1
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Do HQ, Pirayesh E, Ferreira G, Pandhare A, Gallardo ZR, Jansen M. A bupropion modulatory site in the Gloeobacter violaceus ligand-gated ion channel. Biophys J 2024; 123:2185-2198. [PMID: 38678367 PMCID: PMC11309978 DOI: 10.1016/j.bpj.2024.04.027] [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] [Received: 10/09/2023] [Revised: 01/27/2024] [Accepted: 04/25/2024] [Indexed: 04/29/2024] Open
Abstract
Bupropion is an atypical antidepressant and smoking cessation drug that causes adverse effects such as insomnia, irritability, and anxiety. Bupropion inhibits dopamine and norepinephrine reuptake transporters and eukaryotic cation-conducting pentameric ligand-gated ion channels, such as nicotinic acetylcholine and serotonin type 3A receptors, at clinically relevant concentrations. Here, we demonstrate that bupropion also inhibits a prokaryotic homolog of pentameric ligand-gated ion channels, the Gloeobacter violaceus ligand-gated ion channel (GLIC). Using the GLIC as a model, we used molecular docking to predict binding sites for bupropion. Bupropion was found to bind to several sites within the transmembrane domain, with the predominant site being localized to the interface between transmembrane segments M1 and M3 of two adjacent subunits. Residues W213, T214, and W217 in the first transmembrane segment, M1, and F267 and I271 in the third transmembrane segment, M3, most frequently reside within a 4 Å distance from bupropion. We then used single amino acid substitutions at these positions and two-electrode voltage-clamp recordings to determine their impact on bupropion inhibitory effects. The substitution T214F alters bupropion potency by shifting the half-maximal inhibitory concentration to a 13-fold higher value compared to wild-type GLIC. Residue T214 is found within a previously identified binding pocket for neurosteroids and lipids in the GLIC. This intersubunit binding pocket is structurally conserved and almost identical to a binding pocket described for neurosteroids in γ-aminobutyric acid type A receptors. Our data thus suggest that the T214 that lines a previously identified lipophilic binding pocket in GLIC and γ-aminobutyric acid type A receptors is also a modulatory site for bupropion interaction with the GLIC.
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Affiliation(s)
- Hoa Quynh Do
- Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas
| | - Elham Pirayesh
- Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas
| | - Garren Ferreira
- Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas
| | - Akash Pandhare
- Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas
| | - Zackary Ryan Gallardo
- Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas
| | - Michaela Jansen
- Cell Physiology and Molecular Biophysics, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas.
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2
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Bharambe N, Li Z, Seiferth D, Balakrishna AM, Biggin PC, Basak S. Cryo-EM structures of prokaryotic ligand-gated ion channel GLIC provide insights into gating in a lipid environment. Nat Commun 2024; 15:2967. [PMID: 38580666 PMCID: PMC10997623 DOI: 10.1038/s41467-024-47370-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 03/28/2024] [Indexed: 04/07/2024] Open
Abstract
GLIC, a proton-activated prokaryotic ligand-gated ion channel, served as a model system for understanding the eukaryotic counterparts due to their structural and functional similarities. Despite extensive studies conducted on GLIC, the molecular mechanism of channel gating in the lipid environment requires further investigation. Here, we present the cryo-EM structures of nanodisc-reconstituted GLIC at neutral and acidic pH in the resolution range of 2.6 - 3.4 Å. In our apo state at pH 7.5, the extracellular domain (ECD) displays conformational variations compared to the existing apo structures. At pH 4.0, three distinct conformational states (C1, C2 and O states) are identified. The protonated structures exhibit a compacted and counter-clockwise rotated ECD compared with our apo state. A gradual widening of the pore in the TMD is observed upon reducing the pH, with the widest pore in O state, accompanied by several layers of water pentagons. The pore radius and molecular dynamics (MD) simulations suggest that the O state represents an open conductive state. We also observe state-dependent interactions between several lipids and proteins that may be involved in the regulation of channel gating. Our results provide comprehensive insights into the importance of lipids impact on gating.
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Affiliation(s)
- Nikhil Bharambe
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Zhuowen Li
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - David Seiferth
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Philip C Biggin
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Sandip Basak
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 639798, Singapore.
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3
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Kumari M, Khatoon N, Sharma R, Adusumilli S, Auerbach A, Kashyap HK, Nayak TK. Mechanism of hydrophobic gating in the acetylcholine receptor channel pore. J Gen Physiol 2024; 156:e202213189. [PMID: 38153395 PMCID: PMC10757554 DOI: 10.1085/jgp.202213189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/16/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023] Open
Abstract
Neuromuscular acetylcholine receptors (AChRs) are hetero-pentameric, ligand-gated ion channels. The binding of the neurotransmitter acetylcholine (ACh) to two target sites promotes a global conformational change of the receptor that opens the channel and allows ion conduction through the channel pore. Here, by measuring free-energy changes from single-channel current recordings and using molecular dynamics simulations, we elucidate how a constricted hydrophobic region acts as a "gate" to regulate the channel opening in the pore of AChRs. Mutations of gate residues, including those implicated in congenital myasthenia syndrome, lower the permeation barrier of the channel substantially and increase the unliganded gating equilibrium constant (constitutive channel openings). Correlations between hydrophobicity and the observed free-energy changes, supported by calculations of water densities in the wild-type versus mutant channel pores, provide evidence for hydrophobic wetting-dewetting transition at the gate. The analysis of a coupled interaction network provides insight into the molecular mechanism of closed- versus open-state conformational changes at the gate. Studies of the transition state by "phi"(φ)-value analysis indicate that agonist binding serves to stabilize both the transition and the open state. Intersubunit interaction energy measurements and molecular dynamics simulations suggest that channel opening involves tilting of the pore-lining M2 helices, asymmetric outward rotation of amino acid side chains, and wetting transition of the gate region that lowers the barrier to ion permeation and stabilizes the channel open conformation. Our work provides new insight into the hydrophobic gate opening and shows why the gate mutations result in constitutive AChR channel activity.
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Affiliation(s)
- Monika Kumari
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Nadira Khatoon
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Rachita Sharma
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Sushanth Adusumilli
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Anthony Auerbach
- Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Hemant K. Kashyap
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
| | - Tapan K. Nayak
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India
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4
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Van Renterghem C, Nemecz Á, Medjebeur K, Corringer P. Short-chain mono-carboxylates as negative modulators of allosteric transitions in Gloeobacter violaceus ligand-gated ion channel, and impact of a pre-β5 strand (Loop Ω) double mutation on crotonate, not butyrate effect. Physiol Rep 2024; 12:e15916. [PMID: 38343277 PMCID: PMC10859675 DOI: 10.14814/phy2.15916] [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: 09/21/2023] [Revised: 12/24/2023] [Accepted: 01/03/2024] [Indexed: 02/15/2024] Open
Abstract
Using the bacterial proton-activated pentameric receptor-channel Gloeobacter violaceus ligand-gated ion channel (GLIC): (1) We characterize saturated, mono-carboxylates as negative modulators of GLIC (as previously shown for crotonate; Alqazzaz et al., Biochemistry, 2016, 55, 5947). Butyrate and crotonate have indistinguishable properties regarding negative modulation of wt GLIC. (2) We identify a locus in the pre-β5 strand (Loop Ω) whose mutation inverses the effect of the mono-carboxylate crotonate from negative to positive modulation of the allosteric transitions, suggesting an involvement of the pre-β5 strand in coupling the extracellular orthotopic receptor to pore gating. (3) As an extension to the previously proposed "in series" mechanism, we suggest that a orthotopic/orthosteric site-vestibular site-Loop Ω-β5-β6 "sandwich"-Pro-Loop/Cys-Loop series may be an essential component of orthotopic/orthosteric compound-elicited gating control in this pentameric ligand-gated ion channel, on top of which compounds targeting the vestibular site may provide modulation.
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Affiliation(s)
| | - Ákos Nemecz
- Channel‐Receptors Unit, Institut Pasteur, CNRS UMR3571Université Paris CitéParisFrance
| | - Karima Medjebeur
- Channel‐Receptors Unit, Institut Pasteur, CNRS UMR3571Université Paris CitéParisFrance
| | - Pierre‐Jean Corringer
- Channel‐Receptors Unit, Institut Pasteur, CNRS UMR3571Université Paris CitéParisFrance
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5
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Bergh C, Rovšnik U, Howard R, Lindahl E. Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM. eLife 2024; 12:RP86016. [PMID: 38289224 PMCID: PMC10945520 DOI: 10.7554/elife.86016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024] Open
Abstract
Ligand-gated ion channels transduce electrochemical signals in neurons and other excitable cells. Aside from canonical ligands, phospholipids are thought to bind specifically to the transmembrane domain of several ion channels. However, structural details of such lipid contacts remain elusive, partly due to limited resolution of these regions in experimental structures. Here, we discovered multiple lipid interactions in the channel GLIC by integrating cryo-electron microscopy and large-scale molecular simulations. We identified 25 bound lipids in the GLIC closed state, a conformation where none, to our knowledge, were previously known. Three lipids were associated with each subunit in the inner leaflet, including a buried interaction disrupted in mutant simulations. In the outer leaflet, two intrasubunit sites were evident in both closed and open states, while a putative intersubunit site was preferred in open-state simulations. This work offers molecular details of GLIC-lipid contacts particularly in the ill-characterized closed state, testable hypotheses for state-dependent binding, and a multidisciplinary strategy for modeling protein-lipid interactions.
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Affiliation(s)
- Cathrine Bergh
- Science for Life Laboratory & Swedish e-Science Research Center, Department of Applied Physics, KTH Royal Institute of TechnologyStockholmSweden
| | - Urška Rovšnik
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | - Rebecca Howard
- Science for Life Laboratory & Swedish e-Science Research Center, Department of Applied Physics, KTH Royal Institute of TechnologyStockholmSweden
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
| | - Erik Lindahl
- Science for Life Laboratory & Swedish e-Science Research Center, Department of Applied Physics, KTH Royal Institute of TechnologyStockholmSweden
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm UniversityStockholmSweden
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6
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Stevens MJ, Rempe SLB. Binding of carboxylate and water to monovalent cations. Phys Chem Chem Phys 2023; 25:29881-29893. [PMID: 37889481 DOI: 10.1039/d3cp04200f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The interactions of carboxylate anions with water and cations are important for a wide variety of systems, both biological and synthetic. To gain insight on properties of the local complexes, we apply density functional theory, to treat the complex electrostatic interactions, and investigate mixtures with varied numbers of carboxylate anions (acetate) and waters binding to monovalent cations, Li+, Na+ and K+. The optimal structure with overall lowest free energy contains two acetates and two waters such that the cation is four-fold coordinated, similar to structures found earlier for pure water or pure carboxylate ligands. More generally, the complexes with two acetates have the lowest free energy. In transitioning from the overall optimal state, exchanging an acetate for water has a lower free energy barrier than exchanging water for an acetate. In most cases, the carboxylates are monodentate and in the first solvation shell. As water is added to the system, hydrogen bonding between waters and carboxylate O atoms further stabilizes monodentate structures. These structures, which have strong electrostatic interactions that involve hydrogen bonds of varying strength, are significantly polarized, with ChelpG partial charges that vary substantially as the bonding geometry varies. Overall, these results emphasize the increasing importance of water as a component of binding sites as the number of ligands increases, thus affecting the preferential solvation of specific metal ions and clarifying Hofmeister effects. Finally, structural analysis correlated with free energy analysis supports the idea that binding to more than the preferred number of carboxylates under architectural constraints are a key to ion transport.
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Affiliation(s)
- Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
| | - Susan L B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
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7
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Ives CM, Thomson NJ, Zachariae U. A cooperative knock-on mechanism underpins Ca2+-selective cation permeation in TRPV channels. J Gen Physiol 2023; 155:213957. [PMID: 36943243 PMCID: PMC10038842 DOI: 10.1085/jgp.202213226] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 11/15/2022] [Accepted: 02/28/2023] [Indexed: 03/23/2023] Open
Abstract
The selective exchange of ions across cellular membranes is a vital biological process. Ca2+-mediated signaling is implicated in a broad array of physiological processes in cells, while elevated intracellular concentrations of Ca2+ are cytotoxic. Due to the significance of this cation, strict Ca2+ concentration gradients are maintained across the plasma and organelle membranes. Therefore, Ca2+ signaling relies on permeation through selective ion channels that control the flux of Ca2+ ions. A key family of Ca2+-permeable membrane channels is the polymodal signal-detecting transient receptor potential (TRP) ion channels. TRP channels are activated by a wide variety of cues including temperature, small molecules, transmembrane voltage, and mechanical stimuli. While most members of this family permeate a broad range of cations non-selectively, TRPV5 and TRPV6 are unique due to their strong Ca2+ selectivity. Here, we address the question of how some members of the TRPV subfamily show a high degree of Ca2+ selectivity while others conduct a wider spectrum of cations. We present results from all-atom molecular dynamics simulations of ion permeation through two Ca2+-selective and two non-selective TRPV channels. Using a new method to quantify permeation cooperativity based on mutual information, we show that Ca2+-selective TRPV channel permeation occurs by a three-binding site knock-on mechanism, whereas a two-binding site knock-on mechanism is observed in non-selective TRPV channels. Each of the ion binding sites involved displayed greater affinity for Ca2+ over Na+. As such, our results suggest that coupling to an extra binding site in the Ca2+-selective TRPV channels underpins their increased selectivity for Ca2+ over Na+ ions. Furthermore, analysis of all available TRPV channel structures shows that the selectivity filter entrance region is wider for the non-selective TRPV channels, slightly destabilizing ion binding at this site, which is likely to underlie mechanistic decoupling.
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Affiliation(s)
- Callum M Ives
- Computational Biology, School of Life Sciences, University of Dundee , Dundee, UK
| | - Neil J Thomson
- Computational Biology, School of Life Sciences, University of Dundee , Dundee, UK
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee , Dundee, UK
- Biochemistry and Drug Discovery, School of Life Sciences, University of Dundee , Dundee, UK
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8
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Aho N, Buslaev P, Jansen A, Bauer P, Groenhof G, Hess B. Scalable Constant pH Molecular Dynamics in GROMACS. J Chem Theory Comput 2022; 18:6148-6160. [PMID: 36128977 PMCID: PMC9558312 DOI: 10.1021/acs.jctc.2c00516] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Noora Aho
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014Jyväskylä, Finland
| | - Pavel Buslaev
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014Jyväskylä, Finland
| | - Anton Jansen
- Department of Applied Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44Stockholm, Sweden
| | - Paul Bauer
- Department of Applied Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44Stockholm, Sweden
| | - Gerrit Groenhof
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, 40014Jyväskylä, Finland
| | - Berk Hess
- Department of Applied Physics and Swedish e-Science Research Center, Science for Life Laboratory, KTH Royal Institute of Technology, 100 44Stockholm, Sweden
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9
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Stevens MJ, Rempe SLB. Carboxylate binding prefers two cations to one. Phys Chem Chem Phys 2022; 24:22198-22205. [PMID: 36093927 DOI: 10.1039/d2cp03561h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Almost all studies of specific ion binding by carboxylates (-COO-) have considered only a single cation, but clustering of ions and ligands is a common phenomenon. We apply density functional theory to investigate how variations in the number of acetate ligands in binding to two monovalent cations affects ion binding preferences. We study a series of monovalent (Li+, Na+, K+, Cs+) ions relevant to experimental work on many topics, including ion channels, battery storage, water purification and solar cells. We find that the preferred optimal structure has 3 acetates except for Cs+, which has 2 acetates. The optimal coordination of the cation by the carboxylate O atoms is 4 for both Na+ and K+, and 3 for Li+ and Cs+. There is a 4-fold coordination minimum just a few kcal mol-1 higher than the optimal 3-fold structure for Li+. For two cations, multiple minima occur in the vicinity of the lowest free energy state. We find that, for Li, Na and K, the preferred optimal structure with two cations is favored over a mixture of single cation complexes, providing a basis for understanding ionic cluster formation that is relevant for engineering proteins and other materials for rapid, selective ion transport.
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Affiliation(s)
- Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA.
| | - Susan L B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, NM 87185, USA. .,CBRN Defense and Energy Technologies, Sandia National Laboratories, Albuquerque, NM, 87185, USA.
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10
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Heavy Atom Detergent/Lipid Combined X-ray Crystallography for Elucidating the Structure-Function Relationships of Membrane Proteins. MEMBRANES 2021; 11:membranes11110823. [PMID: 34832053 PMCID: PMC8625833 DOI: 10.3390/membranes11110823] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/22/2021] [Accepted: 10/23/2021] [Indexed: 02/03/2023]
Abstract
Membrane proteins reside in the lipid bilayer of biomembranes and the structure and function of these proteins are closely related to their interactions with lipid molecules. Structural analyses of interactions between membrane proteins and lipids or detergents that constitute biological or artificial model membranes are important for understanding the functions and physicochemical properties of membrane proteins and biomembranes. Determination of membrane protein structures is much more difficult when compared with that of soluble proteins, but the development of various new technologies has accelerated the elucidation of the structure-function relationship of membrane proteins. This review summarizes the development of heavy atom derivative detergents and lipids that can be used for structural analysis of membrane proteins and their interactions with detergents/lipids, including their application with X-ray free-electron laser crystallography.
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11
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Bergh C, Heusser SA, Howard R, Lindahl E. Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channel. eLife 2021; 10:68369. [PMID: 34652272 PMCID: PMC8635979 DOI: 10.7554/elife.68369] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 10/14/2021] [Indexed: 01/03/2023] Open
Abstract
Ligand-gated ion channels conduct currents in response to chemical stimuli, mediating electrochemical signaling in neurons and other excitable cells. For many channels, the details of gating remain unclear, partly due to limited structural data and simulation timescales. Here, we used enhanced sampling to simulate the pH-gated channel GLIC, and construct Markov state models (MSMs) of gating. Consistent with new functional recordings, we report in oocytes, our analysis revealed differential effects of protonation and mutation on free-energy wells. Clustering of closed- versus open-like states enabled estimation of open probabilities and transition rates, while higher-order clustering affirmed conformational trends in gating. Furthermore, our models uncovered state- and protonation-dependent symmetrization. This demonstrates the applicability of MSMs to map energetic and conformational transitions between ion-channel functional states, and how they reproduce shifts upon activation or mutation, with implications for modeling neuronal function and developing state-selective drugs.
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Affiliation(s)
- Cathrine Bergh
- Science for Life Laboratory and Swedish e-Science Research Center, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden
| | - Stephanie A Heusser
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Rebecca Howard
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Erik Lindahl
- Science for Life Laboratory and Swedish e-Science Research Center, Department of Applied Physics, KTH Royal Institute of Technology, Solna, Sweden.,Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
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12
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Lefebvre SN, Taly A, Menny A, Medjebeur K, Corringer PJ. Mutational analysis to explore long-range allosteric couplings involved in a pentameric channel receptor pre-activation and activation. eLife 2021; 10:60682. [PMID: 34590583 PMCID: PMC8504973 DOI: 10.7554/elife.60682] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/29/2021] [Indexed: 01/23/2023] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) mediate chemical signaling through a succession of allosteric transitions that are yet not completely understood as intermediate states remain poorly characterized by structural approaches. In a previous study on the prototypic bacterial proton-gated channel GLIC, we generated several fluorescent sensors of the protein conformation that report a fast transition to a pre-active state, which precedes the slower process of activation with pore opening. Here, we explored the phenotype of a series of allosteric mutations, using simultaneous steady-state fluorescence and electrophysiological measurements over a broad pH range. Our data, fitted to a three-state Monod-Wyman-Changeux model, show that mutations at the subunit interface in the extracellular domain (ECD) principally alter pre-activation, while mutations in the lower ECD and in the transmembrane domain principally alter activation. We also show that propofol alters both transitions. Data are discussed in the framework of transition pathways generated by normal mode analysis (iModFit). It further supports that pre-activation involves major quaternary compaction of the ECD, and suggests that activation involves principally a reorganization of a ‘central gating region’ involving a contraction of the ECD β-sandwich and the tilt of the channel lining M2 helix.
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Affiliation(s)
- Solène N Lefebvre
- Institut Pasteur, Université de Paris, CNRS UMR 3571,Channel-Receptors Unit, Paris, France.,Sorbonne Université, Collège doctoral, Paris, France
| | - Antoine Taly
- Institut de Biologie Physico-chimique, Fondation Edmond de Rothschild, PSL Research University, Paris, France.,Laboratoire de Biochimie Théorique, CNRS, Université de Paris, UPR 9080, Paris, France
| | - Anaïs Menny
- Institut Pasteur, Université de Paris, CNRS UMR 3571,Channel-Receptors Unit, Paris, France.,Sorbonne Université, Collège doctoral, Paris, France
| | - Karima Medjebeur
- Institut Pasteur, Université de Paris, CNRS UMR 3571,Channel-Receptors Unit, Paris, France
| | - Pierre-Jean Corringer
- Institut Pasteur, Université de Paris, CNRS UMR 3571,Channel-Receptors Unit, Paris, France
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13
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Lycksell M, Rovšnik U, Bergh C, Johansen NT, Martel A, Porcar L, Arleth L, Howard RJ, Lindahl E. Probing solution structure of the pentameric ligand-gated ion channel GLIC by small-angle neutron scattering. Proc Natl Acad Sci U S A 2021; 118:e2108006118. [PMID: 34504004 PMCID: PMC8449418 DOI: 10.1073/pnas.2108006118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2021] [Indexed: 02/03/2023] Open
Abstract
Pentameric ligand-gated ion channels undergo subtle conformational cycling to control electrochemical signal transduction in many kingdoms of life. Several crystal structures have now been reported in this family, but the functional relevance of such models remains unclear. Here, we used small-angle neutron scattering (SANS) to probe ambient solution-phase properties of the pH-gated bacterial ion channel GLIC under resting and activating conditions. Data collection was optimized by inline paused-flow size-exclusion chromatography, and exchanging into deuterated detergent to hide the micelle contribution. Resting-state GLIC was the best-fit crystal structure to SANS curves, with no evidence for divergent mechanisms. Moreover, enhanced-sampling molecular-dynamics simulations enabled differential modeling in resting versus activating conditions, with the latter corresponding to an intermediate ensemble of both the extracellular and transmembrane domains. This work demonstrates state-dependent changes in a pentameric ion channel by SANS, an increasingly accessible method for macromolecular characterization with the coming generation of neutron sources.
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Affiliation(s)
- Marie Lycksell
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Urška Rovšnik
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Cathrine Bergh
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, 10044 Stockholm, Sweden
| | - Nicolai T Johansen
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Anne Martel
- Institut Laue-Langevin, 38042 Grenoble, France
| | | | - Lise Arleth
- Structural Biophysics, X-ray and Neutron Science, The Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Rebecca J Howard
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 10691 Stockholm, Sweden
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, 10691 Stockholm, Sweden;
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, 10044 Stockholm, Sweden
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14
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Rovšnik U, Zhuang Y, Forsberg BO, Carroni M, Yvonnesdotter L, Howard RJ, Lindahl E. Dynamic closed states of a ligand-gated ion channel captured by cryo-EM and simulations. Life Sci Alliance 2021; 4:e202101011. [PMID: 34210687 PMCID: PMC8326787 DOI: 10.26508/lsa.202101011] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 11/25/2022] Open
Abstract
Ligand-gated ion channels are critical mediators of electrochemical signal transduction across evolution. Biophysical and pharmacological characterization of these receptor proteins relies on high-quality structures in multiple, subtly distinct functional states. However, structural data in this family remain limited, particularly for resting and intermediate states on the activation pathway. Here, we report cryo-electron microscopy (cryo-EM) structures of the proton-activated Gloeobacter violaceus ligand-gated ion channel (GLIC) under three pH conditions. Decreased pH was associated with improved resolution and side chain rearrangements at the subunit/domain interface, particularly involving functionally important residues in the β1-β2 and M2-M3 loops. Molecular dynamics simulations substantiated flexibility in the closed-channel extracellular domains relative to the transmembrane ones and supported electrostatic remodeling around E35 and E243 in proton-induced gating. Exploration of secondary cryo-EM classes further indicated a low-pH population with an expanded pore. These results allow us to define distinct protonation and activation steps in pH-stimulated conformational cycling in GLIC, including interfacial rearrangements largely conserved in the pentameric channel family.
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Affiliation(s)
- Urška Rovšnik
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Yuxuan Zhuang
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Björn O Forsberg
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Marta Carroni
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Linnea Yvonnesdotter
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Rebecca J Howard
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden
- Department of Applied Physics, Science for Life Laboratory, Kungliga Tekniska Högskolan Royal Institute of Technology, Solna, Sweden
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15
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Elephants in the Dark: Insights and Incongruities in Pentameric Ligand-gated Ion Channel Models. J Mol Biol 2021; 433:167128. [PMID: 34224751 DOI: 10.1016/j.jmb.2021.167128] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 02/06/2023]
Abstract
The superfamily of pentameric ligand-gated ion channels (pLGICs) comprises key players in electrochemical signal transduction across evolution, including historic model systems for receptor allostery and targets for drug development. Accordingly, structural studies of these channels have steadily increased, and now approach 250 depositions in the protein data bank. This review contextualizes currently available structures in the pLGIC family, focusing on morphology, ligand binding, and gating in three model subfamilies: the prokaryotic channel GLIC, the cation-selective nicotinic acetylcholine receptor, and the anion-selective glycine receptor. Common themes include the challenging process of capturing and annotating channels in distinct functional states; partially conserved gating mechanisms, including remodeling at the extracellular/transmembrane-domain interface; and diversity beyond the protein level, arising from posttranslational modifications, ligands, lipids, and signaling partners. Interpreting pLGIC structures can be compared to describing an elephant in the dark, relying on touch alone to comprehend the many parts of a monumental beast: each structure represents a snapshot in time under specific experimental conditions, which must be integrated with further structure, function, and simulations data to build a comprehensive model, and understand how one channel may fundamentally differ from another.
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16
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Wilson MA, Pohorille A. Electrophysiological Properties from Computations at a Single Voltage: Testing Theory with Stochastic Simulations. ENTROPY 2021; 23:e23050571. [PMID: 34066581 PMCID: PMC8148522 DOI: 10.3390/e23050571] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 04/24/2021] [Accepted: 04/28/2021] [Indexed: 12/13/2022]
Abstract
We use stochastic simulations to investigate the performance of two recently developed methods for calculating the free energy profiles of ion channels and their electrophysiological properties, such as current–voltage dependence and reversal potential, from molecular dynamics simulations at a single applied voltage. These methods require neither knowledge of the diffusivity nor simulations at multiple voltages, which greatly reduces the computational effort required to probe the electrophysiological properties of ion channels. They can be used to determine the free energy profiles from either forward or backward one-sided properties of ions in the channel, such as ion fluxes, density profiles, committor probabilities, or from their two-sided combination. By generating large sets of stochastic trajectories, which are individually designed to mimic the molecular dynamics crossing statistics of models of channels of trichotoxin, p7 from hepatitis C and a bacterial homolog of the pentameric ligand-gated ion channel, GLIC, we find that the free energy profiles obtained from stochastic simulations corresponding to molecular dynamics simulations of even a modest length are burdened with statistical errors of only 0.3 kcal/mol. Even with many crossing events, applying two-sided formulas substantially reduces statistical errors compared to one-sided formulas. With a properly chosen reference voltage, the current–voltage curves can be reproduced with good accuracy from simulations at a single voltage in a range extending for over 200 mV. If possible, the reference voltages should be chosen not simply to drive a large current in one direction, but to observe crossing events in both directions.
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Affiliation(s)
- Michael A. Wilson
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA;
- SETI Institute, 189 Bernardo Ave, Suite 200, Mountain View, CA 94043, USA
| | - Andrew Pohorille
- Exobiology Branch, MS 239-4, NASA Ames Research Center, Moffett Field, CA 94035, USA;
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94132, USA
- Correspondence: ; Tel.: +1-650-604-5759
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17
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Maldonado-Hernández R, Quesada O, Colón-Sáez JO, Lasalde-Dominicci JA. Sequential purification and characterization of Torpedo californica nAChR-DC supplemented with CHS for high-resolution crystallization studies. Anal Biochem 2020; 610:113887. [PMID: 32763308 DOI: 10.1016/j.ab.2020.113887] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/14/2020] [Accepted: 07/22/2020] [Indexed: 01/26/2023]
Abstract
Over the past 10 years we have been developing a multi-attribute analytical platform that allows for the preparation of milligram amounts of functional, high-pure, and stable Torpedo (muscle-type) nAChR detergent complexes for crystallization purpose. In the present work, we have been able to significantly improve and optimize the purity and yield of nicotinic acetylcholine receptors in detergent complexes (nAChR-DC) without compromising stability and functionality. We implemented new methods in the process, such as analysis and rapid production of samples for future crystallization preparations. Native nAChR was extracted from the electric organ of Torpedo californica using the lipid-like detergent LysoFos Choline 16 (LFC-16), followed by three consecutive steps of chromatography purification. We evaluated the effect of cholesteryl hemisuccinate (CHS) supplementation during the affinity purification steps of nAChR-LFC-16 in terms of receptor secondary structure, stability and functionality. CHS produced significant changes in the degree of β-secondary structure, these changes compromise the diffusion of the nAChR-LFC-16 in lipid cubic phase. The behavior was reversed by Methyl-β-Cyclodextrin treatment. Also, CHS decreased acetylcholine evoked currents of Xenopus leavis oocyte injected with nAChR-LFC-16 in a concentration-dependent manner. Methyl-β-Cyclodextrin treatment do not reverse functionality, however column delipidation produced a functional protein similar to nAChR-LFC-16 without CHS treatment.
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Affiliation(s)
- Rafael Maldonado-Hernández
- Department of the Biology, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico; Molecular Sciences Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Orestes Quesada
- Department of Physical Sciences, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico; Molecular Sciences Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - José O Colón-Sáez
- Pharmaceutical Sciences, University of Puerto Rico Medical Science Campus, Puerto Rico
| | - José A Lasalde-Dominicci
- Department of the Biology, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico; Molecular Sciences Research Center, University of Puerto Rico, San Juan, Puerto Rico; Institute of Neurobiology, University of Puerto Rico Medical Science Campus, Puerto Rico.
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18
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Faulkner C, de Leeuw NH. In silico studies of the interactions between propofol and fentanyl using Gaussian accelerated molecular dynamics. J Biomol Struct Dyn 2020; 40:312-324. [PMID: 32909527 DOI: 10.1080/07391102.2020.1814415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Fentanyl is a potent opioid analgesic, which for decades has been used routinely in surgical and therapeutic applications. In addition to its analgesic properties, fentanyl also possesses anesthetic properties, which are not well understood. Fentanyl is used in the general anesthesia process to induce and maintain anesthesia in combination with the general anesthetic propofol, which fentanyl is known to potentiate. As the atomic-level mechanism behind the potentiation of propofol is unclear, we have used classical molecular dynamics simulations to study the interactions of these drugs with the Gloeobacter violaceus ion channel (GLIC). This ion channel has been identified as a target for many anesthetic drugs. We identified multiple binding sites using flooding style and Gaussian accelerated molecular dynamics (GaMD) simulations, showing fentanyl acting as a stabiliser that holds propofol within binding sites. Our extensive GaMD simulations were also able to show the pathway by which propofol blocks the channel pore, which has previously been suggested as a mechanism for ion channel modulation. General anesthesia is a multi-drug process and this study provides the first insight into the interactions between two different drugs in the anesthesia process in a relevant biological environment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Nora H de Leeuw
- School of Chemistry, Cardiff University, Cardiff, UK.,School of Chemistry, University of Leeds, Leeds, UK
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19
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Fourati Z, Sauguet L, Delarue M. Structural evidence for the binding of monocarboxylates and dicarboxylates at pharmacologically relevant extracellular sites of a pentameric ligand-gated ion channel. Acta Crystallogr D Struct Biol 2020; 76:668-675. [PMID: 32627739 PMCID: PMC7336382 DOI: 10.1107/s205979832000772x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 06/05/2020] [Indexed: 11/21/2022] Open
Abstract
GLIC is a bacterial homologue of the pentameric ligand-gated ion channels (pLGICs) that mediate the fast chemical neurotransmission of nerve signalling in eukaryotes. Because the activation and allosteric modulation features are conserved among prokaryotic and eukaryotic pLGICs, GLIC is commonly used as a model to study the allosteric transition and structural pharmacology of pLGICs. It has previously been shown that GLIC is inhibited by some carboxylic acid derivatives. Here, experimental evidence for carboxylate binding to GLIC is provided by solving its X-ray structures with a series of monocarboxylate and dicarboxylate derivatives, and two carboxylate-binding sites are described: (i) the `intersubunit' site that partially overlaps the canonical pLGIC orthosteric site and (ii) the `intrasubunit' vestibular site, which is only occupied by a subset of the described derivatives. While the intersubunit site is widely conserved in all pLGICs, the intrasubunit site is only conserved in cationic eukaryotic pLGICs. This study sheds light on the importance of these two extracellular modulation sites as potential drug targets in pLGICs.
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Affiliation(s)
- Zaineb Fourati
- Unité Dynamique Structurale des Macromolécules, Institut Pasteur, 25 Rue du Docteur Roux, F-75015 Paris, France
- Centre National de la Recherche Scientifique, CNRS UMR3528, Biologie Structurale des Processus Cellulaires et Maladies Infectieuses, 25 Rue du Docteur Roux, F-75015 Paris, France
| | - Ludovic Sauguet
- Unité Dynamique Structurale des Macromolécules, Institut Pasteur, 25 Rue du Docteur Roux, F-75015 Paris, France
- Centre National de la Recherche Scientifique, CNRS UMR3528, Biologie Structurale des Processus Cellulaires et Maladies Infectieuses, 25 Rue du Docteur Roux, F-75015 Paris, France
| | - Marc Delarue
- Unité Dynamique Structurale des Macromolécules, Institut Pasteur, 25 Rue du Docteur Roux, F-75015 Paris, France
- Centre National de la Recherche Scientifique, CNRS UMR3528, Biologie Structurale des Processus Cellulaires et Maladies Infectieuses, 25 Rue du Docteur Roux, F-75015 Paris, France
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20
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Structural basis for allosteric transitions of a multidomain pentameric ligand-gated ion channel. Proc Natl Acad Sci U S A 2020; 117:13437-13446. [PMID: 32482881 DOI: 10.1073/pnas.1922701117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) are allosteric receptors that mediate rapid electrochemical signal transduction in the animal nervous system through the opening of an ion pore upon binding of neurotransmitters. Orthologs have been found and characterized in prokaryotes and they display highly similar structure-function relationships to eukaryotic pLGICs; however, they often encode greater architectural diversity involving additional amino-terminal domains (NTDs). Here we report structural, functional, and normal-mode analysis of two conformational states of a multidomain pLGIC, called DeCLIC, from a Desulfofustis deltaproteobacterium, including a periplasmic NTD fused to the conventional ligand-binding domain (LBD). X-ray structure determination revealed an NTD consisting of two jelly-roll domains interacting across each subunit interface. Binding of Ca2+ at the LBD subunit interface was associated with a closed transmembrane pore, with resolved monovalent cations intracellular to the hydrophobic gate. Accordingly, DeCLIC-injected oocytes conducted currents only upon depletion of extracellular Ca2+; these were insensitive to quaternary ammonium block. Furthermore, DeCLIC crystallized in the absence of Ca2+ with a wide-open pore and remodeled periplasmic domains, including increased contacts between the NTD and classic LBD agonist-binding sites. Functional, structural, and dynamical properties of DeCLIC paralleled those of sTeLIC, a pLGIC from another symbiotic prokaryote. Based on these DeCLIC structures, we would reclassify the previous structure of bacterial ELIC (the first high-resolution structure of a pLGIC) as a "locally closed" conformation. Taken together, structures of DeCLIC in multiple conformations illustrate dramatic conformational state transitions and diverse regulatory mechanisms available to ion channels in pLGICs, particularly involving Ca2+ modulation and periplasmic NTDs.
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21
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Sanchis-Juan A, Hasenahuer MA, Baker JA, McTague A, Barwick K, Kurian MA, Duarte ST, Carss KJ, Thornton J, Raymond FL. Structural analysis of pathogenic missense mutations in GABRA2 and identification of a novel de novo variant in the desensitization gate. Mol Genet Genomic Med 2020; 8:e1106. [PMID: 32347641 PMCID: PMC7336760 DOI: 10.1002/mgg3.1106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/29/2019] [Accepted: 12/10/2019] [Indexed: 12/19/2022] Open
Abstract
Background Cys‐loop receptors control neuronal excitability in the brain and their dysfunction results in numerous neurological disorders. Recently, six missense variants in GABRA2, a member of this family, have been associated with early infantile epileptic encephalopathy (EIEE). We identified a novel de novo missense variant in GABRA2 in a patient with EIEE and performed protein structural analysis of the seven variants. Methods The novel variant was identified by trio whole‐genome sequencing. We performed protein structural analysis of the seven variants, and compared them to previously reported pathogenic mutations at equivalent positions in other Cys‐loop receptors. Additionally, we studied the distribution of disease‐associated variants in the transmembrane helices of these proteins. Results The seven variants are in the transmembrane domain, either close to the desensitization gate, the activation gate, or in inter‐subunit interfaces. Six of them have pathogenic mutations at equivalent positions in other Cys‐loop receptors, emphasizing the importance of these residues. Also, pathogenic mutations are more common in the pore‐lining helix, consistent with this region being highly constrained for variation in control populations. Conclusion Our study reports a novel pathogenic variant in GABRA2, characterizes the regions where pathogenic mutations are in the transmembrane helices, and underscores the value of considering sequence, evolutionary, and structural information as a strategy for variant interpretation of novel missense mutations.
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Affiliation(s)
- Alba Sanchis-Juan
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Cambridge, UK.,NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Marcia A Hasenahuer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.,Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - James A Baker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Amy McTague
- Developmental Neurosciences, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Katy Barwick
- Developmental Neurosciences, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Manju A Kurian
- Developmental Neurosciences, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Sofia T Duarte
- Hospital Dona Estefânia, Centro Hospitalar de Lisboa Central, Lisbon, Portugal
| | | | - Keren J Carss
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Cambridge, UK.,NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Janet Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - F Lucy Raymond
- NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK.,Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
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22
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Progress in nicotinic receptor structural biology. Neuropharmacology 2020; 171:108086. [PMID: 32272141 DOI: 10.1016/j.neuropharm.2020.108086] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/31/2020] [Indexed: 02/07/2023]
Abstract
Here we begin by briefly reviewing landmark structural studies on the nicotinic acetylcholine receptor. We highlight challenges that had to be overcome to push through resolution barriers, then focus on what has been gleaned in the past few years from crystallographic and single particle cryo-EM studies of different nicotinic receptor subunit assemblies and ligand complexes. We discuss insights into ligand recognition, ion permeation, and allosteric gating. We then highlight some foundational aspects of nicotinic receptor structural biology that remain unresolved and are areas ripe for future exploration. This article is part of the special issue on 'Contemporary Advances in Nicotine Neuropharmacology'.
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23
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Cryo-EM structures of a lipid-sensitive pentameric ligand-gated ion channel embedded in a phosphatidylcholine-only bilayer. Proc Natl Acad Sci U S A 2020; 117:1788-1798. [PMID: 31911476 PMCID: PMC6983364 DOI: 10.1073/pnas.1906823117] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The lipid dependence of the nicotinic acetylcholine receptor from the Torpedo electric organ has long been recognized, and one of the most consistent experimental observations is that, when reconstituted in membranes formed by zwitterionic phospholipids alone, exposure to agonist fails to elicit ion-flux activity. More recently, it has been suggested that the bacterial homolog ELIC (Erwinia chrysanthemi ligand-gated ion channel) has a similar lipid sensitivity. As a first step toward the elucidation of the structural basis of this phenomenon, we solved the structures of ELIC embedded in palmitoyl-oleoyl-phosphatidylcholine- (POPC-) only nanodiscs in both the unliganded (4.1-Å resolution) and agonist-bound (3.3 Å) states using single-particle cryoelectron microscopy. Comparison of the two structural models revealed that the largest differences occur at the level of loop C-at the agonist-binding sites-and the loops at the interface between the extracellular and transmembrane domains (ECD and TMD, respectively). On the other hand, the transmembrane pore is occluded in a remarkably similar manner in both structures. A straightforward interpretation of these findings is that POPC-only membranes frustrate the ECD-TMD coupling in such a way that the "conformational wave" of liganded-receptor gating takes place in the ECD and the interfacial M2-M3 linker but fails to penetrate the membrane and propagate into the TMD. Furthermore, analysis of the structural models and molecular simulations suggested that the higher affinity for agonists characteristic of the open- and desensitized-channel conformations results, at least in part, from the tighter confinement of the ligand to its binding site; this limits the ligand's fluctuations, and thus delays its escape into bulk solvent.
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24
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Dämgen MA, Biggin PC. A Refined Open State of the Glycine Receptor Obtained via Molecular Dynamics Simulations. Structure 2020; 28:130-139.e2. [PMID: 31753620 PMCID: PMC6945115 DOI: 10.1016/j.str.2019.10.019] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 10/11/2019] [Accepted: 10/30/2019] [Indexed: 01/22/2023]
Abstract
Pentameric ligand-gated ion channels are key players in mediating fast neurotransmission. Glycine receptors are chloride-selective members of this receptor family that mediate inhibitory synaptic transmission and are implicated in neurological disorders including autism and hyperekplexia. They have been structurally characterized by both X-ray crystallography and cryoelectron microscopy (cryo-EM) studies, with the latter giving rise to what was proposed as a possible open state. However, recent work has questioned the physiological relevance of this open state structure, since it rapidly collapses in molecular dynamics simulations. Here, we show that the collapse can be avoided by a careful equilibration protocol that reconciles the more problematic regions of the original density map and gives a stable open state that shows frequent selective chloride permeation. The protocol developed in this work provides a means to refine open-like structures of the whole pentameric ligand-gated ion channel superfamily and reconciles the previous issues with the cryo-EM structure.
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Affiliation(s)
- Marc A Dämgen
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Philip C Biggin
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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25
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Faulkner C, Plant DF, de Leeuw NH. Modulation of the Gloeobacter violaceus Ion Channel by Fentanyl: A Molecular Dynamics Study. Biochemistry 2019; 58:4804-4808. [PMID: 31718178 DOI: 10.1021/acs.biochem.9b00881] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fentanyl is an opioid analgesic, which is routinely used in general surgery to suppress the sensation of pain and as the analgesic component in the induction and maintenance of anesthesia. Fentanyl is also used as the main component to induce anesthesia and as a potentiator to the general anesthetic propofol. The mechanism by which fentanyl induces its anesthetic action is still unclear, and we have therefore employed fully atomistic molecular dynamics simulations to probe this process by simulating the interactions of fentanyl with the Gloeobacter violaceus ligand-gated ion channel (GLIC). In this paper, we identify multiple extracellular fentanyl binding sites, which are different from the transmembrane general anesthetic binding sites observed for propofol and other general anesthetics. Our simulations identify a novel fentanyl binding site within the GLIC that results in conformational changes that inhibit conduction through the channel.
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Affiliation(s)
- Christopher Faulkner
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff CF10 3AT , United Kingdom
| | - David F Plant
- Atomic Weapons Establishment (AWE) , Aldermaston, Reading RG7 4PR , United Kingdom
| | - Nora H de Leeuw
- School of Chemistry , Cardiff University , Main Building, Park Place , Cardiff CF10 3AT , United Kingdom
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26
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Abstract
Recently, two groups of rhodopsin genes were identified in large double-stranded DNA viruses. The structure and function of viral rhodopsins are unknown. We present functional characterization and high-resolution structure of an Organic Lake Phycodnavirus rhodopsin II (OLPVRII) of group 2. It forms a pentamer, with a symmetrical, bottle-like central channel with the narrow vestibule in the cytoplasmic part covered by a ring of 5 arginines, whereas 5 phenylalanines form a hydrophobic barrier in its exit. The proton donor E42 is placed in the helix B. The structure is unique among the known rhodopsins. Structural and functional data and molecular dynamics suggest that OLPVRII might be a light-gated pentameric ion channel analogous to pentameric ligand-gated ion channels, however, future patch clamp experiments should prove this directly. The data shed light on a fundamentally distinct branch of rhodopsins and may contribute to the understanding of virus-host interactions in ecologically important marine protists.
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27
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Fourati Z, Howard RJ, Heusser SA, Hu H, Ruza RR, Sauguet L, Lindahl E, Delarue M. Structural Basis for a Bimodal Allosteric Mechanism of General Anesthetic Modulation in Pentameric Ligand-Gated Ion Channels. Cell Rep 2019; 23:993-1004. [PMID: 29694907 DOI: 10.1016/j.celrep.2018.03.108] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 02/02/2018] [Accepted: 03/23/2018] [Indexed: 10/17/2022] Open
Abstract
Ion channel modulation by general anesthetics is a vital pharmacological process with implications for receptor biophysics and drug development. Functional studies have implicated conserved sites of both potentiation and inhibition in pentameric ligand-gated ion channels, but a detailed structural mechanism for these bimodal effects is lacking. The prokaryotic model protein GLIC recapitulates anesthetic modulation of human ion channels, and it is accessible to structure determination in both apparent open and closed states. Here, we report ten X-ray structures and electrophysiological characterization of GLIC variants in the presence and absence of general anesthetics, including the surgical agent propofol. We show that general anesthetics can allosterically favor closed channels by binding in the pore or favor open channels via various subsites in the transmembrane domain. Our results support an integrated, multi-site mechanism for allosteric modulation, and they provide atomic details of both potentiation and inhibition by one of the most common general anesthetics.
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Affiliation(s)
- Zaineb Fourati
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 75015 Paris, France
| | - Rebecca J Howard
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, 17165 Solna, Sweden
| | - Stephanie A Heusser
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, 17165 Solna, Sweden
| | - Haidai Hu
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 75015 Paris, France; Sorbonne Universités, UPMC University Paris 6, 75005 Paris, France
| | - Reinis R Ruza
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 75015 Paris, France
| | - Ludovic Sauguet
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 75015 Paris, France
| | - Erik Lindahl
- Department of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, 17165 Solna, Sweden; Swedish e-Science Research Center, KTH Royal Institute of Technology, 11428 Stockholm, Sweden
| | - Marc Delarue
- Unit of Structural Dynamics of Macromolecules, Institut Pasteur and UMR 3528 du CNRS, 75015 Paris, France.
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28
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Duncan AL, Song W, Sansom MSP. Lipid-Dependent Regulation of Ion Channels and G Protein-Coupled Receptors: Insights from Structures and Simulations. Annu Rev Pharmacol Toxicol 2019; 60:31-50. [PMID: 31506010 DOI: 10.1146/annurev-pharmtox-010919-023411] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ion channels and G protein-coupled receptors (GPCRs) are regulated by lipids in their membrane environment. Structural studies combined with biophysical and molecular simulation investigations reveal interaction sites for specific lipids on membrane protein structures. For K channels, PIP2 plays a key role in regulating Kv and Kir channels. Likewise, several recent cryo-EM structures of TRP channels have revealed bound lipids, including PIP2 and cholesterol. Among the pentameric ligand-gated ion channel family, structural and biophysical studies suggest the M4 TM helix may act as a lipid sensor, e.g., forming part of the binding sites for neurosteroids on the GABAA receptor. Structures of GPCRs have revealed multiple cholesterol sites, which may modulate both receptor dynamics and receptor oligomerization. PIP2 also interacts with GPCRs and may modulate their interactions with G proteins. Overall, it is evident that multiple lipid binding sites exist on channels and receptors that modulate their function allosterically and are potential druggable sites.
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Affiliation(s)
- Anna L Duncan
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom;
| | - Wanling Song
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom;
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom;
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29
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Gharpure A, Teng J, Zhuang Y, Noviello CM, Walsh RM, Cabuco R, Howard RJ, Zaveri NT, Lindahl E, Hibbs RE. Agonist Selectivity and Ion Permeation in the α3β4 Ganglionic Nicotinic Receptor. Neuron 2019; 104:501-511.e6. [PMID: 31488329 DOI: 10.1016/j.neuron.2019.07.030] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/01/2019] [Accepted: 07/25/2019] [Indexed: 12/16/2022]
Abstract
Nicotinic acetylcholine receptors are pentameric ion channels that mediate fast chemical neurotransmission. The α3β4 nicotinic receptor subtype forms the principal relay between the central and peripheral nervous systems in the autonomic ganglia. This receptor is also expressed focally in brain areas that affect reward circuits and addiction. Here, we present structures of the α3β4 nicotinic receptor in lipidic and detergent environments, using functional reconstitution to define lipids appropriate for structural analysis. The structures of the receptor in complex with nicotine, as well as the α3β4-selective ligand AT-1001, complemented by molecular dynamics, suggest principles of agonist selectivity. The structures further reveal much of the architecture of the intracellular domain, where mutagenesis experiments and simulations define residues governing ion conductance.
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Affiliation(s)
- Anant Gharpure
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jinfeng Teng
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yuxuan Zhuang
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna 17121, Sweden
| | - Colleen M Noviello
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Richard M Walsh
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rico Cabuco
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rebecca J Howard
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna 17121, Sweden
| | | | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna 17121, Sweden; Department of Applied Physics, Swedish e-Science Research Center, KTH Royal Institute of Technology, Solna 17121, Sweden
| | - Ryan E Hibbs
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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30
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Sugasawa Y, Bracamontes JR, Krishnan K, Covey DF, Reichert DE, Akk G, Chen Q, Tang P, Evers AS, Cheng WWL. The molecular determinants of neurosteroid binding in the GABA(A) receptor. J Steroid Biochem Mol Biol 2019; 192:105383. [PMID: 31150831 PMCID: PMC6708749 DOI: 10.1016/j.jsbmb.2019.105383] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/11/2019] [Accepted: 05/26/2019] [Indexed: 10/26/2022]
Abstract
Neurosteroids positively modulate GABA-A receptor (GABAAR) channel activity by binding to a transmembrane domain intersubunit site. Understanding the interactions in this site that determine neurosteroid binding and its effect is essential for the design of neurosteroid-based therapeutics. Using photo-affinity labeling and an ELIC-α1GABAAR chimera, we investigated the impact of mutations (Q242L, Q242W and W246L) within the intersubunit site on neurosteroid binding. These mutations, which abolish the thermal stabilizing effect of allopregnanolone on the chimera, reduce neither photolabeling within the intersubunit site nor competitive prevention of labeling by allopregnanolone. Instead, these mutations change the orientation of neurosteroid photolabeling. Molecular docking of allopregnanolone in WT and Q242W receptors confirms that the mutation favors re-orientation of allopregnanolone within the binding pocket. Collectively, the data indicate that mutations at Gln242 or Trp246 that eliminate neurosteroid effects do not eliminate neurosteroid binding within the intersubunit site, but significantly alter the preferred orientation of the neurosteroid within the site. The interactions formed by Gln242 and Trp246 within this pocket play a vital role in determining the orientation of the neurosteroid that may be necessary for its functional effect.
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Affiliation(s)
- Yusuke Sugasawa
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO 63110, USA.
| | - John R Bracamontes
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO 63110, USA.
| | - Kathiresan Krishnan
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO 63110, USA.
| | - Douglas F Covey
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO 63110, USA; Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO 63110, USA; Department of Psychiatry, Washington University in St. Louis, St. Louis, MO 63110, USA; Taylor Family Institute for Innovative Psychiatric Research, Washington University in St. Louis, St. Louis, MO 63110, USA.
| | - David E Reichert
- Department of Radiology, Washington University in St. Louis, St. Louis, MO 63110, USA; Taylor Family Institute for Innovative Psychiatric Research, Washington University in St. Louis, St. Louis, MO 63110, USA.
| | - Gustav Akk
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO 63110, USA; Taylor Family Institute for Innovative Psychiatric Research, Washington University in St. Louis, St. Louis, MO 63110, USA.
| | - Qiang Chen
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
| | - Pei Tang
- Department of Anesthesiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA; Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA.
| | - Alex S Evers
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO 63110, USA; Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO 63110, USA; Taylor Family Institute for Innovative Psychiatric Research, Washington University in St. Louis, St. Louis, MO 63110, USA.
| | - Wayland W L Cheng
- Department of Anesthesiology, Washington University in St. Louis, St. Louis, MO 63110, USA.
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31
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Flood E, Boiteux C, Lev B, Vorobyov I, Allen TW. Atomistic Simulations of Membrane Ion Channel Conduction, Gating, and Modulation. Chem Rev 2019; 119:7737-7832. [DOI: 10.1021/acs.chemrev.8b00630] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Emelie Flood
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Céline Boiteux
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Bogdan Lev
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Igor Vorobyov
- Department of Physiology & Membrane Biology/Department of Pharmacology, University of California, Davis, 95616, United States
| | - Toby W. Allen
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
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32
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Crnjar A, Comitani F, Melis C, Molteni C. Mutagenesis computer experiments in pentameric ligand-gated ion channels: the role of simulation tools with different resolution. Interface Focus 2019; 9:20180067. [PMID: 31065340 PMCID: PMC6501341 DOI: 10.1098/rsfs.2018.0067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2019] [Indexed: 12/21/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) are an important class of widely expressed membrane neuroreceptors, which play a crucial role in fast synaptic communications and are involved in several neurological conditions. They are activated by the binding of neurotransmitters, which trigger the transmission of an electrical signal via facilitated ion flux. They can also be activated, inhibited or modulated by a number of drugs. Mutagenesis electrophysiology experiments, with natural or unnatural amino acids, have provided a large body of functional data that, together with emerging structural information from X-ray spectroscopy and cryo-electron microscopy, are helping unravel the complex working mechanisms of these neuroreceptors. Computer simulations are complementing these mutagenesis experiments, with insights at various levels of accuracy and resolution. Here, we review how a selection of computational tools, including first principles methods, classical molecular dynamics and enhanced sampling techniques, are contributing to construct a picture of how pLGICs function and can be pharmacologically targeted to treat the disorders they are responsible for.
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Affiliation(s)
- Alessandro Crnjar
- King’s College London, Department of Physics, Strand, London WC2R 2LS, UK
| | - Federico Comitani
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Claudio Melis
- Universitá degli Studi di Cagliari, Complesso Universitario di Monserrato, Dipartimento di Fisica, S.P. Monserrato-Sestu Km 0,700, Monserrato (CA) 09042, Italy
| | - Carla Molteni
- King’s College London, Department of Physics, Strand, London WC2R 2LS, UK
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33
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Indexed: 12/23/2022]
Abstract
Biological membranes are tricky to investigate. They are complex in terms of molecular composition and structure, functional over a wide range of time scales, and characterized by nonequilibrium conditions. Because of all of these features, simulations are a great technique to study biomembrane behavior. A significant part of the functional processes in biological membranes takes place at the molecular level; thus computer simulations are the method of choice to explore how their properties emerge from specific molecular features and how the interplay among the numerous molecules gives rise to function over spatial and time scales larger than the molecular ones. In this review, we focus on this broad theme. We discuss the current state-of-the-art of biomembrane simulations that, until now, have largely focused on a rather narrow picture of the complexity of the membranes. Given this, we also discuss the challenges that we should unravel in the foreseeable future. Numerous features such as the actin-cytoskeleton network, the glycocalyx network, and nonequilibrium transport under ATP-driven conditions have so far received very little attention; however, the potential of simulations to solve them would be exceptionally high. A major milestone for this research would be that one day we could say that computer simulations genuinely research biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Matti Javanainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy
of Sciences, Flemingovo naḿesti 542/2, 16610 Prague, Czech Republic
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Waldemar Kulig
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
| | - Ilpo Vattulainen
- Department
of Physics, University of
Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
- Computational
Physics Laboratory, Tampere University, P.O. Box 692, FI-33014 Tampere, Finland
- MEMPHYS-Center
for Biomembrane Physics
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34
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Harpole TJ, Grosman C. A Crucial Role for Side-Chain Conformation in the Versatile Charge Selectivity of Cys-Loop Receptors. Biophys J 2019; 116:1667-1681. [PMID: 31005237 PMCID: PMC6506641 DOI: 10.1016/j.bpj.2019.03.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 03/18/2019] [Accepted: 03/25/2019] [Indexed: 10/27/2022] Open
Abstract
Whether synaptic transmission is excitatory or inhibitory depends, to a large extent, on whether the ion channels that open upon binding the released neurotransmitter conduct cations or anions. The mechanistic basis of the opposite charge selectivities of Cys-loop receptors has only recently begun to emerge. It is now clear that ionized side chains-whether pore-facing or buried-in the first α-helical turn of the second transmembrane segments underlie this phenomenon and that the electrostatics of backbone atoms are not critically involved. Moreover, on the basis of electrophysiological observations, it has recently been suggested that not only the sign of charged side chains but also their conformation are crucial determinants of cation-anion selectivity. To challenge these ideas with the chemical and structural rigor that electrophysiological observations naturally lack, we performed molecular dynamics, Brownian dynamics, and electrostatics calculations of ion permeation. To this end, we used structural models of the open-channel conformation of the α1 glutamate-gated Cl- channel and the α1 glycine receptor. Our results provided full support to the notion that the conformation of charged sides chains matters for charge selectivity. Indeed, whereas some rotamers of the buried arginines at position 0' conferred high selectivity for anions, others supported the permeation of cations and anions at similar rates or even allowed the faster permeation of cations. Furthermore, we found that modeling glutamates at position -1' of the anion-selective α1 glycine receptor open-state structure-instead of the five native alanines-switches charge selectivity also in a conformation-dependent manner, with some glutamate rotamers being much more effective at conferring selectivity for cations than others. Regarding pore size, we found that the mere expansion of the pore has only a minimal impact on cation-anion selectivity. Overall, these results bring to light the previously unappreciated impact of side-chain conformation on charge selectivity in Cys-loop receptors.
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Affiliation(s)
- Tyler J Harpole
- Center for Biophysics and Quantitative Biology, Urbana, Illinois
| | - Claudio Grosman
- Center for Biophysics and Quantitative Biology, Urbana, Illinois; Department of Molecular and Integrative Physiology, Urbana, Illinois; Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, Illinois.
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35
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Abstract
The pentameric γ-aminobutyric acid type A receptors are ion channels activated by ligands, which intervene in the rapid inhibitory transmission in the mammalian CNS. Due to their rich pharmacology and therapeutic potential, it is essential to understand their structure and function thoroughly. This deep characterization was hampered by the lack of experimental structural information for many years. Thus, computational techniques have been extensively combined with experimental data, in order to undertake the study of γ-aminobutyric acid type A receptors and their interaction with drugs. Here, we review the exciting journey made to assess the structures of these receptors and outline major outcomes. Finally, we discuss the brand new structure of the α1β2γ2 subtype and the amazing advances it brings to the field.
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36
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Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel. Proc Natl Acad Sci U S A 2018; 115:E12172-E12181. [PMID: 30541892 DOI: 10.1073/pnas.1813378116] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The pentameric ligand-gated ion channel (pLGIC) from Gloeobacter violaceus (GLIC) has provided insightful structure-function views on the permeation process and the allosteric regulation of the pLGICs family. However, GLIC is activated by pH instead of a neurotransmitter and a clear picture for the gating transition driven by protons is still lacking. We used an electrostatics-based (finite difference Poisson-Boltzmann/Debye-Hückel) method to predict the acidities of all aspartic and glutamic residues in GLIC, both in its active and closed-channel states. Those residues with a predicted pKa close to the experimental pH50 were individually replaced by alanine and the resulting variant receptors were titrated by ATR/FTIR spectroscopy. E35, located in front of loop F far away from the orthosteric site, appears as the key proton sensor with a measured individual pKa at 5.8. In the GLIC open conformation, E35 is connected through a water-mediated hydrogen-bond network first to the highly conserved electrostatic triad R192-D122-D32 and then to Y197-Y119-K248, both located at the extracellular domain-transmembrane domain interface. The second triad controls a cluster of hydrophobic side chains from the M2-M3 loop that is remodeled during the gating transition. We solved 12 crystal structures of GLIC mutants, 6 of them being trapped in an agonist-bound but nonconductive conformation. Combined with previous data, this reveals two branches of a continuous network originating from E35 that reach, independently, the middle transmembrane region of two adjacent subunits. We conclude that GLIC's gating proceeds by making use of loop F, already known as an allosteric site in other pLGICs, instead of the classic orthosteric site.
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37
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Budelier MM, Cheng WWL, Chen ZW, Bracamontes JR, Sugasawa Y, Krishnan K, Mydock-McGrane L, Covey DF, Evers AS. Common binding sites for cholesterol and neurosteroids on a pentameric ligand-gated ion channel. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1864:128-136. [PMID: 30471426 DOI: 10.1016/j.bbalip.2018.11.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/20/2018] [Accepted: 11/16/2018] [Indexed: 11/16/2022]
Abstract
Cholesterol is an essential component of cell membranes, and is required for mammalian pentameric ligand-gated ion channel (pLGIC) function. Computational studies suggest direct interactions between cholesterol and pLGICs but experimental evidence identifying specific binding sites is limited. In this study, we mapped cholesterol binding to Gloeobacter ligand-gated ion channel (GLIC), a model pLGIC chosen for its high level of expression, existing crystal structure, and previous use as a prototypic pLGIC. Using two cholesterol analogue photolabeling reagents with the photoreactive moiety on opposite ends of the sterol, we identified two cholesterol binding sites: an intersubunit site between TM3 and TM1 of adjacent subunits and an intrasubunit site between TM1 and TM4. In both the inter- and intrasubunit sites, cholesterol is oriented such that the 3‑OH group points toward the center of the transmembrane domains rather than toward either the cytosolic or extracellular surfaces. We then compared this binding to that of the cholesterol metabolite, allopregnanolone, a neurosteroid that allosterically modulates pLGICs. The same binding pockets were identified for allopregnanolone and cholesterol, but the binding orientation of the two ligands was markedly different, with the 3‑OH group of allopregnanolone pointing to the intra- and extracellular termini of the transmembrane domains rather than to their centers. We also found that cholesterol increases, whereas allopregnanolone decreases the thermal stability of GLIC. These data indicate that cholesterol and neurosteroids bind to common hydrophobic pockets in the model pLGIC, GLIC, but that their effects depend on the orientation and specific molecular interactions unique to each sterol.
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Affiliation(s)
- Melissa M Budelier
- Department of Anesthesiology, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA
| | - Wayland W L Cheng
- Department of Anesthesiology, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA
| | - Zi-Wei Chen
- Department of Anesthesiology, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA; Taylor Family Institute for Innovative Psychiatric Research, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA
| | - John R Bracamontes
- Department of Anesthesiology, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA
| | - Yusuke Sugasawa
- Department of Anesthesiology, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA
| | - Kathiresan Krishnan
- Department of Developmental Biology, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA
| | - Laurel Mydock-McGrane
- Department of Developmental Biology, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA
| | - Douglas F Covey
- Department of Anesthesiology, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA; Taylor Family Institute for Innovative Psychiatric Research, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA; Department of Developmental Biology, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA; Department of Psychiatry, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA
| | - Alex S Evers
- Department of Anesthesiology, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA; Taylor Family Institute for Innovative Psychiatric Research, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA; Department of Developmental Biology, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA.
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38
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Chiodo L, Malliavin TE, Giuffrida S, Maragliano L, Cottone G. Closed-Locked and Apo-Resting State Structures of the Human α7 Nicotinic Receptor: A Computational Study. J Chem Inf Model 2018; 58:2278-2293. [PMID: 30359518 DOI: 10.1021/acs.jcim.8b00412] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nicotinic acetylcholine receptors, belonging to the Cys-loop superfamily of ligand-gated ion channels (LGICs), are membrane proteins present in neurons and at neuromuscular junctions. They are responsible for signal transmission, and their function is regulated by neurotransmitters, agonists, and antagonists drugs. A detailed knowledge of their conformational transition in response to ligand binding is critical to understanding the basis of ligand-receptor interaction, in view of new pharmacological approaches to control receptor activity. However, the scarcity of experimentally derived structures of human channels makes this perspective extremely challenging. To contribute overcoming this issue, we have recently reported structural models for the open and the desensitized states of the human α7 nicotinic receptor. Here, we provide all-atom structural models of the same receptor in two different nonconductive states. The first structure, built via homology modeling and relaxed with extensive Molecular Dynamics simulations, represents the receptor bound to the natural antagonist α-conotoxin ImI. After comparison with available experimental data and computational models of other eukaryotic LGICs, we deem it consistent with the "closed-locked" state. The second model, obtained with simulations from the spontaneous relaxation of the open, agonist-bound α7 structure after ligand removal, recapitulates the characteristics of the apo-resting state of the receptor. These results add to our previous work on the active and desensitized state conformations, contributing to the structural characterization of the conformational landscape of the human α7 receptor and suggesting benchmarks to discriminate among conformations found in experiments or in simulations of LGICs. In particular key interactions at the interface between the extracellular domain and the transmembrane domain are identified, that could be critical to the α7 receptor function.
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Affiliation(s)
- Letizia Chiodo
- Department of Engineering , Campus Bio-Medico University of Rome , Via Á. del Portillo 21 , 00128 Rome , Italy
| | - Thérèse E Malliavin
- Institut Pasteur and CNRS UMR 3528, Unité de Bioinformatique Structurale , 25-28 rue du Dr Roux , 75015 Paris , France.,Centre de Bioinformatique, Biostatistique et Biologie Intégrative , Institut Pasteur and CNRS USR 3756 , 25-28 rue du Dr Roux , 75015 Paris , France
| | - Sergio Giuffrida
- Department of Physics and Chemistry , University of Palermo , Viale delle Scienze Ed. 17 , 90128 Palermo , Italy
| | - Luca Maragliano
- Center for Synaptic Neuroscience and Technology (NSYN@UniGe) , Istituto Italiano di Tecnologia , Largo Rosanna Benzi, 10 , 16132 Genoa , Italy.,IRCCS Ospedale Policlinico San Martino , Largo Rosanna Benzi 10 , 16132 Genoa , Italy
| | - Grazia Cottone
- Department of Physics and Chemistry , University of Palermo , Viale delle Scienze Ed. 17 , 90128 Palermo , Italy
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39
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Cerdan AH, Martin NÉ, Cecchini M. An Ion-Permeable State of the Glycine Receptor Captured by Molecular Dynamics. Structure 2018; 26:1555-1562.e4. [DOI: 10.1016/j.str.2018.07.019] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 05/07/2018] [Accepted: 07/26/2018] [Indexed: 11/16/2022]
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40
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Allosteric potentiation of a ligand-gated ion channel is mediated by access to a deep membrane-facing cavity. Proc Natl Acad Sci U S A 2018; 115:10672-10677. [PMID: 30275330 PMCID: PMC6196478 DOI: 10.1073/pnas.1809650115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Theories of general anesthesia have shifted in focus from bulk lipid effects to specific interactions with membrane proteins. Target receptors include several subtypes of pentameric ligand-gated ion channels; however, structures of physiologically relevant proteins in this family have yet to define anesthetic binding at high resolution. Recent cocrystal structures of the bacterial protein GLIC provide snapshots of state-dependent binding sites for the common surgical agent propofol (PFL), offering a detailed model system for anesthetic modulation. Here, we combine molecular dynamics and oocyte electrophysiology to reveal differential motion and modulation upon modification of a transmembrane binding site within each GLIC subunit. WT channels exhibited net inhibition by PFL, and a contraction of the cavity away from the pore-lining M2 helix in the absence of drug. Conversely, in GLIC variants exhibiting net PFL potentiation, the cavity was persistently expanded and proximal to M2. Mutations designed to favor this deepened site enabled sensitivity even to subclinical concentrations of PFL, and a uniquely prolonged mode of potentiation evident up to ∼30 min after washout. Dependence of these prolonged effects on exposure time implicated the membrane as a reservoir for a lipid-accessible binding site. However, at the highest measured concentrations, potentiation appeared to be masked by an acute inhibitory effect, consistent with the presence of a discrete, water-accessible site of inhibition. These results support a multisite model of transmembrane allosteric modulation, including a possible link between lipid- and receptor-based theories that could inform the development of new anesthetics.
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41
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The Role of Proton Transport in Gating Current in a Voltage Gated Ion Channel, as Shown by Quantum Calculations. SENSORS 2018; 18:s18093143. [PMID: 30231473 PMCID: PMC6163810 DOI: 10.3390/s18093143] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/05/2018] [Accepted: 09/12/2018] [Indexed: 11/25/2022]
Abstract
Over two-thirds of a century ago, Hodgkin and Huxley proposed the existence of voltage gated ion channels (VGICs) to carry Na+ and K+ ions across the cell membrane to create the nerve impulse, in response to depolarization of the membrane. The channels have multiple physiological roles, and play a central role in a wide variety of diseases when they malfunction. The first channel structure was found by MacKinnon and coworkers in 1998. Subsequently, the structure of a number of VGICs was determined in the open (ion conducting) state. This type of channel consists of four voltage sensing domains (VSDs), each formed from four transmembrane (TM) segments, plus a pore domain through which ions move. Understanding the gating mechanism (how the channel opens and closes) requires structures. One TM segment (S4) has an arginine in every third position, with one such segment per domain. It is usually assumed that these arginines are all ionized, and in the resting state are held toward the intracellular side of the membrane by voltage across the membrane. They are assumed to move outward (extracellular direction) when released by depolarization of this voltage, producing a capacitive gating current and opening the channel. We suggest alternate interpretations of the evidence that led to these models. Measured gating current is the total charge displacement of all atoms in the VSD; we propose that the prime, but not sole, contributor is proton motion, not displacement of the charges on the arginines of S4. It is known that the VSD can conduct protons. Quantum calculations on the Kv1.2 potassium channel VSD show how; the key is the amphoteric nature of the arginine side chain, which allows it to transfer a proton. This appears to be the first time the arginine side chain has had its amphoteric character considered. We have calculated one such proton transfer in detail: this proton starts from a tyrosine that can ionize, transferring to the NE of the third arginine on S4; that arginine’s NH then transfers a proton to a glutamate. The backbone remains static. A mutation predicted to affect the proton transfer has been qualitatively confirmed experimentally, from the change in the gating current-voltage curve. The total charge displacement in going from a normal closed potential of −70 mV across the membrane to 0 mV (open), is calculated to be approximately consistent with measured values, although the error limits on the calculation require caution in interpretation.
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42
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Phulera S, Zhu H, Yu J, Claxton DP, Yoder N, Yoshioka C, Gouaux E. Cryo-EM structure of the benzodiazepine-sensitive α1β1γ2S tri-heteromeric GABA A receptor in complex with GABA. eLife 2018; 7:39383. [PMID: 30044221 PMCID: PMC6086659 DOI: 10.7554/elife.39383] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 07/24/2018] [Indexed: 12/12/2022] Open
Abstract
Fast inhibitory neurotransmission in the mammalian nervous system is largely mediated by GABAA receptors, chloride-selective members of the superfamily of pentameric Cys-loop receptors. Native GABAA receptors are heteromeric assemblies sensitive to many important drugs, from sedatives to anesthetics and anticonvulsant agents, with mutant forms of GABAA receptors implicated in multiple neurological diseases. Despite the profound importance of heteromeric GABAA receptors in neuroscience and medicine, they have proven recalcitrant to structure determination. Here we present the structure of a tri-heteromeric α1β1γ2SEM GABAA receptor in complex with GABA, determined by single particle cryo-EM at 3.1–3.8 Å resolution, elucidating molecular principles of receptor assembly and agonist binding. Remarkable N-linked glycosylation on the α1 subunit occludes the extracellular vestibule of the ion channel and is poised to modulate receptor assembly and perhaps ion channel gating. Our work provides a pathway to structural studies of heteromeric GABAA receptors and a framework for rational design of novel therapeutic agents.
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Affiliation(s)
- Swastik Phulera
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Hongtao Zhu
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Jie Yu
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Derek P Claxton
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Nate Yoder
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Craig Yoshioka
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Eric Gouaux
- Vollum Institute, Oregon Health and Science University, Portland, United States.,Howard Hughes Medical Institute, Oregon Health and Science University, Portland, United States
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43
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Gielen M, Corringer P. The dual-gate model for pentameric ligand-gated ion channels activation and desensitization. J Physiol 2018; 596:1873-1902. [PMID: 29484660 PMCID: PMC5978336 DOI: 10.1113/jp275100] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 01/17/2018] [Accepted: 01/17/2018] [Indexed: 12/15/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) mediate fast neurotransmission in the nervous system. Their dysfunction is associated with psychiatric, neurological and neurodegenerative disorders such as schizophrenia, epilepsy and Alzheimer's disease. Understanding their biophysical and pharmacological properties, at both the functional and the structural level, thus holds many therapeutic promises. In addition to their agonist-elicited activation, most pLGICs display another key allosteric property, namely desensitization, in which they enter a shut state refractory to activation upon sustained agonist binding. While the activation mechanisms of several pLGICs have been revealed at near-atomic resolution, the structural foundation of desensitization has long remained elusive. Recent structural and functional data now suggest that the activation and desensitization gates are distinct, and are located at both sides of the ion channel. Such a 'dual gate mechanism' accounts for the marked allosteric effects of channel blockers, a feature illustrated herein by theoretical kinetics simulations. Comparison with other classes of ligand- and voltage-gated ion channels shows that this dual gate mechanism emerges as a common theme for the desensitization and inactivation properties of structurally unrelated ion channels.
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Affiliation(s)
- Marc Gielen
- Channel Receptors UnitInstitut PasteurCNRS UMR 3571ParisFrance
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44
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Crystal structures of a pentameric ion channel gated by alkaline pH show a widely open pore and identify a cavity for modulation. Proc Natl Acad Sci U S A 2018; 115:E3959-E3968. [PMID: 29632192 DOI: 10.1073/pnas.1717700115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) constitute a widespread class of ion channels, present in archaea, bacteria, and eukaryotes. Upon binding of their agonists in the extracellular domain, the transmembrane pore opens, allowing ions to go through, via a gating mechanism that can be modulated by a number of drugs. Even though high-resolution structural information on pLGICs has increased in a spectacular way in recent years, both in bacterial and in eukaryotic systems, the structure of the open channel conformation of some intensively studied receptors whose structures are known in a nonactive (closed) form, such as Erwinia chrysanthemi pLGIC (ELIC), is still lacking. Here we describe a gammaproteobacterial pLGIC from an endo-symbiont of Tevnia jerichonana (sTeLIC), whose sequence is closely related to the pLGIC from ELIC with 28% identity. We provide an X-ray crystallographic structure at 2.3 Å in an active conformation, where the pore is found to be more open than any current conformation found for pLGICs. In addition, two charged restriction rings are present in the vestibule. Functional characterization shows sTeLIC to be a cationic channel activated at alkaline pH. It is inhibited by divalent cations, but not by quaternary ammonium ions, such as tetramethylammonium. Additionally, we found that sTeLIC is allosterically potentiated by aromatic amino acids Phe and Trp, as well as their derivatives, such as 4-bromo-cinnamate, whose cocrystal structure reveals a vestibular binding site equivalent to, but more deeply buried than, the one already described for benzodiazepines in ELIC.
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45
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Chen Q, Xu Y, Tang P. X-Ray Crystallographic Studies for Revealing Binding Sites of General Anesthetics in Pentameric Ligand-Gated Ion Channels. Methods Enzymol 2018; 603:21-47. [PMID: 29673527 DOI: 10.1016/bs.mie.2018.01.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
X-ray crystallography is a powerful tool in structural biology and can offer insight into structured-based understanding of general anesthetic action on various relevant molecular targets, including pentameric ligand-gated ion channels (pLGICs). In this chapter, we outline the procedures for expression and purification of pLGICs. Optimization of crystallization conditions, especially to achieve high-resolution structures of pLGICs bound with general anesthetics, is also presented. Case studies of pLGICs bound with the volatile general anesthetic isoflurane, 2-bromoethanol, and the intravenous general anesthetic ketamine are revisited.
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Affiliation(s)
- Qiang Chen
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Yan Xu
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Pei Tang
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.
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46
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Bondarenko V, Wells M, Xu Y, Tang P. Solution NMR Studies of Anesthetic Interactions with Ion Channels. Methods Enzymol 2018; 603:49-66. [PMID: 29673534 DOI: 10.1016/bs.mie.2018.01.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
NMR spectroscopy is one of the major tools to provide atomic resolution protein structural information. It has been used to elucidate the molecular details of interactions between anesthetics and ion channels, to identify anesthetic binding sites, and to characterize channel dynamics and changes introduced by anesthetics. In this chapter, we present solution NMR methods essential for investigating interactions between ion channels and general anesthetics, including both volatile and intravenous anesthetics. Case studies are provided with a focus on pentameric ligand-gated ion channels and the voltage-gated sodium channel NaChBac.
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Affiliation(s)
- Vasyl Bondarenko
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Marta Wells
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Yan Xu
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Pei Tang
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.
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47
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Basak S, Gicheru Y, Samanta A, Molugu SK, Huang W, Fuente MLD, Hughes T, Taylor DJ, Nieman MT, Moiseenkova-Bell V, Chakrapani S. Cryo-EM structure of 5-HT 3A receptor in its resting conformation. Nat Commun 2018; 9:514. [PMID: 29410406 PMCID: PMC5802770 DOI: 10.1038/s41467-018-02997-4] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/10/2018] [Indexed: 11/24/2022] Open
Abstract
Serotonin receptors (5-HT3AR) directly regulate gut movement, and drugs that inhibit 5-HT3AR function are used to control emetic reflexes associated with gastrointestinal pathologies and cancer therapies. The 5-HT3AR function involves a finely tuned orchestration of three domain movements that include the ligand-binding domain, the pore domain, and the intracellular domain. Here, we present the structure from the full-length 5-HT3AR channel in the apo-state determined by single-particle cryo-electron microscopy at a nominal resolution of 4.3 Å. In this conformation, the ligand-binding domain adopts a conformation reminiscent of the unliganded state with the pore domain captured in a closed conformation. In comparison to the 5-HT3AR crystal structure, the full-length channel in the apo-conformation adopts a more expanded conformation of all the three domains with a characteristic twist that is implicated in gating. Serotonin receptor (5-HT3AR), a pentameric ligand-gated ion channel, regulates numerous gastrointestinal functions. Here the authors provide a cryo-electron microscopic structure from the full-length 5-HT3AR in the apo-state which corresponds to a resting conformation of the channel.
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Affiliation(s)
- Sandip Basak
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Yvonne Gicheru
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Amrita Samanta
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Sudheer Kumar Molugu
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Maria la de Fuente
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Taylor Hughes
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Marvin T Nieman
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Vera Moiseenkova-Bell
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA.,Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Sudha Chakrapani
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA. .,Department of Neuroscience, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106-4970, USA.
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48
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Cheng WWL, Chen ZW, Bracamontes JR, Budelier MM, Krishnan K, Shin DJ, Wang C, Jiang X, Covey DF, Akk G, Evers AS. Mapping two neurosteroid-modulatory sites in the prototypic pentameric ligand-gated ion channel GLIC. J Biol Chem 2018; 293:3013-3027. [PMID: 29301936 DOI: 10.1074/jbc.ra117.000359] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 12/21/2017] [Indexed: 12/20/2022] Open
Abstract
Neurosteroids are endogenous sterols that potentiate or inhibit pentameric ligand-gated ion channels (pLGICs) and can be effective anesthetics, analgesics, or anti-epileptic drugs. The complex effects of neurosteroids on pLGICs suggest the presence of multiple binding sites in these receptors. Here, using a series of novel neurosteroid-photolabeling reagents combined with top-down and middle-down mass spectrometry, we have determined the stoichiometry, sites, and orientation of binding for 3α,5α-pregnane neurosteroids in the Gloeobacter ligand-gated ion channel (GLIC), a prototypic pLGIC. The neurosteroid-based reagents photolabeled two sites per GLIC subunit, both within the transmembrane domain; one site was an intrasubunit site, and the other was located in the interface between subunits. By using reagents with photoreactive groups positioned throughout the neurosteroid backbone, we precisely map the orientation of neurosteroid binding within each site. Amino acid substitutions introduced at either site altered neurosteroid modulation of GLIC channel activity, demonstrating the functional role of both sites. These results provide a detailed molecular model of multisite neurosteroid modulation of GLIC, which may be applicable to other mammalian pLGICs.
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Affiliation(s)
| | - Zi-Wei Chen
- Department of Anesthesiology; Taylor Family Institute for Innovative Psychiatric Research, Washington University, St. Louis, Missouri 63110
| | | | | | | | | | | | | | - Douglas F Covey
- Department of Anesthesiology; Taylor Family Institute for Innovative Psychiatric Research, Washington University, St. Louis, Missouri 63110; Department of Developmental Biology; Department of Psychiatry
| | - Gustav Akk
- Department of Anesthesiology; Taylor Family Institute for Innovative Psychiatric Research, Washington University, St. Louis, Missouri 63110
| | - Alex S Evers
- Department of Anesthesiology; Taylor Family Institute for Innovative Psychiatric Research, Washington University, St. Louis, Missouri 63110; Department of Developmental Biology.
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49
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Nemecz Á, Hu H, Fourati Z, Van Renterghem C, Delarue M, Corringer PJ. Full mutational mapping of titratable residues helps to identify proton-sensors involved in the control of channel gating in the Gloeobacter violaceus pentameric ligand-gated ion channel. PLoS Biol 2017; 15:e2004470. [PMID: 29281623 PMCID: PMC5760087 DOI: 10.1371/journal.pbio.2004470] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 01/09/2018] [Accepted: 12/04/2017] [Indexed: 11/19/2022] Open
Abstract
The Gloeobacter violaceus ligand-gated ion channel (GLIC) has been extensively studied by X-ray crystallography and other biophysical techniques. This provided key insights into the general gating mechanism of pentameric ligand-gated ion channel (pLGIC) signal transduction. However, the GLIC is activated by lowering the pH and the location of its putative proton activation site(s) still remain(s) unknown. To this end, every Asp, Glu, and His residue was mutated individually or in combination and investigated by electrophysiology. In addition to the mutational analysis, key mutations were structurally resolved to address whether particular residues contribute to proton sensing, or alternatively to GLIC-gating, independently of the side chain protonation. The data show that multiple residues located below the orthosteric site, notably E26, D32, E35, and D122 in the lower part of the extracellular domain (ECD), along with E222, H235, E243, and H277 in the transmembrane domain (TMD), alter GLIC activation. D122 and H235 were found to also alter GLIC expression. E35 is identified as a key proton-sensing residue, whereby neutralization of its side chain carboxylate stabilizes the active state. Thus, proton activation occurs allosterically to the orthosteric site, at the level of multiple loci with a key contribution of the coupling interface between the ECD and TMD. Pentameric ligand-gated ion channels are an important class of receptors that are involved in many neurological diseases. They have been extensively studied but a full understanding of their mechanism of action has yet to be achieved. In an effort to bypass obstacles in the research of human receptors, bacterial versions have been used to characterize the family’s structure-function relationship. One key bacterial receptor, known as GLIC, has lead the way in structural resolution of various mechanistic states along the gating pathway, yet its activation by protons is significantly less understood than its human counterparts. To define the site(s) involved in proton gating, we systematically mutated all titratable residues near the pH50 of activation: Asp, Glu, and His. We determined that a previously established His residue in the transmembrane domain is structurally important but likely plays little or no role in proton gating. We instead found that proton activation is a complex multiple loci mechanism, with the key contribution stemming from the coupling interface between the extracellular and transmembrane domain, with E35 acting as a key proton-sensing residue.
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Affiliation(s)
- Ákos Nemecz
- Unité Récepteurs-Canaux, Unité Mixte de Recherche 3571 du Centre National de la Recherche Scientifique, Institut Pasteur, Paris, France
| | - Haidai Hu
- Unité de Dynamique Structurale des Macromolécules, Unité Mixte de Recherche 3528 du Centre National de la Recherche Scientifique, Institut Pasteur, Paris, France
| | - Zaineb Fourati
- Unité de Dynamique Structurale des Macromolécules, Unité Mixte de Recherche 3528 du Centre National de la Recherche Scientifique, Institut Pasteur, Paris, France
| | - Catherine Van Renterghem
- Unité Récepteurs-Canaux, Unité Mixte de Recherche 3571 du Centre National de la Recherche Scientifique, Institut Pasteur, Paris, France
| | - Marc Delarue
- Unité de Dynamique Structurale des Macromolécules, Unité Mixte de Recherche 3528 du Centre National de la Recherche Scientifique, Institut Pasteur, Paris, France
| | - Pierre-Jean Corringer
- Unité Récepteurs-Canaux, Unité Mixte de Recherche 3571 du Centre National de la Recherche Scientifique, Institut Pasteur, Paris, France
- * E-mail:
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50
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Delbart F, Brams M, Gruss F, Noppen S, Peigneur S, Boland S, Chaltin P, Brandao-Neto J, von Delft F, Touw WG, Joosten RP, Liekens S, Tytgat J, Ulens C. An allosteric binding site of the α7 nicotinic acetylcholine receptor revealed in a humanized acetylcholine-binding protein. J Biol Chem 2017; 293:2534-2545. [PMID: 29237730 PMCID: PMC5818190 DOI: 10.1074/jbc.m117.815316] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/24/2017] [Indexed: 11/06/2022] Open
Abstract
Nicotinic acetylcholine receptors (nAChRs) belong to the family of pentameric ligand-gated ion channels and mediate fast excitatory transmission in the central and peripheral nervous systems. Among the different existing receptor subtypes, the homomeric α7 nAChR has attracted considerable attention because of its possible implication in several neurological and psychiatric disorders, including cognitive decline associated with Alzheimer's disease or schizophrenia. Allosteric modulators of ligand-gated ion channels are of particular interest as therapeutic agents, as they modulate receptor activity without affecting normal fluctuations of synaptic neurotransmitter release. Here, we used X-ray crystallography and surface plasmon resonance spectroscopy of α7-acetylcholine-binding protein (AChBP), a humanized chimera of a snail AChBP, which has 71% sequence similarity with the extracellular ligand-binding domain of the human α7 nAChR, to investigate the structural determinants of allosteric modulation. We extended previous observations that an allosteric site located in the vestibule of the receptor offers an attractive target for receptor modulation. We introduced seven additional humanizing mutations in the vestibule-located binding site of AChBP to improve its suitability as a model for studying allosteric binding. Using a fragment-based screening approach, we uncovered an allosteric binding site located near the β8-β9 loop, which critically contributes to coupling ligand binding to channel opening in human α7 nAChR. This work expands our understanding of the topology of allosteric binding sites in AChBP and, by extrapolation, in the human α7 nAChR as determined by electrophysiology measurements. Our insights pave the way for drug design strategies targeting nAChRs involved in ion channel-mediated disorders.
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Affiliation(s)
- Florian Delbart
- From the Department of Cellular and Molecular Medicine, Laboratory of Structural Neurobiology, Faculty of Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Marijke Brams
- From the Department of Cellular and Molecular Medicine, Laboratory of Structural Neurobiology, Faculty of Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Fabian Gruss
- From the Department of Cellular and Molecular Medicine, Laboratory of Structural Neurobiology, Faculty of Medicine, KU Leuven, 3000 Leuven, Belgium
| | - Sam Noppen
- the Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Steve Peigneur
- the Laboratory of Toxicology and Pharmacology, Faculty of Pharmaceutical Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Sandro Boland
- the Center for Innovation and Stimulation of Drug Discovery Leuven, Cistim Leuven vzw, 3001 Heverlee, Belgium
| | - Patrick Chaltin
- the Center for Innovation and Stimulation of Drug Discovery Leuven, Cistim Leuven vzw, 3001 Heverlee, Belgium.,the Center for Innovation and Stimulation of Drug Discovery Leuven and Center for Drug Design and Discovery, KU Leuven, 3001 Heverlee, Belgium
| | - Jose Brandao-Neto
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom, and
| | - Frank von Delft
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0QX, United Kingdom, and
| | - Wouter G Touw
- the Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Robbie P Joosten
- the Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Sandra Liekens
- the Department of Microbiology and Immunology, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, 3000 Leuven, Belgium
| | - Jan Tytgat
- the Laboratory of Toxicology and Pharmacology, Faculty of Pharmaceutical Sciences, KU Leuven, 3000 Leuven, Belgium
| | - Chris Ulens
- From the Department of Cellular and Molecular Medicine, Laboratory of Structural Neurobiology, Faculty of Medicine, KU Leuven, 3000 Leuven, Belgium,
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