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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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2
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Martinez-Corral R, Nam KM, DePace AH, Gunawardena J. The Hill function is the universal Hopfield barrier for sharpness of input-output responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.587054. [PMID: 38585761 PMCID: PMC10996692 DOI: 10.1101/2024.03.27.587054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The Hill functions, ℋ h ( x ) = x h / 1 + x h , have been widely used in biology for over a century but, with the exception of ℋ 1 , they have had no justification other than as a convenient fit to empirical data. Here, we show that they are the universal limit for the sharpness of any input-output response arising from a Markov process model at thermodynamic equilibrium. Models may represent arbitrary molecular complexity, with multiple ligands, internal states, conformations, co-regulators, etc, under core assumptions that are detailed in the paper. The model output may be any linear combination of steady-state probabilities, with components other than the chosen input ligand held constant. This formulation generalises most of the responses in the literature. We use a coarse-graining method in the graph-theoretic linear framework to show that two sharpness measures for input-output responses fall within an effectively bounded region of the positive quadrant, Ω m ⊂ ℝ + 2 , for any equilibrium model with m input binding sites. Ω m exhibits a cusp which approaches, but never exceeds, the sharpness of ℋ m but the region and the cusp can be exceeded when models are taken away from thermodynamic equilibrium. Such fundamental thermodynamic limits are called Hopfield barriers and our results provide a biophysical justification for the Hill functions as the universal Hopfield barriers for sharpness. Our results also introduce an object, Ω m , whose structure may be of mathematical interest, and suggest the importance of characterising Hopfield barriers for other forms of cellular information processing.
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Affiliation(s)
| | - Kee-Myoung Nam
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Angela H. DePace
- Howard Hughes Medical Institute, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jeremy Gunawardena
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
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3
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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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Gibbs E, Klemm E, Seiferth D, Kumar A, Ilca SL, Biggin PC, Chakrapani S. Conformational transitions and allosteric modulation in a heteromeric glycine receptor. Nat Commun 2023; 14:1363. [PMID: 36914669 PMCID: PMC10011588 DOI: 10.1038/s41467-023-37106-7] [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: 07/22/2022] [Accepted: 03/02/2023] [Indexed: 03/16/2023] Open
Abstract
Glycine Receptors (GlyRs) provide inhibitory neuronal input in the spinal cord and brainstem, which is critical for muscle coordination and sensory perception. Synaptic GlyRs are a heteromeric assembly of α and β subunits. Here we present cryo-EM structures of full-length zebrafish α1βBGlyR in the presence of an antagonist (strychnine), agonist (glycine), or agonist with a positive allosteric modulator (glycine/ivermectin). Each structure shows a distinct pore conformation with varying degrees of asymmetry. Molecular dynamic simulations found the structures were in a closed (strychnine) and desensitized states (glycine and glycine/ivermectin). Ivermectin binds at all five interfaces, but in a distinct binding pose at the β-α interface. Subunit-specific features were sufficient to solve structures without a fiduciary marker and to confirm the 4α:1β stoichiometry recently observed. We also report features of the extracellular and intracellular domains. Together, our results show distinct compositional and conformational properties of α1βGlyR and provide a framework for further study of this physiologically important channel.
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Affiliation(s)
- Eric Gibbs
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Emily Klemm
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - David Seiferth
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Arvind Kumar
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Serban L Ilca
- New York Structural Biology Center, New York, NY, 10027, USA
- Simons Electron Microscopy Center, New York, NY, 10027, USA
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - 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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Wang H, Zhu X, Zhao Y, Zang Y, Zhang J, Kang Y, Yang Z, Lin P, Zhang L, Zhang S. Markov State Models Underlying the N-Terminal Premodel of TOPK/PBK. J Phys Chem B 2022; 126:10662-10671. [PMID: 36512332 DOI: 10.1021/acs.jpcb.2c06559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Lymphokine-activated killer T-cell-originated protein kinase (TOPK) is a potential target for cancer therapy. To explore the micromechanism, we proposed the N-terminal premodel (NTPM) of the TOPK monomer via homology modeling and molecular dynamic simulations and analyzed the conformational dynamics by Markov state model analysis. The electronegative insert (ENI) motif of the NTPM can be opened with a small probability under wild type, regulated by the so-called "N-C" interaction zone consisting of the N-terminal head, the coil between β3-strand and αC-helix, and the ENI motif. Glutamate substitution at threonine residue 9 or tyrosine residue 74 promotes the closed-open transition, revealing the details of phosphorylation. Allosteric effects induce functionally relevant structural changes, such as increased structural flexibility and active sites, which are thought to be necessary for further activation or binding. These findings provide rational structural templates for designing state-dependent inhibitors and give insight into the molecular regulatory mechanisms of TOPK monomers.
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Affiliation(s)
- He Wang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Xun Zhu
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Yongjian Zang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Jianwen Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Ying Kang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Peng Lin
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an710032, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
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Heusser SA, Borg CB, Colding JM, Pless SA. Conformational decoupling in acid-sensing ion channels uncovers mechanism and stoichiometry of PcTx1-mediated inhibition. eLife 2022; 11:73384. [PMID: 35156612 PMCID: PMC8871370 DOI: 10.7554/elife.73384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 02/11/2022] [Indexed: 01/10/2023] Open
Abstract
Acid-sensing ion channels (ASICs) are trimeric proton-gated cation channels involved in fast synaptic transmission. Pharmacological inhibition of ASIC1a reduces neurotoxicity and stroke infarct volumes, with the cysteine knot toxin psalmotoxin-1 (PcTx1) being one of the most potent and selective inhibitors. PcTx1 binds at the subunit interface in the extracellular domain (ECD), but the mechanism and conformational consequences of the interaction, as well as the number of toxin molecules required for inhibition, remain unknown. Here, we use voltage-clamp fluorometry and subunit concatenation to decipher the mechanism and stoichiometry of PcTx1 inhibition of ASIC1a. Besides the known inhibitory binding mode, we propose PcTx1 to have at least two additional binding modes that are decoupled from the pore. One of these modes induces a long-lived ECD conformation that reduces the activity of an endogenous neuropeptide. This long-lived conformational state is proton-dependent and can be destabilized by a mutation that decreases PcTx1 sensitivity. Lastly, the use of concatemeric channel constructs reveals that disruption of a single PcTx1 binding site is sufficient to destabilize the toxin-induced conformation, while functional inhibition is not impaired until two or more binding sites are mutated. Together, our work provides insight into the mechanism of PcTx1 inhibition of ASICs and uncovers a prolonged conformational change with possible pharmacological implications.
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Affiliation(s)
- Stephanie A Heusser
- Department of Drug Design and Pharmacology, University of Copenhagen, Copehagen, Denmark
| | - Christian B Borg
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Janne M Colding
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Stephan A Pless
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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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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