, functional motifs, protein glycosylation, and codon usage phenotypes related to genetic evolution and gene expression. In addition, we propose intriguing questions related to ORF3 protein that we hope to stimulate further studies and encourage collaboration among virologists worldwide to provide constructive knowledge about the unique characteristics and biological functions of ORF3 protein, by which their potential role in clarifying viral behavior and pathogenesis can be possible.
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Affiliation(s)
- Fusheng Si
- Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, P.R. China
| | - Shuai Song
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture of Rural Affairs, and Key Laboratory of Animal Disease Prevention of Guangdong Province, Guangzhou 510640, P.R. China
| | - Ruisong Yu
- Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, P.R. China
| | - Zhen Li
- Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, P.R. China
| | - Wenqiang Wei
- Department of Microbiology, School of Basic Medical Sciences, Henan University, Kaifeng, Henan 475004, P.R. China
| | - Chao Wu
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, MO 63110, USA
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4
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Minniberger S, Abdolvand S, Braunbeck S, Sun H, Plested AJR. Asymmetry and Ion Selectivity Properties of Bacterial Channel NaK Mutants Derived from Ionotropic Glutamate Receptors. J Mol Biol 2023; 435:167970. [PMID: 36682679 DOI: 10.1016/j.jmb.2023.167970] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/17/2022] [Accepted: 01/12/2023] [Indexed: 01/22/2023]
Abstract
Ionotropic glutamate receptors are ligand-gated cation channels that play essential roles in the excitatory synaptic transmission throughout the central nervous system. A number of open-pore structures of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic-acid (AMPA)-type glutamate receptors became available recently by cryo-electron microscopy (cryo-EM). These structures provide valuable insights into the conformation of the selectivity filter (SF), the part of the ion channel that determines the ion selectivity. Nonetheless, due to the moderate resolution of the cryo-EM structures, detailed information such as ion occupancy of monovalent and divalent cations as well as positioning of the side-chains in the SF is still missing. Here, in an attempt to obtain high-resolution information about glutamate receptor SFs, we incorporated partial SF sequences of the AMPA and kainate receptors into the bacterial tetrameric cation channel NaK, which served as a structural scaffold. We determined a series of X-ray structures of NaK-CDI, NaK-SDI and NaK-SELM mutants at 1.42-2.10 Å resolution, showing distinct ion occupation of different monovalent cations. Molecular dynamics (MD) simulations of NaK-CDI indicated the channel to be conductive to monovalent cations, which agrees well with our electrophysiology recordings. Moreover, previously unobserved structural asymmetry of the SF was revealed by the X-ray structures and MD simulations, implying its importance in ion non-selectivity of tetrameric cation channels.
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Affiliation(s)
- Sonja Minniberger
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, 10115 Berlin, Germany; NeuroCure, Charité Universitätsmedizin, 10117 Berlin, Germany; Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Saeid Abdolvand
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, 10115 Berlin, Germany; NeuroCure, Charité Universitätsmedizin, 10117 Berlin, Germany; Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Sebastian Braunbeck
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, 10115 Berlin, Germany; NeuroCure, Charité Universitätsmedizin, 10117 Berlin, Germany; Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Han Sun
- Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institute of Chemistry, Department of Chemistry, Technische Universität Berlin, 10623 Berlin, Germany.
| | - Andrew J R Plested
- Institute of Biology, Cellular Biophysics, Humboldt Universität zu Berlin, 10115 Berlin, Germany; NeuroCure, Charité Universitätsmedizin, 10117 Berlin, Germany; Leibniz Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany.
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5
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Lu J, Jiang G, Zhang H, Qian B, Zhu H, Gu Q, Yan Y, Liu JZ, Freeman BD, Jiang L, Wang H. An artificial sodium-selective subnanochannel. SCIENCE ADVANCES 2023; 9:eabq1369. [PMID: 36706186 PMCID: PMC9882983 DOI: 10.1126/sciadv.abq1369] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
Single-ion selectivity with high precision has long been pursued for fundamental bioinspired engineering and applications such as in ion separation and energy conversion. However, it remains a challenge to develop artificial ion channels to achieve single-ion selectivity comparable to their biological analogs, especially for high Na+/K+ selectivity. Here, we report an artificial sodium channel by subnanoconfinement of 4'-aminobenzo-15-crown-5 ethers (15C5s) into ~6-Å-sized metal-organic framework subnanochannel (MOFSNC). The resulting 15C5-MOFSNC shows an unprecedented Na+/K+ selectivity of tens to 102 and Na+/Li+ selectivity of 103 under multicomponent permeation conditions, comparable to biological sodium channels. A co-ion-responsive single-file transport mechanism in 15C-MOFSNC is proposed for the preferential transport of Na+ over K+ due to the synergetic effects of size exclusion, charge selectivity, local hydrophobicity, and preferential binding with functional groups. This study provides an alternative strategy for developing potential single-ion selective channels and membranes for many applications.
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Affiliation(s)
- Jun Lu
- Department of Chemical and Biological Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Gengping Jiang
- Department of Applied Physics, College of Science, Wuhan University of Science and Technology, Wuhan 430072, China
| | - Huacheng Zhang
- Chemical and Environmental Engineering, School of Engineering, RMIT University, Melbourne, Victoria 3000, Australia
| | - Binbin Qian
- Department of Chemical and Biological Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Haijin Zhu
- Institute for Frontier Materials, Deakin University Waurn Ponds Campus, Geelong, Victoria 3216, Australia
| | - Qinfen Gu
- ANSTO, Australian Synchrotron, 800 Blackburn Rd., Clayton, Victoria 3168, Australia
| | - Yuan Yan
- Department of Mechanical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jefferson Zhe Liu
- Department of Mechanical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Benny D. Freeman
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Lei Jiang
- Department of Chemical and Biological Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Huanting Wang
- Department of Chemical and Biological Engineering, Monash University, Clayton, Victoria 3800, Australia
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6
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Matamoros M, Ng XW, Brettmann JB, Piston DW, Nichols CG. Conformational plasticity of NaK2K and TREK2 potassium channel selectivity filters. Nat Commun 2023; 14:89. [PMID: 36609575 PMCID: PMC9822992 DOI: 10.1038/s41467-022-35756-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 12/23/2022] [Indexed: 01/07/2023] Open
Abstract
The K+ channel selectivity filter (SF) is defined by TxGYG amino acid sequences that generate four identical K+ binding sites (S1-S4). Only two sites (S3, S4) are present in the non-selective bacterial NaK channel, but a four-site K+-selective SF is obtained by mutating the wild-type TVGDGN SF sequence to a canonical K+ channel TVGYGD sequence (NaK2K mutant). Using single molecule FRET (smFRET), we show that the SF of NaK2K, but not of non-selective NaK, is ion-dependent, with the constricted SF configuration stabilized in high K+ conditions. Patch-clamp electrophysiology and non-canonical fluorescent amino acid incorporation show that NaK2K selectivity is reduced by crosslinking to limit SF conformational movement. Finally, the eukaryotic K+ channel TREK2 SF exhibits essentially identical smFRET-reported ion-dependent conformations as in prokaryotic K+ channels. Our results establish the generality of K+-induced SF conformational stability across the K+ channel superfamily, and introduce an approach to study manipulation of channel selectivity.
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Affiliation(s)
- Marcos Matamoros
- Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Xue Wen Ng
- Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Joshua B Brettmann
- Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Millipore-Sigma Inc., St. Louis, MO, USA
| | - David W Piston
- Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Colin G Nichols
- Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO, USA.
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA.
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7
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Kurauskas V, Tonelli M, Henzler-Wildman K. Full opening of helix bundle crossing does not lead to NaK channel activation. J Gen Physiol 2022; 154:213659. [PMID: 36326620 PMCID: PMC9640265 DOI: 10.1085/jgp.202213196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/11/2022] [Accepted: 10/10/2022] [Indexed: 11/05/2022] Open
Abstract
A critical part of ion channel function is the ability to open and close in response to stimuli and thus conduct ions in a regulated fashion. While x-ray diffraction studies of ion channels suggested a general steric gating mechanism located at the helix bundle crossing (HBC), recent functional studies on several channels indicate that the helix bundle crossing is wide-open even in functionally nonconductive channels. Two NaK channel variants were crystallized in very different open and closed conformations, which served as important models of the HBC gating hypothesis. However, neither of these NaK variants is conductive in liposomes unless phenylalanine 92 is mutated to alanine (F92A). Here, we use NMR to probe distances at near-atomic resolution of the two NaK variants in lipid bicelles. We demonstrate that in contrast to the crystal structures, both NaK variants are in a fully open conformation, akin to Ca2+-bound MthK channel structure where the HBC is widely open. While we were not able to determine what a conductive NaK structure is like, our further inquiry into the gating mechanism suggests that the selectivity filter and pore helix are coupled to the M2 helix below and undergo changes in the structure when F92 is mutated. Overall, our data show that NaK exhibits coupling between the selectivity filter and HBC, similar to K+ channels, and has a more complex gating mechanism than previously thought, where the full opening of HBC does not lead to channel activation.
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Affiliation(s)
- Vilius Kurauskas
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin—Madison, Madison, WI
| | - Katherine Henzler-Wildman
- Department of Biochemistry, University of Wisconsin—Madison, Madison, WI
- National Magnetic Resonance Facility at Madison, University of Wisconsin—Madison, Madison, WI
- Correspondence to Katherine Henzler-Wildman:
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8
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Rothberg BS. Interrogating the gating motions of the NaK channel. J Gen Physiol 2022; 154:e202213257. [PMID: 36326621 PMCID: PMC9640267 DOI: 10.1085/jgp.202213257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Previous crystallographic studies depicted a physical gate of the NaK channel localized at a bundle crossing of pore-lining helices, but solution NMR studies in the current issue of JGP suggest otherwise.
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Affiliation(s)
- Brad S Rothberg
- Department of Medical Genetics and Molecular Biochemistry, Temple University Lewis Katz School of Medicine, Philadelphia, PA
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9
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Molecular Events behind the Selectivity and Inactivation Properties of Model NaK-Derived Ion Channels. Int J Mol Sci 2022; 23:ijms23169246. [PMID: 36012519 PMCID: PMC9409022 DOI: 10.3390/ijms23169246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/10/2022] [Accepted: 08/14/2022] [Indexed: 11/17/2022] Open
Abstract
Y55W mutants of non-selective NaK and partly K+-selective NaK2K channels have been used to explore the conformational dynamics at the pore region of these channels as they interact with either Na+ or K+. A major conclusion is that these channels exhibit a remarkable pore conformational flexibility. Homo-FRET measurements reveal a large change in W55–W55 intersubunit distances, enabling the selectivity filter (SF) to admit different species, thus, favoring poor or no selectivity. Depending on the cation, these channels exhibit wide-open conformations of the SF in Na+, or tight induced-fit conformations in K+, most favored in the four binding sites containing NaK2K channels. Such conformational flexibility seems to arise from an altered pattern of restricting interactions between the SF and the protein scaffold behind it. Additionally, binding experiments provide clues to explain such poor selectivity. Compared to the K+-selective KcsA channel, these channels lack a high affinity K+ binding component and do not collapse in Na+. Thus, they cannot properly select K+ over competing cations, nor reject Na+ by collapsing, as K+-selective channels do. Finally, these channels do not show C-type inactivation, likely because their submillimolar K+ binding affinities prevent an efficient K+ loss from their SF, thus favoring permanently open channel states.
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10
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Ahrari S, Ozturk TN, D'Avanzo N. ION BEHAVIOUR IN THE SELECTIVITY FILTER OF HCN1 CHANNELS. Biophys J 2022; 121:2206-2218. [PMID: 35474263 DOI: 10.1016/j.bpj.2022.04.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/20/2022] [Accepted: 04/20/2022] [Indexed: 11/26/2022] Open
Abstract
Hyperpolarization-activated cyclic nucleotide-gated channels (HCNs) are responsible for the generation of pacemaker currents (If or Ih) in cardiac and neuronal cells. Despite the overall structural similarity to voltage-gated potassium (Kv) channels, HCNs show much lower selectivity for K+ over Na+ ions. This increased permeability to Na+ is critical to their role in membrane depolarization. HCNs can also select between Na+ and Li+ ions. Here we investigate the unique ion selectivity properties of HCNs using molecular dynamics simulations. Our simulations suggest that the HCN1 pore is flexible and dilated compared to Kv channels with only one stable ion binding site within the selectivity filter. We also observe that ion coordination and hydration differ within the HCN1 selectivity filter compared to those in Kv and CNG channels. Additionally, the C358T mutation further stabilizes the symmetry of the binding site and provides a more fit space for ion coordination, particularly for Li+. STATEMENT OF SIGNIFICANCE: Hyperpolarization-activated cyclic-nucleotide gated (HCN) channels represent the molecular correlate of the currents If or Ih in cardiomyocytes and neurons. Here we study the unique low conductance and semi-selective properties of HCNs. The conductance and selectivity mechanisms of ion channels are tightly associated with their physiological role and contribute to the specific properties of the excitable cells in which they are expressed.
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Affiliation(s)
- Sajjad Ahrari
- Département de pharmacologie et physiologie, Université de Montréal, 2960 Chemin de la Tour, Montréal, Canada, H3T 1J4
| | - Tugba N Ozturk
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, 223 McDonnell Sciences Building, St. Louis, US, 63110; Theoretical Molecular Biophysics Laboratory, National Heart, Lung and Blood Institute, National Institutes of Health, 10 Center Drive, Bethesda, Maryland, 20814
| | - Nazzareno D'Avanzo
- Département de pharmacologie et physiologie, Université de Montréal, 2960 Chemin de la Tour, Montréal, Canada, H3T 1J4.
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11
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Öster C, Tekwani Movellan K, Goold B, Hendriks K, Lange S, Becker S, de Groot BL, Kopec W, Andreas LB, Lange A. Direct Detection of Bound Ammonium Ions in the Selectivity Filter of Ion Channels by Solid-State NMR. J Am Chem Soc 2022; 144:4147-4157. [PMID: 35200002 PMCID: PMC8915258 DOI: 10.1021/jacs.1c13247] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Indexed: 01/16/2023]
Abstract
The flow of ions across cell membranes facilitated by ion channels is an important function for all living cells. Despite the huge amount of structural data provided by crystallography, elucidating the exact interactions between the selectivity filter atoms and bound ions is challenging. Here, we detect bound 15N-labeled ammonium ions as a mimic for potassium ions in ion channels using solid-state NMR under near-native conditions. The non-selective ion channel NaK showed two ammonium peaks corresponding to its two ion binding sites, while its potassium-selective mutant NaK2K that has a signature potassium-selective selectivity filter with four ion binding sites gave rise to four ammonium peaks. Ions bound in specific ion binding sites were identified based on magnetization transfer between the ions and carbon atoms in the selectivity filters. Magnetization transfer between bound ions and water molecules revealed that only one out of four ions in the selectivity filter of NaK2K is in close contact with water, which is in agreement with the direct knock-on ion conduction mechanism where ions are conducted through the channel by means of direct interactions without water molecules in between. Interestingly, the potassium-selective ion channels investigated here (NaK2K and, additionally, KcsA-Kv1.3) showed remarkably different chemical shifts for their bound ions, despite having identical amino acid sequences and crystal structures of their selectivity filters. Molecular dynamics simulations show similar ion binding and conduction behavior between ammonium and potassium ions and identify the origin of the differences between the investigated potassium channels.
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Affiliation(s)
- Carl Öster
- Department
of Molecular Biophysics, Leibniz-Forschungsinstitut
für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Kumar Tekwani Movellan
- Department
of NMR-Based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Benjamin Goold
- Faculty
of Engineering and Physical Sciences, University
of Southampton, University Road, SO17 1BJ Southampton, U.K.
- Computational
Biomolecular Dynamics Group, Max Planck
Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kitty Hendriks
- Department
of Molecular Biophysics, Leibniz-Forschungsinstitut
für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Sascha Lange
- Department
of Molecular Biophysics, Leibniz-Forschungsinstitut
für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Stefan Becker
- Department
of NMR-Based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Bert L. de Groot
- Computational
Biomolecular Dynamics Group, Max Planck
Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Wojciech Kopec
- Computational
Biomolecular Dynamics Group, Max Planck
Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Loren B. Andreas
- Department
of NMR-Based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Adam Lange
- Department
of Molecular Biophysics, Leibniz-Forschungsinstitut
für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
- Institut
für Biologie, Humboldt-Universität
zu Berlin, Invalidenstr.
42, 10115 Berlin, Germany
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12
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Studying membrane proteins with MicroED. Biochem Soc Trans 2022; 50:231-239. [PMID: 35191473 PMCID: PMC9022970 DOI: 10.1042/bst20210911] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 12/27/2022]
Abstract
The structural investigation of biological macromolecules is indispensable in understanding the molecular mechanisms underlying diseases. Several structural biology techniques have been introduced to unravel the structural facets of biomolecules. Among these, the electron cryomicroscopy (cryo-EM) method microcrystal electron diffraction (MicroED) has produced atomic resolution structures of important biological and small molecules. Since its inception in 2013, MicroED established a demonstrated ability for solving structures of difficult samples using vanishingly small crystals. However, membrane proteins remain the next big frontier for MicroED. The intrinsic properties of membrane proteins necessitate improved sample handling and imaging techniques to be developed and optimized for MicroED. Here, we summarize the milestones of electron crystallography of two-dimensional crystals leading to MicroED of three-dimensional crystals. Then, we focus on four different membrane protein families and discuss representatives from each family solved by MicroED.
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13
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Zhang H, Li X, Hou J, Jiang L, Wang H. Angstrom-scale ion channels towards single-ion selectivity. Chem Soc Rev 2022; 51:2224-2254. [PMID: 35225300 DOI: 10.1039/d1cs00582k] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Artificial ion channels with ion permeability and selectivity comparable to their biological counterparts are highly desired for efficient separation, biosensing, and energy conversion technologies. In the past two decades, both nanoscale and sub-nanoscale ion channels have been successfully fabricated to mimic biological ion channels. Although nanoscale ion channels have achieved intelligent gating and rectification properties, they cannot realize high ion selectivity, especially single-ion selectivity. Artificial angstrom-sized ion channels with narrow pore sizes <1 nm and well-defined pore structures mimicking biological channels have accomplished high ion conductivity and single-ion selectivity. This review comprehensively summarizes the research progress in the rational design and synthesis of artificial subnanometer-sized ion channels with zero-dimensional to three-dimensional pore structures. Then we discuss cation/anion, mono-/di-valent cation, mono-/di-valent anion, and single-ion selectivities of the synthetic ion channels and highlight their potential applications in high-efficiency ion separation, energy conversion, and biological therapeutics. The gaps of single-ion selectivity between artificial and natural channels and the connections between ion selectivity and permeability of synthetic ion channels are covered. Finally, the challenges that need to be addressed in this research field and the perspective of angstrom-scale ion channels are discussed.
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Affiliation(s)
- Huacheng Zhang
- Chemical and Environmental Engineering, School of Engineering, RMIT University, Melbourne, Victoria 3000, Australia.
| | - Xingya Li
- Department of Applied Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, P. R. China.
| | - Jue Hou
- Manufacturing, CSIRO, Clayton, Victoria 3168, Australia
| | - Lei Jiang
- Department of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Huanting Wang
- Department of Chemical Engineering, Monash University, Clayton, Victoria 3800, Australia
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14
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Hendriks K, Öster C, Lange A. Structural Plasticity of the Selectivity Filter in Cation Channels. Front Physiol 2021; 12:792958. [PMID: 34950061 PMCID: PMC8689586 DOI: 10.3389/fphys.2021.792958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/17/2021] [Indexed: 11/13/2022] Open
Abstract
Ion channels allow for the passage of ions across biological membranes, which is essential for the functioning of a cell. In pore loop channels the selectivity filter (SF) is a conserved sequence that forms a constriction with multiple ion binding sites. It is becoming increasingly clear that there are several conformations and dynamic states of the SF in cation channels. Here we outline specific modes of structural plasticity observed in the SFs of various pore loop channels: disorder, asymmetry, and collapse. We summarize the multiple atomic structures with varying SF conformations as well as asymmetric and more dynamic states that were discovered recently using structural biology, spectroscopic, and computational methods. Overall, we discuss here that structural plasticity within the SF is a key molecular determinant of ion channel gating behavior.
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Affiliation(s)
- Kitty Hendriks
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Carl Öster
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany.,Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
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15
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Jiang Y, Idikuda V, Chanda B. Preparation of Giant Escherichia coli spheroplasts for Electrophysiological Recordings. Bio Protoc 2021; 11:e4261. [PMID: 35087920 PMCID: PMC8720513 DOI: 10.21769/bioprotoc.4261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/27/2021] [Accepted: 10/05/2021] [Indexed: 07/07/2024] Open
Abstract
Prokaryotic ion channels have been instrumental in furthering our understanding of many fundamental aspects of ion channels' structure and function. However, characterizing the biophysical properties of a prokaryotic ion channel in a native membrane system using patch-clamp electrophysiology is technically challenging. Patch-clamp is regarded as a gold standard technique to study ion channel properties in both native and heterologous expression systems. The presence of a cell wall and the small size of bacterial cells makes it impossible to directly patch clamp using microelectrodes. Here, we describe a method for the preparation of giant E. coli spheroplasts in order to investigate the electrophysiological properties of bacterial cell membranes. Spheroplasts are formed by first inhibiting bacterial cell wall synthesis, followed by enzymatic digestion of the outer cell wall in the presence of a permeabilizing agent. This protocol can be used to characterize the function of any heterologous ion channels or ion transporters expressed in E. coli membranes.
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Affiliation(s)
- Yihao Jiang
- Department of Psychiatry of First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- The MOE Frontier Research Center of Brain & Brain-machine Integration, Zhejiang University School of Brain Science and Brain Medicine, China
| | - Vinay Idikuda
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for the Investigation of Membrane Excitability Diseases (CIMED)
| | - Baron Chanda
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Center for the Investigation of Membrane Excitability Diseases (CIMED)
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16
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Lewis A, Kurauskas V, Tonelli M, Henzler-Wildman K. Ion-dependent structure, dynamics, and allosteric coupling in a non-selective cation channel. Nat Commun 2021; 12:6225. [PMID: 34711838 PMCID: PMC8553846 DOI: 10.1038/s41467-021-26538-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/05/2021] [Indexed: 11/09/2022] Open
Abstract
The selectivity filter (SF) determines which ions are efficiently conducted through ion channel pores. NaK is a non-selective cation channel that conducts Na+ and K+ with equal efficiency. Crystal structures of NaK suggested a rigid SF structure, but later solid-state NMR and MD simulations questioned this interpretation. Here, we use solution NMR to characterize how bound Na+ vs. K+ affects NaK SF structure and dynamics. We find that the extracellular end of the SF is flexible on the ps-ns timescale regardless of bound ion. On a slower timescale, we observe a structural change between the Na+ and K+-bound states, accompanied by increased structural heterogeneity in Na+. We also show direct evidence that the SF structure is communicated to the pore via I88 on the M2 helix. These results support a dynamic SF with multiple conformations involved in non-selective conduction. Our data also demonstrate allosteric coupling between the SF and pore-lining helices in a non-selective cation channel that is analogous to the allosteric coupling previously demonstrated for K+-selective channels, supporting the generality of this model. NaK is a bacterial non-selective cation channel. Here, the authors use solution NMR to show that selectivity filter (SF) in NaK is dynamic, with structural differences between the Na+ and K + -bound states. The conformation of the SF is communicated to the pore-lining helices similarly as in the K + -selective channels.
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Affiliation(s)
- Adam Lewis
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Vilius Kurauskas
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Katherine Henzler-Wildman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA. .,National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-Madison, Madison, WI, 53706, USA.
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17
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Hendriks K, Öster C, Shi C, Sun H, Lange A. Sodium Ions Do Not Stabilize the Selectivity Filter of a Potassium Channel. J Mol Biol 2021; 433:167091. [PMID: 34090923 DOI: 10.1016/j.jmb.2021.167091] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/12/2021] [Accepted: 05/27/2021] [Indexed: 11/28/2022]
Abstract
Ion conduction is an essential function for electrical activity in all organisms. The non-selective ion channel NaK was previously shown to adopt two stable conformations of the selectivity filter. Here, we present solid-state NMR measurements of NaK demonstrating a population shift between these conformations induced by changing the ions in the sample while the overall structure of NaK is not affected. We show that two K+-selective mutants (NaK2K and NaK2K-Y66F) suffer a complete loss of selectivity filter stability under Na+ conditions, but do not collapse into a defined structure. Widespread chemical shift perturbations are seen between the Na+ and K+ states of the K+-selective mutants in the region of the pore helix indicating structural changes. We conclude that the stronger link between the selectivity filter and the pore helix in the K+-selective mutants, compared to the non-selective wild-type NaK channel, reduces the ion-dependent conformational flexibility of the selectivity filter.
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Affiliation(s)
- Kitty Hendriks
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Carl Öster
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Chaowei Shi
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany; Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Huangshan Road 443, Hefei 230027, China
| | - Han Sun
- Structural Chemistry and Computational Biophysics Group, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Str. 10, 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, Invalidenstraße 42, 10115 Berlin, Germany.
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18
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Roy RN, Hendriks K, Kopec W, Abdolvand S, Weiss KL, de Groot BL, Lange A, Sun H, Coates L. Structural plasticity of the selectivity filter in a nonselective ion channel. IUCRJ 2021; 8:421-430. [PMID: 33953928 PMCID: PMC8086165 DOI: 10.1107/s205225252100213x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/23/2021] [Indexed: 06/12/2023]
Abstract
The sodium potassium ion channel (NaK) is a nonselective ion channel that conducts both sodium and potassium across the cellular membrane. A new crystallographic structure of NaK reveals conformational differences in the residues that make up the selectivity filter between the four subunits that form the ion channel and the inner helix of the ion channel. The crystallographic structure also identifies a side-entry, ion-conduction pathway for Na+ permeation that is unique to NaK. NMR studies and molecular dynamics simulations confirmed the dynamical nature of the top part of the selectivity filter and the inner helix in NaK as also observed in the crystal structure. Taken together, these results indicate that the structural plasticity of the selectivity filter combined with the dynamics of the inner helix of NaK are vital for the efficient conduction of different ions through the non-selective ion channel of NaK.
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Affiliation(s)
- Raktim N. Roy
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Kitty Hendriks
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Wojciech Kopec
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Saeid Abdolvand
- Structural Chemistry and Computational Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Kevin L. Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Bert L. de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Han Sun
- Structural Chemistry and Computational Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany
| | - Leighton Coates
- Second Target Station, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
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19
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Matamoros M, Nichols CG. Pore-forming transmembrane domains control ion selectivity and selectivity filter conformation in the KirBac1.1 potassium channel. J Gen Physiol 2021; 153:211923. [PMID: 33779689 PMCID: PMC8008366 DOI: 10.1085/jgp.202012683] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 11/23/2020] [Accepted: 03/09/2021] [Indexed: 01/10/2023] Open
Abstract
Potassium (K+) channels are membrane proteins with the remarkable ability to very selectively conduct K+ ions across the membrane. High-resolution structures have revealed that dehydrated K+ ions permeate through the narrowest region of the pore, formed by the backbone carbonyls of the signature selectivity filter (SF) sequence TxGYG. However, the existence of nonselective channels with similar SF sequences, as well as effects of mutations in other regions on selectivity, suggest that the SF is not the sole determinant of selectivity. We changed the selectivity of the KirBac1.1 channel by introducing mutations at residue I131 in transmembrane helix 2 (TM2). These mutations increase Na+ flux in the absence of K+ and introduce significant proton conductance. Consistent with K+ channel crystal structures, single-molecule FRET experiments show that the SF is conformationally constrained and stable in high-K+ conditions but undergoes transitions to dilated low-FRET states in high-Na+/low-K+ conditions. Relative to wild-type channels, I131M mutants exhibit marked shifts in the K+ and Na+ dependence of SF dynamics to higher K+ and lower Na+ concentrations. These results illuminate the role of I131, and potentially other structural elements outside the SF, in controlling ion selectivity, by suggesting that the physical interaction of these elements with the SF contributes to the relative stability of the constrained K+-induced SF configuration versus nonselective dilated conformations.
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Affiliation(s)
- Marcos Matamoros
- Center for Investigation of Membrane Excitability Diseases, and Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO
| | - Colin G Nichols
- Center for Investigation of Membrane Excitability Diseases, and Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO
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20
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Structural mechanisms of gating and selectivity of human rod CNGA1 channel. Neuron 2021; 109:1302-1313.e4. [PMID: 33651975 DOI: 10.1016/j.neuron.2021.02.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/22/2021] [Accepted: 02/03/2021] [Indexed: 11/22/2022]
Abstract
Mammalian cyclic nucleotide-gated (CNG) channels play an essential role in the signal transduction of the visual and olfactory sensory systems. Here we reveal the structural mechanism of ligand gating in human rod CNGA1 channel by determining its cryo-EM structures in both the apo closed and cGMP-bound open states. Distinct from most other members of voltage-gated tetrameric cation channels, CNGA1 forms a central channel gate in the middle of the membrane, occluding the central cavity. Structural analyses of ion binding profiles in the selectivity filters of the wild-type channel and the E365Q filter mutant allow us to unambiguously define the two Ca2+ binding sites inside the selectivity filter, providing structural insights into Ca2+ blockage and permeation in CNG channels. The structure of the E365Q mutant also reveals two alternative side-chain conformations at Q365, providing a plausible explanation for the voltage-dependent gating of CNG channel acquired upon E365 mutation.
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21
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Schmidt M, Schroeder I, Bauer D, Thiel G, Hamacher K. Inferring functional units in ion channel pores via relative entropy. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2021; 50:37-57. [PMID: 33523249 PMCID: PMC7872957 DOI: 10.1007/s00249-020-01480-7] [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] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 10/11/2020] [Accepted: 11/09/2020] [Indexed: 11/25/2022]
Abstract
Coarse-grained protein models approximate the first-principle physical potentials. Among those modeling approaches, the relative entropy framework yields promising and physically sound results, in which a mapping from the target protein structure and dynamics to a model is defined and subsequently adjusted by an entropy minimization of the model parameters. Minimization of the relative entropy is equivalent to maximization of the likelihood of reproduction of (configurational ensemble) observations by the model. In this study, we extend the relative entropy minimization procedure beyond parameter fitting by a second optimization level, which identifies the optimal mapping to a (dimension-reduced) topology. We consider anisotropic network models of a diverse set of ion channels and assess our findings by comparison to experimental results.
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Affiliation(s)
- Michael Schmidt
- Department of Physics, TU Darmstadt, Karolinenpl. 5, 64289 Darmstadt, Germany
| | - Indra Schroeder
- Department of Biology, TU Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Daniel Bauer
- Department of Biology, TU Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Gerhard Thiel
- Department of Biology, TU Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
| | - Kay Hamacher
- Department of Physics, Department of Biology, Department of Computer Science, TU Darmstadt, Schnittspahnstr. 10, 64287 Darmstadt, Germany
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22
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Jiang Y, Idikuda V, Chowdhury S, Chanda B. Activation of the archaeal ion channel MthK is exquisitely regulated by temperature. eLife 2020; 9:e59055. [PMID: 33274718 PMCID: PMC7717905 DOI: 10.7554/elife.59055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 11/17/2020] [Indexed: 11/13/2022] Open
Abstract
Physiological response to thermal stimuli in mammals is mediated by a structurally diverse class of ion channels, many of which exhibit polymodal behavior. To probe the diversity of biophysical mechanisms of temperature-sensitivity, we characterized the temperature-dependent activation of MthK, a two transmembrane calcium-activated potassium channel from thermophilic archaebacteria. Our functional complementation studies show that these channels are more efficient at rescuing K+ transport at 37°C than at 24°C. Electrophysiological activity of the purified MthK is extremely sensitive (Q10 >100) to heating particularly at low-calcium concentrations whereas channels lacking the calcium-sensing RCK domain are practically insensitive. By analyzing single-channel activities at limiting calcium concentrations, we find that temperature alters the coupling between the cytoplasmic RCK domains and the pore domain. These findings reveal a hitherto unexplored mechanism of temperature-dependent regulation of ion channel gating and shed light on ancient origins of temperature-sensitivity.
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Affiliation(s)
- Yihao Jiang
- Department of Anesthesiology, Washington University School of MedicineSt. LouisUnited States
- Center for the Investigation of Membrane Excitability Diseases (CIMED)St. LouisUnited States
| | - Vinay Idikuda
- Department of Anesthesiology, Washington University School of MedicineSt. LouisUnited States
- Center for the Investigation of Membrane Excitability Diseases (CIMED)St. LouisUnited States
| | - Sandipan Chowdhury
- Department of Anesthesiology, Washington University School of MedicineSt. LouisUnited States
- Center for the Investigation of Membrane Excitability Diseases (CIMED)St. LouisUnited States
| | - Baron Chanda
- Department of Anesthesiology, Washington University School of MedicineSt. LouisUnited States
- Center for the Investigation of Membrane Excitability Diseases (CIMED)St. LouisUnited States
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23
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Lolicato M, Natale AM, Abderemane-Ali F, Crottès D, Capponi S, Duman R, Wagner A, Rosenberg JM, Grabe M, Minor DL. K 2P channel C-type gating involves asymmetric selectivity filter order-disorder transitions. SCIENCE ADVANCES 2020; 6:6/44/eabc9174. [PMID: 33127683 PMCID: PMC7608817 DOI: 10.1126/sciadv.abc9174] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/10/2020] [Indexed: 05/05/2023]
Abstract
K2P potassium channels regulate cellular excitability using their selectivity filter (C-type) gate. C-type gating mechanisms, best characterized in homotetrameric potassium channels, remain controversial and are attributed to selectivity filter pinching, dilation, or subtle structural changes. The extent to which such mechanisms control C-type gating of innately heterodimeric K2Ps is unknown. Here, combining K2P2.1 (TREK-1) x-ray crystallography in different potassium concentrations, potassium anomalous scattering, molecular dynamics, and electrophysiology, we uncover unprecedented, asymmetric, potassium-dependent conformational changes that underlie K2P C-type gating. These asymmetric order-disorder transitions, enabled by the K2P heterodimeric architecture, encompass pinching and dilation, disrupt the S1 and S2 ion binding sites, require the uniquely long K2P SF2-M4 loop and conserved "M3 glutamate network," and are suppressed by the K2P C-type gate activator ML335. These findings demonstrate that two distinct C-type gating mechanisms can operate in one channel and underscore the SF2-M4 loop as a target for K2P channel modulator development.
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Affiliation(s)
- Marco Lolicato
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA
| | - Andrew M Natale
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA
| | - Fayal Abderemane-Ali
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA
| | - David Crottès
- Department of Physiology, University of California, San Francisco, CA 93858-2330, USA
| | - Sara Capponi
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA
| | - Ramona Duman
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Armin Wagner
- Science Division, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - John M Rosenberg
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Michael Grabe
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA.
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 93858-2330, USA
| | - Daniel L Minor
- Cardiovascular Research Institute, University of California, San Francisco, CA 93858-2330, USA.
- Departments of Biochemistry and Biophysics, and Cellular and Molecular Pharmacology, University of California, San Francisco, CA 93858-2330, USA
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 93858-2330, USA
- Kavli Institute for Fundamental Neuroscience, University of California, San Francisco, CA, 93858-2330, USA
- Molecular Biophysics and Integrated Bio-imaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720 USA
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24
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Langan PS, Vandavasi VG, Kopec W, Sullivan B, Afonne PV, Weiss KL, de Groot BL, Coates L. The structure of a potassium-selective ion channel reveals a hydrophobic gate regulating ion permeation. IUCRJ 2020; 7:835-843. [PMID: 32939275 PMCID: PMC7467165 DOI: 10.1107/s2052252520008271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
Protein dynamics are essential to function. One example of this is the various gating mechanisms within ion channels, which are transmembrane proteins that act as gateways into the cell. Typical ion channels switch between an open and closed state via a conformational transition which is often triggered by an external stimulus, such as ligand binding or pH and voltage differences. The atomic resolution structure of a potassium-selective ion channel named NaK2K has allowed us to observe that a hydro-phobic residue at the bottom of the selectivity filter, Phe92, appears in dual conformations. One of the two conformations of Phe92 restricts the diameter of the exit pore around the selectivity filter, limiting ion flow through the channel, while the other conformation of Phe92 provides a larger-diameter exit pore from the selectivity filter. Thus, it can be concluded that Phe92 acts as a hydro-phobic gate, regulating the flow of ions through the selectivity filter.
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Affiliation(s)
- Patricia S. Langan
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
- Lentigen Technologies, 910 Clopper Road, Gaithersburg, MD 20878, USA
| | - Venu Gopal Vandavasi
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
- Department of Chemistry, Princeton University, Princeton, NJ 08540, USA
| | - Wojciech Kopec
- Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Brendan Sullivan
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Pavel V. Afonne
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kevin L. Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Bert L. de Groot
- Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
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25
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Coates L. Ion permeation in potassium ion channels. Acta Crystallogr D Struct Biol 2020; 76:326-331. [PMID: 32254056 PMCID: PMC7137105 DOI: 10.1107/s2059798320003599] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/10/2020] [Indexed: 11/11/2022] Open
Abstract
The study of ion channels dates back to the 1950s and the groundbreaking electrophysiology work of Hodgin and Huxley, who used giant squid axons to probe how action potentials in neurons were initiated and propagated. More recently, several experiments using different structural biology techniques and approaches have been conducted to try to understand how potassium ions permeate through the selectivity filter of potassium ion channels. Two mechanisms of permeation have been proposed, and each of the two mechanisms is supported by different experiments. The key structural biology experiments conducted so far to try to understand how ion permeation takes place in potassium ion channels are reviewed and discussed. Protein crystallography has made, and continues to make, key contributions in this field, often through the use of anomalous scattering. Other structural biology techniques used to study the contents of the selectivity filter include solid-state nuclear magnetic resonance and two-dimensional infrared spectroscopy, both of which make clever use of isotopic labeling techniques, while molecular-dynamics simulations of ion flow through the selectivity filter have been enabled by the growing number of potassium ion channel structures deposited in the Protein Data Bank.
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Affiliation(s)
- Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
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26
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Durham RJ, Paudyal N, Carrillo E, Bhatia NK, Maclean DM, Berka V, Dolino DM, Gorfe AA, Jayaraman V. Conformational spread and dynamics in allostery of NMDA receptors. Proc Natl Acad Sci U S A 2020; 117:3839-3847. [PMID: 32015122 PMCID: PMC7035515 DOI: 10.1073/pnas.1910950117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Allostery can be manifested as a combination of repression and activation in multidomain proteins allowing for fine tuning of regulatory mechanisms. Here we have used single molecule fluorescence resonance energy transfer (smFRET) and molecular dynamics simulations to study the mechanism of allostery underlying negative cooperativity between the two agonists glutamate and glycine in the NMDA receptor. These data show that binding of one agonist leads to conformational flexibility and an increase in conformational spread at the second agonist site. Mutational and cross-linking studies show that the dimer-dimer interface at the agonist-binding domain mediates the allostery underlying the negative cooperativity. smFRET on the transmembrane segments shows that they are tightly coupled in the unliganded and single agonist-bound form and only upon binding both agonists the transmembrane domain explores looser packing which would facilitate activation.
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Affiliation(s)
- Ryan J Durham
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Nabina Paudyal
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Elisa Carrillo
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Nidhi Kaur Bhatia
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030
| | - David M Maclean
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642
| | - Vladimir Berka
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Drew M Dolino
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Alemayehu A Gorfe
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, TX 77030
| | - Vasanthi Jayaraman
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030;
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030
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27
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Selectivity filter modalities and rapid inactivation of the hERG1 channel. Proc Natl Acad Sci U S A 2020; 117:2795-2804. [PMID: 31980532 DOI: 10.1073/pnas.1909196117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The human ether-á-go-go-related gene (hERG1) channel conducts small outward K+ currents that are critical for cardiomyocyte membrane repolarization. The gain-of-function mutation N629D at the outer mouth of the selectivity filter (SF) disrupts inactivation and K+-selective transport in hERG1, leading to arrhythmogenic phenotypes associated with long-QT syndrome. Here, we combined computational electrophysiology with Markov state model analysis to investigate how SF-level gating modalities control selective cation transport in wild-type (WT) and mutant (N629D) hERG1 variants. Starting from the recently reported cryogenic electron microscopy (cryo-EM) open-state channel structure, multiple microseconds-long molecular-dynamics (MD) trajectories were generated using different cation configurations at the filter, voltages, electrolyte concentrations, and force-field parameters. Most of the K+ permeation events observed in hERG1-WT simulations occurred at microsecond timescales, influenced by the spontaneous dehydration/rehydration dynamics at the filter. The SF region displayed conductive, constricted, occluded, and dilated states, in qualitative agreement with the well-documented flickering conductance of hERG1. In line with mutagenesis studies, these gating modalities resulted from dynamic interaction networks involving residues from the SF, outer-mouth vestibule, P-helices, and S5-P segments. We found that N629D mutation significantly stabilizes the SF in a state that is permeable to both K+ and Na+, which is reminiscent of the SF in the nonselective bacterial NaK channel. Increasing the external K+ concentration induced "WT-like" SF dynamics in N629D, in qualitative agreement with the recovery of flickering currents in experiments. Overall, our findings provide an understanding of the molecular mechanisms controlling selective transport in K+ channels with a nonconventional SF sequence.
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Yuan P. Structural biology of thermoTRPV channels. Cell Calcium 2019; 84:102106. [PMID: 31726322 DOI: 10.1016/j.ceca.2019.102106] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 11/15/2022]
Abstract
Essential for physiology, transient receptor potential (TRP) channels constitute a large and diverse family of cation channels functioning as cellular sensors responding to a vast array of physical and chemical stimuli. Detailed understanding of the inner workings of TRP channels has been hampered by a lack of atomic structures, though structural biology of TRP channels has been an enthusiastic endeavor since their molecular identification two decades ago. These multi-domain integral membrane proteins, exhibiting complex polymodal gating behavior, have been a challenge for traditional X-ray crystallography, which requires formation of well-ordered protein crystals. X-ray structures remain limited to a few TRP channel proteins to date. Fortunately, recent breakthroughs in single-particle cryo-electron microscopy (cryo-EM) have enabled rapid growth of the number of TRP channel structures, providing tremendous insights into channel gating and regulation mechanisms and serving as foundations for further mechanistic investigations. This brief review focuses on recent exciting developments in structural biology of a subset of TRP channels, the calcium-permeable, non-selective and thermosensitive vanilloid subfamily of TRP channels (TRPV1-4), and the permeation and gating mechanisms revealed by structures.
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Affiliation(s)
- Peng Yuan
- Department of Cell Biology and Physiology, Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, Missouri 63110, USA.
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29
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Structure, function, and ion-binding properties of a K + channel stabilized in the 2,4-ion-bound configuration. Proc Natl Acad Sci U S A 2019; 116:16829-16834. [PMID: 31387976 DOI: 10.1073/pnas.1901888116] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Here, we present the atomic resolution crystallographic structure, the function, and the ion-binding properties of the KcsA mutants, G77A and G77C, that stabilize the 2,4-ion-bound configuration (i.e., water, K+, water, K+-ion-bound configuration) of the K+ channel's selectivity filter. A full functional and thermodynamic characterization of the G77A mutant revealed wild-type-like ion selectivity and apparent K+-binding affinity, in addition to showing a lack of C-type inactivation gating and a marked reduction in its single-channel conductance. These structures validate, from a structural point of view, the notion that 2 isoenergetic ion-bound configurations coexist within a K+ channel's selectivity filter, which fully agrees with the water-K+-ion-coupled transport detected by streaming potential measurements.
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Langan PS, Vandavasi VG, Sullivan B, Harp J, Weiss K, Coates L. Crystallization of a potassium ion channel and X-ray and neutron data collection. Acta Crystallogr F Struct Biol Commun 2019; 75:435-438. [PMID: 31204690 PMCID: PMC6572099 DOI: 10.1107/s2053230x19006630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/08/2019] [Indexed: 11/10/2022] Open
Abstract
The mechanism by which potassium ions are transported through ion channels is currently being investigated by several groups using many different techniques. Clarification of the location of water molecules during transport is central to understanding how these integral membrane proteins function. Neutrons have a unique sensitivity to both hydrogen and potassium, rendering neutron crystallography capable of distinguishing waters from K+ ions. Here, the collection of a complete neutron data set from a potassium ion channel to a resolution of 3.55 Å using the Macromolecular Neutron Diffractometer (MaNDi) is reported. A room-temperature X-ray data set was also collected from the same crystal to a resolution of 2.50 Å. Upon further refinement, these results will help to further clarify the ion/water population within the selectivity filter of potassium ion channels.
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Affiliation(s)
- Patricia S. Langan
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Venu Gopal Vandavasi
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Brendan Sullivan
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Joel Harp
- Department of Biochemistry and Center for Structural Biology, Vanderbilt University School of Medicine, 1161 21st Avenue South, Nashville, TN 37232, USA
| | - Kevin Weiss
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
| | - Leighton Coates
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA
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31
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He Y, Zhang B, Dong H, Xu P, Cai X, Zhou T, Yu M, Liang J, Zheng X, Tian C. Equilibria between the K + binding and cation vacancy conformations of potassium channels. Protein Cell 2019; 10:533-537. [PMID: 30805873 PMCID: PMC6588643 DOI: 10.1007/s13238-019-0609-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Yao He
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Bo Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Hao Dong
- Kuang Yaming Honors School and Institute for Brain Sciences, Nanjing University, Nanjing, 210023, China.
| | - Penglin Xu
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Chemistry and Material Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Xiaoying Cai
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Ting Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Chemistry and Material Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Mu Yu
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Jun Liang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China
| | - Xiao Zheng
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Chemistry and Material Sciences, University of Science and Technology of China, Hefei, 230026, China.
| | - Changlin Tian
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, 230027, China.
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32
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Babakhanian M, Yang L, Nowroozi B, Saddik G, Boodaghians L, Blount P, Grundfest W. Effects of Low Intensity Focused Ultrasound on Liposomes Containing Channel proteins. Sci Rep 2018; 8:17250. [PMID: 30467339 PMCID: PMC6250712 DOI: 10.1038/s41598-018-35486-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/06/2018] [Indexed: 02/08/2023] Open
Abstract
The ability to reversibly and non-invasively modulate region-specific brain activity in vivo suggests Low Intensity Focused Ultrasound (LIFU) as potential therapeutics for neurological dysfunctions such as epilepsy and Parkinson's disease. While in vivo studies provide evidence of the bioeffects of LIFU on neuronal activity, they merely hint at potential mechanisms but do not fully explain how this technology achieves these effects. One potential hypothesis is that LIFU produces local membrane depolarization by mechanically perturbing the neuronal cell membrane, or activating channels or other proteins embedded in the membrane. Proteins that sense mechanical perturbations of the membrane, such as those gated by membrane tension, are prime candidates for activating in response to LIFU and thus leading to the neurological responses that have been measured. Here we use the bacterial mechanosensitive channel MscL, which has been purified and reconstituted in liposomes, to determine how LIFU may affect the activation of this membrane-tension gated channel. Two bacterial voltage-gated channels, KvAP and NaK2K F92A channels were also studied. Surprisingly, the results suggest that ultrasound modulation and membrane perturbation does not induce channel gating, but rather induces pore formation at the membrane protein-lipid interface. However, in vesicles with high MscL mechanosensitive channel concentrations, apparent decreases in pore formation are observed, suggesting that this membrane-tension-sensitive protein may serve to increase the elasticity of the membrane, presumably because of expansion of the channel in the plane of the membrane independent of channel gating.
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Affiliation(s)
- Meghedi Babakhanian
- Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA
- Center for Advanced Surgical and Interventional Technology (CASIT), University of California, Los Angeles, CA, 90095, USA
| | - Limin Yang
- Department of Physiology, UT Southwestern Medical Center, Dallas, TX, 75390-9040, USA
| | - Bryan Nowroozi
- Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA
- Center for Advanced Surgical and Interventional Technology (CASIT), University of California, Los Angeles, CA, 90095, USA
| | - George Saddik
- Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA
- Center for Advanced Surgical and Interventional Technology (CASIT), University of California, Los Angeles, CA, 90095, USA
| | - Lilian Boodaghians
- Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA
- Center for Advanced Surgical and Interventional Technology (CASIT), University of California, Los Angeles, CA, 90095, USA
| | - Paul Blount
- Department of Physiology, UT Southwestern Medical Center, Dallas, TX, 75390-9040, USA.
| | - Warren Grundfest
- Department of Bioengineering, University of California, Los Angeles, CA, 90095, USA.
- Center for Advanced Surgical and Interventional Technology (CASIT), University of California, Los Angeles, CA, 90095, USA.
- Department of Electrical Engineering, University of California, Los Angeles, CA, 90095, USA.
- David Geffen School of Medicine, University of California, Los Angeles, USA.
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33
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Anomalous X-ray diffraction studies of ion transport in K + channels. Nat Commun 2018; 9:4540. [PMID: 30382100 PMCID: PMC6208422 DOI: 10.1038/s41467-018-06957-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/24/2018] [Indexed: 11/16/2022] Open
Abstract
Potassium ion channels utilize a highly selective filter to rapidly transport K+ ions across cellular membranes. This selectivity filter is composed of four binding sites which display almost equal electron density in crystal structures with high potassium ion concentrations. This electron density can be interpreted to reflect a superposition of alternating potassium ion and water occupied states or as adjacent potassium ions. Here, we use single wavelength anomalous dispersion (SAD) X-ray diffraction data collected near the potassium absorption edge to show experimentally that all ion binding sites within the selectivity filter are fully occupied by K+ ions. These data support the hypothesis that potassium ion transport occurs by direct Coulomb knock-on, and provide an example of solving the phase problem by K-SAD. The number of K+ occupied binding sites in the selectivity filter of potassium ion channels is still under debate. Here, the authors collect diffraction data on the K+ selective NaK channel NaK2K at a wavelength of 3.35 Å, close to the K absorption edge, revealing that all four binding sites in the selectivity filter are fully occupied by K+ ions.
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34
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MacLean DM, Durham RJ, Jayaraman V. Mapping the Conformational Landscape of Glutamate Receptors Using Single Molecule FRET. Trends Neurosci 2018; 42:128-139. [PMID: 30385052 DOI: 10.1016/j.tins.2018.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/27/2018] [Accepted: 10/02/2018] [Indexed: 10/28/2022]
Abstract
The ionotropic glutamate receptors mediate excitatory neurotransmission in the mammalian central nervous system. These receptors provide a range of temporally diverse signals which stem from subunit composition and also from the inherent ability of each member to occupy multiple functional states, the distribution of which can be altered by small molecule modulators and binding partners. Hence it becomes essential to characterize the conformational landscape of the receptors under this variety of different conditions. This has recently become possible due to single molecule fluorescence resonance energy transfer measurements, along with the rich foundation of existing structures allowing for direct correlations between conformational and functional diversity.
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Affiliation(s)
- David M MacLean
- Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Ryan J Durham
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Biochemistry and Cell Biology Graduate Program, Graduate School of Biomedical Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Vasanthi Jayaraman
- Center for Membrane Biology, Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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35
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Kopec W, Köpfer DA, Vickery ON, Bondarenko AS, Jansen TLC, de Groot BL, Zachariae U. Direct knock-on of desolvated ions governs strict ion selectivity in K+ channels. Nat Chem 2018; 10:813-820. [DOI: 10.1038/s41557-018-0105-9] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/15/2018] [Indexed: 01/26/2023]
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Abstract
Sodium (Na+) is a ubiquitous and important inorganic salt mediating many critical biological processes such as neuronal excitation, signaling, and facilitation of various transporters. The hydration states of Na+ are proposed to play critical roles in determining the conductance and the selectivity of Na+ channels, yet they are rarely captured by conventional structural biology means. Here we use the emerging cryo-electron microscopy (cryoEM) method micro-electron diffraction (MicroED) to study the structure of a prototypical tetrameric Na+-conducting channel, NaK, to 2.5 Å resolution from nano-crystals. Two new conformations at the external site of NaK are identified, allowing us to visualize a partially hydrated Na+ ion at the entrance of the channel pore. A process of dilation coupled with Na+ movement is identified leading to valuable insights into the mechanism of ion conduction and gating. This study lays the ground work for future studies using MicroED in membrane protein biophysics. Through a MicroED structure of NaK ion channel, Shian Liu and Tamir Gonen identify a process of dilation coupled with Na+ movement, providing mechanistic insights into ion conduction and gating. This study lays the ground work for future studies using MicroED in membrane protein biophysics.
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37
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Niitsu A, Heal JW, Fauland K, Thomson AR, Woolfson DN. Membrane-spanning α-helical barrels as tractable protein-design targets. Philos Trans R Soc Lond B Biol Sci 2018. [PMID: 28630153 DOI: 10.1098/rstb.2016.0213] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The rational (de novo) design of membrane-spanning proteins lags behind that for water-soluble globular proteins. This is due to gaps in our knowledge of membrane-protein structure, and experimental difficulties in studying such proteins compared to water-soluble counterparts. One limiting factor is the small number of experimentally determined three-dimensional structures for transmembrane proteins. By contrast, many tens of thousands of globular protein structures provide a rich source of 'scaffolds' for protein design, and the means to garner sequence-to-structure relationships to guide the design process. The α-helical coiled coil is a protein-structure element found in both globular and membrane proteins, where it cements a variety of helix-helix interactions and helical bundles. Our deep understanding of coiled coils has enabled a large number of successful de novo designs. For one class, the α-helical barrels-that is, symmetric bundles of five or more helices with central accessible channels-there are both water-soluble and membrane-spanning examples. Recent computational designs of water-soluble α-helical barrels with five to seven helices have advanced the design field considerably. Here we identify and classify analogous and more complicated membrane-spanning α-helical barrels from the Protein Data Bank. These provide tantalizing but tractable targets for protein engineering and de novo protein design.This article is part of the themed issue 'Membrane pores: from structure and assembly, to medicine and technology'.
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Affiliation(s)
- Ai Niitsu
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Jack W Heal
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Kerstin Fauland
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Andrew R Thomson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK .,School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK.,BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, UK
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38
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Deng Z, Paknejad N, Maksaev G, Sala-Rabanal M, Nichols CG, Hite RK, Yuan P. Cryo-EM and X-ray structures of TRPV4 reveal insight into ion permeation and gating mechanisms. Nat Struct Mol Biol 2018; 25:252-260. [PMID: 29483651 DOI: 10.1038/s41594-018-0037-5] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 01/26/2018] [Indexed: 12/15/2022]
Abstract
The transient receptor potential (TRP) channel TRPV4 participates in multiple biological processes, and numerous TRPV4 mutations underlie several distinct and devastating diseases. Here we present the cryo-EM structure of Xenopus tropicalis TRPV4 at 3.8-Å resolution. The ion-conduction pore contains an intracellular gate formed by the inner helices, but lacks any extracellular gate in the selectivity filter, as observed in other TRPV channels. Anomalous X-ray diffraction analyses identify a single ion-binding site in the selectivity filter, thus explaining TRPV4 nonselectivity. Structural comparisons with other TRP channels and distantly related voltage-gated cation channels reveal an unprecedented, unique packing interface between the voltage-sensor-like domain and the pore domain, suggesting distinct gating mechanisms. Moreover, our structure begins to provide mechanistic insights to the large set of pathogenic mutations, offering potential opportunities for drug development.
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Affiliation(s)
- Zengqin Deng
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA.,Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Navid Paknejad
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Grigory Maksaev
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA.,Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Monica Sala-Rabanal
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA.,Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Colin G Nichols
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA.,Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Richard K Hite
- Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Peng Yuan
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, USA. .,Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO, USA.
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39
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Andersson AEV, Kasimova MA, Delemotte L. Exploring the Viral Channel Kcv PBCV-1 Function via Computation. J Membr Biol 2018; 251:419-430. [PMID: 29476260 PMCID: PMC6028866 DOI: 10.1007/s00232-018-0022-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 02/15/2018] [Indexed: 11/30/2022]
Abstract
Viral potassium channels (Kcv) are homologous to the pore module of complex \documentclass[12pt]{minimal}
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\begin{document}$$\hbox {K}^+$$\end{document}K+-selective ion channels of cellular organisms. Due to their relative simplicity, they have attracted interest towards understanding the principles of \documentclass[12pt]{minimal}
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\begin{document}$$\hbox {K}^+$$\end{document}K+ conduction and channel gating. In this work, we construct a homology model of the \documentclass[12pt]{minimal}
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\begin{document}$${\hbox {Kcv}}_{\text{PBCV-1}}$$\end{document}KcvPBCV-1 open state, which we validate by studying the binding of known blockers and by monitoring ion conduction through the channel. Molecular dynamics simulations of this model reveal that the re-orientation of selectivity filter carbonyl groups coincides with the transport of potassium ions, suggesting a possible mechanism for fast gating. In addition, we show that the voltage sensitivity of this mechanism can originate from the relocation of potassium ions inside the selectivity filter. We also explore the interaction of \documentclass[12pt]{minimal}
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\begin{document}$${\hbox {Kcv}}_{\text{PBCV-1}}$$\end{document}KcvPBCV-1 with the surrounding bilayer and observe the binding of lipids in the area between two adjacent subunits. The model is available to the scientific community to further explore the structure/function relationship of Kcv channels.
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Affiliation(s)
- Alma E V Andersson
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, SE-171 21, Solna, Sweden
| | - Marina A Kasimova
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, SE-171 21, Solna, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Box 1031, SE-171 21, Solna, Sweden.
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40
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A single NaK channel conformation is not enough for non-selective ion conduction. Nat Commun 2018; 9:717. [PMID: 29459730 PMCID: PMC5818664 DOI: 10.1038/s41467-018-03179-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/24/2018] [Indexed: 01/15/2023] Open
Abstract
NaK and other non-selective channels are able to conduct both sodium (Na+) and potassium (K+) with equally high efficiency. In contrast to previous crystallographic results, we show that the selectivity filter (SF) of NaK in native-like lipid membranes adopts two distinct conformations that are stabilized by either Na+ or K+ ions. The atomic differences of these conformations are resolved by solid-state NMR (ssNMR) spectroscopy and molecular dynamics (MD) simulations. Besides the canonical K+ permeation pathway, we identify a side entry ion-conduction pathway for Na+ permeation unique to NaK. Moreover, under otherwise identical conditions ssNMR spectra of the K+ selective NaK mutant (NaK2K) reveal only a single conformational state. Therefore, we propose that structural plasticity within the SF and the selection of these conformations by different ions are key molecular determinants for highly efficient conduction of different ions in non-selective cation channels.
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41
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Shevkunov SV. Mean force potential of interaction between Na+ and Cl− ions in planar nanopores in contact with water under pressure. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2017. [DOI: 10.1134/s0036024417110243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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42
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The structure-energy landscape of NMDA receptor gating. Nat Chem Biol 2017; 13:1232-1238. [PMID: 28991238 PMCID: PMC5698143 DOI: 10.1038/nchembio.2487] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 08/28/2017] [Indexed: 01/26/2023]
Abstract
N-Methyl-D-aspartate (NMDA) receptors are the main calcium-permeable excitatory receptors in the mammalian central nervous system. The NMDA receptor gating is complex, exhibiting multiple closed, open, and desensitized states; however, central questions regarding the conformations and energetics of the transmembrane domains as they relate to the gating states are still unanswered. Here, using single-molecule Förster resonance energy transfer (smFRET), we map the energy landscape of the first transmembrane segment of the Rattus norvegicus NMDA receptor under resting and various liganded conditions. These results show kinetically and structurally distinct changes associated with apo, agonist-bound, and inhibited receptors linked by a linear mechanism of gating at this site. Furthermore, the smFRET data suggest that allosteric inhibition by zinc occurs by an uncoupling of the agonist-induced changes at the extracellular domains from the gating motions leading to an apo-like state, while dizocilpine, a pore blocker, stabilizes multiple closely packed transmembrane states.
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43
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Lee C, Guo J, Zeng W, Kim S, She J, Cang C, Ren D, Jiang Y. The lysosomal potassium channel TMEM175 adopts a novel tetrameric architecture. Nature 2017; 547:472-475. [PMID: 28723891 PMCID: PMC5901963 DOI: 10.1038/nature23269] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/06/2017] [Indexed: 11/09/2022]
Abstract
TMEM175 is a lysosomal K+ channel that is important for maintaining the membrane potential and pH stability in lysosomes. It contains two homologous copies of a six-transmembrane-helix (6-TM) domain, which has no sequence homology to the canonical tetrameric K+ channels and lacks the TVGYG selectivity filter motif found in these channels. The prokaryotic TMEM175 channel, which is present in a subset of bacteria and archaea, contains only a single 6-TM domain and functions as a tetramer. Here, we present the crystal structure of a prokaryotic TMEM175 channel from Chamaesiphon minutus, CmTMEM175, the architecture of which represents a completely different fold from that of canonical K+ channels. All six transmembrane helices of CmTMEM175 are tightly packed within each subunit without undergoing domain swapping. The highly conserved TM1 helix acts as the pore-lining inner helix, creating an hourglass-shaped ion permeation pathway in the channel tetramer. Three layers of hydrophobic residues on the carboxy-terminal half of the TM1 helices form a bottleneck along the ion conduction pathway and serve as the selectivity filter of the channel. Mutagenesis analysis suggests that the first layer of the highly conserved isoleucine residues in the filter is primarily responsible for channel selectivity. Thus, the structure of CmTMEM175 represents a novel architecture of a tetrameric cation channel whose ion selectivity mechanism appears to be distinct from that of the classical K+ channel family.
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Affiliation(s)
- Changkeun Lee
- Department of Physiology and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815-6789, USA
| | - Jiangtao Guo
- Department of Physiology and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA
| | - Weizhong Zeng
- Department of Physiology and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815-6789, USA
| | - Sunghoon Kim
- Department of Physiology and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815-6789, USA
| | - Ji She
- Department of Physiology and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA
| | - Chunlei Cang
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Dejian Ren
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Youxing Jiang
- Department of Physiology and Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA.,Howard Hughes Medical Institute, Chevy Chase, Maryland 20815-6789, USA
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44
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Mesbahi-Vasey S, Veras L, Yonkunas M, Johnson JW, Kurnikova MG. All atom NMDA receptor transmembrane domain model development and simulations in lipid bilayers and water. PLoS One 2017; 12:e0177686. [PMID: 28582391 PMCID: PMC5459333 DOI: 10.1371/journal.pone.0177686] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 05/01/2017] [Indexed: 11/19/2022] Open
Abstract
N-methyl-d-aspartate receptors (NMDARs) are members of the ionotropic glutamate receptor family that mediate excitatory synaptic transmission in the central nervous system. The channels of NMDARs are permeable to Ca2+ but blocked by Mg2+, distinctive properties that underlie essential brain processes such as induction of synaptic plasticity. However, due to limited structural information about the NMDAR transmembrane ion channel forming domain, the mechanism of divalent cation permeation and block is understood poorly. In this paper we developed an atomistic model of the transmembrane domain (TMD) of NMDARs composed of GluN1 and GluN2A subunits (GluN1/2A receptors). The model was generated using (a) a homology model based on the structure of the NaK channel and a partially resolved structure of an AMPA receptor (AMPAR), and (b) a partially resolved X-ray structure of GluN1/2B NMDARs. Refinement and extensive Molecular Dynamics (MD) simulations of the NMDAR TMD model were performed in explicit lipid bilayer membrane and water. Targeted MD with simulated annealing was introduced to promote structure refinement. Putative positions of the Mg2+ and Ca2+ ions in the ion channel divalent cation binding site are proposed. Differences in the structural and dynamic behavior of the channel protein in the presence of Mg2+ or Ca2+ are analyzed. NMDAR protein conformational flexibility was similar with no ion bound to the divalent cation binding site and with Ca2+ bound, whereas Mg2+ binding reduced protein fluctuations. While bound at the binding site both ions retained their preferred ligand coordination numbers: 6 for Mg2+, and 7–8 for Ca2+. Four asparagine side chain oxygens, a back-bone oxygen, and a water molecule participated in binding a Mg2+ ion. The Ca2+ ion first coordination shell ligands typically included four to five side-chain oxygen atoms of the binding site asparagine residues, two water molecules and zero to two backbone oxygens of the GluN2B subunits. These results demonstrate the importance of high-resolution channel structures for elucidation of mechanisms of NMDAR permeation and block.
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Affiliation(s)
- Samaneh Mesbahi-Vasey
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Lea Veras
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Michael Yonkunas
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Jon W. Johnson
- Department of Neuroscience and Center for Neuroscience, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Maria G. Kurnikova
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
- * E-mail:
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45
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Colledge M, Wallace BA. AnglerFish: a webserver for defining the geometry of α-helices in membrane proteins. Bioinformatics 2017; 33:1233-1234. [PMID: 28035031 PMCID: PMC5860525 DOI: 10.1093/bioinformatics/btw781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/06/2016] [Indexed: 11/14/2022] Open
Abstract
Summary Integral membrane proteins that form helical pores and bundles constitute major drug targets, and many of their structures have been defined by crystallography and cryo-electron microscopy. The gating of channels and ligand binding of transporters generally involve changes in orientation of one or more the constituent helices in the structures. At present there is no standard easily accessible means for defining the orientation of a helix in a membrane protein structure. AnglerFish is a web-based tool for parameterising the angles of transmembrane helices based on PDB coordinates, with the helical orientations defined by the angles ‘tilt’ and ‘swing’. AnglerFish is particularly useful for defining changes in structure between different states, including both symmetric and asymmetric transitions, and can be used to quantitate differences between related structures or different subunits within the same structure. Availability and Implementation AnglerFish is freely available at http://anglerfish.cryst.bbk.ac.uk. The website is implemented in Perl-cgi and Apache and operation in all major browsers is supported. The source code is available at GitHub. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Matthew Colledge
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, UK
- To whom correspondence should be addressed.
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46
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Lee CH, MacKinnon R. Structures of the Human HCN1 Hyperpolarization-Activated Channel. Cell 2017; 168:111-120.e11. [PMID: 28086084 DOI: 10.1016/j.cell.2016.12.023] [Citation(s) in RCA: 258] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 11/29/2016] [Accepted: 12/15/2016] [Indexed: 01/23/2023]
Abstract
Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels underlie the control of rhythmic activity in cardiac and neuronal pacemaker cells. In HCN, the polarity of voltage dependence is uniquely reversed. Intracellular cyclic adenosine monophosphate (cAMP) levels tune the voltage response, enabling sympathetic nerve stimulation to increase the heart rate. We present cryo-electron microscopy structures of the human HCN channel in the absence and presence of cAMP at 3.5 Å resolution. HCN channels contain a K+ channel selectivity filter-forming sequence from which the amino acids create a unique structure that explains Na+ and K+ permeability. The voltage sensor adopts a depolarized conformation, and the pore is closed. An S4 helix of unprecedented length extends into the cytoplasm, contacts the C-linker, and twists the inner helical gate shut. cAMP binding rotates cytoplasmic domains to favor opening of the inner helical gate. These structures advance understanding of ion selectivity, reversed polarity gating, and cAMP regulation in HCN channels.
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Affiliation(s)
- Chia-Hsueh Lee
- Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10065, USA
| | - Roderick MacKinnon
- Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10065, USA.
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47
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A reduced mechanical model for cAMP-modulated gating in HCN channels. Sci Rep 2017; 7:40168. [PMID: 28074902 PMCID: PMC5225470 DOI: 10.1038/srep40168] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/01/2016] [Indexed: 12/29/2022] Open
Abstract
We developed an in silico mechanical model to analyze the process of cAMP-induced conformational modulations in hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, which conduct cations across the membrane of mammalian heart and brain cells. The structural analysis reveals a quaternary twist in the cytosolic parts of the four subunits in the channel tetramer. This motion augments the intrinsic dynamics of the very same protein structure. The pronounced differences between the cAMP bound and unbound form include a mutual interaction between the C-linker of the cyclic nucleotide binding domain (CNBD) and the linker between the S4 and S5 transmembrane domain of the channel. This allows a mechanistic annotation of the twisting motion in relation to the allosteric modulation of voltage-dependent gating of this channel by cAMP.
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48
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Sadhu B, Sundararajan M, Bandyopadhyay T. Divalent ions are potential permeating blockers of the non-selective NaK ion channel: combined QM and MD based investigations. Phys Chem Chem Phys 2017; 19:27611-27622. [DOI: 10.1039/c7cp05586b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interplay between the hydration energy barrier and optimum site-selectivity controls the permeation and blocking features of divalent metal ions.
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Affiliation(s)
- Biswajit Sadhu
- Radiation Safety Systems Division
- Bhabha Atomic Research Centre
- Mumbai 400 085
- India
- Homi Bhabha National Institute
| | - Mahesh Sundararajan
- Theoretical Chemistry Section
- Bhabha Atomic Research Centre
- Mumbai 400 094
- India
| | - Tusar Bandyopadhyay
- Homi Bhabha National Institute
- Mumbai 400 085
- India
- Theoretical Chemistry Section
- Bhabha Atomic Research Centre
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49
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Christensen AP, Akyuz N, Corey DP. The Outer Pore and Selectivity Filter of TRPA1. PLoS One 2016; 11:e0166167. [PMID: 27824920 PMCID: PMC5100928 DOI: 10.1371/journal.pone.0166167] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/23/2016] [Indexed: 11/25/2022] Open
Abstract
TRPA1 (transient-receptor-potential-related ion channel with ankyrin domains) is a direct receptor or indirect effector for a wide variety of nociceptive signals, and thus is a compelling target for development of analgesic pharmaceuticals such as channel blockers. Recently, the structure of TRPA1 was reported, providing insights into channel assembly and pore architecture. Here we report whole-cell and single-channel current recordings of wild-type human TRPA1 as well as TRPA1 bearing point mutations of key charged residues in the outer pore. These measurements demonstrate that the glutamate at position 920 plays an important role in collecting cations into the mouth of the pore, by changing the effective surface potential by ~16 mV, while acidic residues further out have little effect on permeation. Electrophysiology experiments also confirm that the aspartate residue at position 915 represents a constriction site of the TRPA1 pore and is critical in controlling ion permeation.
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Affiliation(s)
- Adam P. Christensen
- Program in Neuroscience, Harvard Medical School, 220 Longwood Ave, Boston, Massachusetts, United States of America
- Department of Neurobiology and Howard Hughes Medical Institute, Harvard Medical School, 220 Longwood Ave, Boston, Massachusetts, United States of America
| | - Nurunisa Akyuz
- Department of Neurobiology and Howard Hughes Medical Institute, Harvard Medical School, 220 Longwood Ave, Boston, Massachusetts, United States of America
| | - David P. Corey
- Program in Neuroscience, Harvard Medical School, 220 Longwood Ave, Boston, Massachusetts, United States of America
- Department of Neurobiology and Howard Hughes Medical Institute, Harvard Medical School, 220 Longwood Ave, Boston, Massachusetts, United States of America
- * E-mail:
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50
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Dhakshnamoorthy B, Rohaim A, Rui H, Blachowicz L, Roux B. Structural and functional characterization of a calcium-activated cation channel from Tsukamurella paurometabola. Nat Commun 2016; 7:12753. [PMID: 27678077 PMCID: PMC5052707 DOI: 10.1038/ncomms12753] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/25/2016] [Indexed: 02/03/2023] Open
Abstract
The selectivity filter is an essential functional element of K+ channels that is highly conserved both in terms of its primary sequence and its three-dimensional structure. Here, we investigate the properties of an ion channel from the Gram-positive bacterium Tsukamurella paurometabola with a selectivity filter formed by an uncommon proline-rich sequence. Electrophysiological recordings show that it is a non-selective cation channel and that its activity depends on Ca2+ concentration. In the crystal structure, the selectivity filter adopts a novel conformation with Ca2+ ions bound within the filter near the pore helix where they are coordinated by backbone oxygen atoms, a recurrent motif found in multiple proteins. The binding of Ca2+ ion in the selectivity filter controls the widening of the pore as shown in crystal structures and in molecular dynamics simulations. The structural, functional and computational data provide a characterization of this calcium-gated cationic channel. Tetrameric cationic channels specificity is determined by the sequence and structural conformation of their selectivity filter. Here, the authors show that a cationic channel from Tsukamurella paurometabola is non-selective due to a Ca2+-binding motif within its unusual proline-rich filter.
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Affiliation(s)
- Balasundaresan Dhakshnamoorthy
- Division of Biological Sciences, Department of Biochemistry and Molecular Biology, The University of Chicago 929 East 57th Street Chicago, Illinois 60637, USA
| | - Ahmed Rohaim
- Division of Biological Sciences, Department of Biochemistry and Molecular Biology, The University of Chicago 929 East 57th Street Chicago, Illinois 60637, USA.,Department of Biophysics, Faculty of Science, Cairo University, Giza, 12613, Egypt
| | - Huan Rui
- Division of Biological Sciences, Department of Biochemistry and Molecular Biology, The University of Chicago 929 East 57th Street Chicago, Illinois 60637, USA
| | - Lydia Blachowicz
- Division of Biological Sciences, Department of Biochemistry and Molecular Biology, The University of Chicago 929 East 57th Street Chicago, Illinois 60637, USA
| | - Benoît Roux
- Division of Biological Sciences, Department of Biochemistry and Molecular Biology, The University of Chicago 929 East 57th Street Chicago, Illinois 60637, USA
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