1
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Hu Z, Yang J. Structural basis of properties, mechanisms, and channelopathy of cyclic nucleotide-gated channels. Channels (Austin) 2023; 17:2273165. [PMID: 37905307 PMCID: PMC10761061 DOI: 10.1080/19336950.2023.2273165] [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: 09/07/2023] [Accepted: 10/07/2023] [Indexed: 11/02/2023] Open
Abstract
Recent years have seen an outpouring of atomic or near atomic resolution structures of cyclic nucleotide-gated (CNG) channels, captured in closed, transition, pre-open, partially open, and fully open states. These structures provide unprecedented molecular insights into the activation, assembly, architecture, regulation, and channelopathy of CNG channels, as well as mechanistic explanations for CNG channel biophysical and pharmacological properties. This article summarizes recent advances in CNG channel structural biology, describes key structural features and elements, and illuminates a detailed conformational landscape of activation by cyclic nucleotides. The review also correlates structures with findings and properties delineated in functional studies, including nonselective monovalent cation selectivity, Ca2+ permeation and block, block by L-cis-diltiazem, location of the activation gate, lack of voltage-dependent gating, and modulation by lipids and calmodulin. A perspective on future research is also offered.
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Affiliation(s)
- Zhengshan Hu
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Jian Yang
- Department of Biological Sciences, Columbia University, New York, NY, USA
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2
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Galvanetto N, Ye Z, Marchesi A, Mortal S, Maity S, Laio A, Torre VA. Unfolding and identification of membrane proteins in situ. eLife 2022; 11:77427. [PMID: 36094473 PMCID: PMC9531951 DOI: 10.7554/elife.77427] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Single-molecule force spectroscopy (SMFS) uses the cantilever tip of an AFM to apply a force able to unfold a single protein. The obtained force-distance curve encodes the unfolding pathway, and from its analysis it is possible to characterize the folded domains. SMFS has been mostly used to study the unfolding of purified proteins, in solution or reconstituted in a lipid bilayer. Here, we describe a pipeline for analyzing membrane proteins based on SMFS, that involves the isolation of the plasma membrane of single cells and the harvesting of force-distance curves directly from it. We characterized and identified the embedded membrane proteins combining, within a Bayesian framework, the information of the shape of the obtained curves, with the information from Mass Spectrometry and proteomic databases. The pipeline was tested with purified/reconstituted proteins and applied to five cell types where we classified the unfolding of their most abundant membrane proteins. We validated our pipeline by overexpressing 4 constructs, and this allowed us to gather structural insights of the identified proteins, revealing variable elements in the loop regions. Our results set the basis for the investigation of the unfolding of membrane proteins in situ, and for performing proteomics from a membrane fragment.
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Affiliation(s)
| | - Zhongjie Ye
- International School for Advanced Studies, Trieste, Italy
| | - Arin Marchesi
- Nano Life Science Institute, Kanazawa Medical University, Kanazawa, Japan
| | - Simone Mortal
- International School for Advanced Studies, Trieste, Italy
| | - Sourav Maity
- Moleculaire Biofysica, University of Groningen, Groningen, Netherlands
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3
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Zhang Y, Zhu X, Zhang H, Yan J, Xu P, Wu P, Wu S, Bai C. Mechanism Study of Proteins under Membrane Environment. MEMBRANES 2022; 12:membranes12070694. [PMID: 35877897 PMCID: PMC9322369 DOI: 10.3390/membranes12070694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 11/24/2022]
Abstract
Membrane proteins play crucial roles in various physiological processes, including molecule transport across membranes, cell communication, and signal transduction. Approximately 60% of known drug targets are membrane proteins. There is a significant need to deeply understand the working mechanism of membrane proteins in detail, which is a challenging work due to the lack of available membrane structures and their large spatial scale. Membrane proteins carry out vital physiological functions through conformational changes. In the current study, we utilized a coarse-grained (CG) model to investigate three representative membrane protein systems: the TMEM16A channel, the family C GPCRs mGlu2 receptor, and the P4-ATPase phospholipid transporter. We constructed the reaction pathway of conformational changes between the two-end structures. Energy profiles and energy barriers were calculated. These data could provide reasonable explanations for TMEM16A activation, the mGlu2 receptor activation process, and P4-ATPase phospholipid transport. Although they all belong to the members of membrane proteins, they behave differently in terms of energy. Our work investigated the working mechanism of membrane proteins and could give novel insights into other membrane protein systems of interest.
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Affiliation(s)
- Yue Zhang
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Xiaohong Zhu
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- School of Chemistry and Materials Science, University of Science and Technology of China, Hefei 230026, China
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Honghui Zhang
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Junfang Yan
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Peiyi Xu
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- Warshel Institute for Computational Biology, Shenzhen 518172, China
| | - Peng Wu
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518055, China;
| | - Song Wu
- South China Hospital, Health Science Center, Shenzhen University, Shenzhen 518116, China
- Correspondence: (S.W.); (C.B.)
| | - Chen Bai
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China; (Y.Z.); (X.Z.); (H.Z.); (J.Y.); (P.X.)
- Warshel Institute for Computational Biology, Shenzhen 518172, China
- Chenzhu Biotechnology Co., Ltd., Hangzhou 310005, China
- Correspondence: (S.W.); (C.B.)
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4
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Gorobchenko A, Mareev S, Nikonenko V. Mathematical Modeling of Monovalent Permselectivity of a Bilayer Ion-Exchange Membrane as a Function of Current Density. Int J Mol Sci 2022; 23:ijms23094711. [PMID: 35563102 PMCID: PMC9104382 DOI: 10.3390/ijms23094711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 12/03/2022] Open
Abstract
Modification of an ion-exchange membrane with a thin layer, the charge of which is opposite to the charge of the substrate membrane, has proven to be an effective approach to obtaining a composite membrane with permselectivity towards monovalent ions. However, the mechanism of permselectivity is not clear enough. We report a 1D model based on the Nernst–Planck–Poisson equation system. Unlike other similar models, we introduce activity coefficients, which change when passing from one layer of the membrane to another. This makes it possible to accurately take into account the fact that the substrate membranes usually selectively sorb multiply charged counterions. We show that the main cause for the change in the permselectivity coefficient, P1/2, with increasing current density, j, is the change in the membrane/solution layer, which controls the fluxes of the competing mono- and divalent ions. At low current densities, counterion fluxes are controlled by transfer through the substrate membrane, which causes selective divalent ion transfer. When the current increases, the kinetic control goes first to the modification layer (which leads to the predominant transfer of monovalent ions) and then, at currents close to the limiting current, to the depleted diffusion layer (which results in a complete loss of the permselectivity). Thus, the dependence P1/2 − j passes through a maximum. An analytical solution is obtained for approximate assessment of the maximum value of P1/2 and the corresponding fluxes of the competing ions. The maximum P1/2 values, plotted as a function of the Na+ ion current density at which this maximum is reached, gives the theoretical trade-off curve between the membrane permselectivity and permeability of the bilayer monovalent selective ion-exchange membrane under consideration.
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Amyot R, Marchesi A, Franz CM, Casuso I, Flechsig H. Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images. PLoS Comput Biol 2022; 18:e1009970. [PMID: 35294442 PMCID: PMC8959186 DOI: 10.1371/journal.pcbi.1009970] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 03/28/2022] [Accepted: 02/25/2022] [Indexed: 11/18/2022] Open
Abstract
Atomic force microscopy (AFM) can visualize the dynamics of single biomolecules under near-physiological conditions. However, the scanning tip probes only the molecular surface with limited resolution, missing details required to fully deduce functional mechanisms from imaging alone. To overcome such drawbacks, we developed a computational framework to reconstruct 3D atomistic structures from AFM surface scans, employing simulation AFM and automatized fitting to experimental images. We provide applications to AFM images ranging from single molecular machines, protein filaments, to large-scale assemblies of 2D protein lattices, and demonstrate how the obtained full atomistic information advances the molecular understanding beyond the original topographic AFM image. We show that simulation AFM further allows for quantitative molecular feature assignment within measured AFM topographies. Implementation of the developed methods into the versatile interactive interface of the BioAFMviewer software, freely available at www.bioafmviewer.com, presents the opportunity for the broad Bio-AFM community to employ the enormous amount of existing structural and modeling data to facilitate the interpretation of resolution-limited AFM images.
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Affiliation(s)
- Romain Amyot
- Aix Marseille University, CNRS, INSERM, LAI, Turing Centre for Living Systems, Marseille, France
| | - Arin Marchesi
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, Japan
| | - Clemens M. Franz
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, Japan
| | - Ignacio Casuso
- Aix Marseille University, CNRS, INSERM, LAI, Turing Centre for Living Systems, Marseille, France
| | - Holger Flechsig
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa, Japan
- * E-mail:
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6
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CNG channel structure, function, and gating: a tale of conformational flexibility. Pflugers Arch 2021; 473:1423-1435. [PMID: 34357442 DOI: 10.1007/s00424-021-02610-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 10/20/2022]
Abstract
Cyclic nucleotide-gated (CNG) channels are key to the signal transduction machinery of certain sensory modalities both in vertebrate and invertebrate organisms. They translate a chemical change in cyclic nucleotide concentration into an electrical signal that can spread through sensory cells. Despite CNG and voltage-gated potassium channels sharing a remarkable amino acid sequence homology and basic architectural plan, their functional properties are dramatically different. While voltage-gated potassium channels are highly selective and require membrane depolarization to open, CNG channels have low ion selectivity and are not very sensitive to voltage. In the last few years, many high-resolution structures of intact CNG channels have been released. This wealth of new structural information has provided enormous progress toward the understanding of the molecular mechanisms and driving forces underpinning CNG channel activation. In this review, we report on the current understanding and controversies surrounding the gating mechanism in CNG channels, as well as the deep intertwining existing between gating, the ion permeation process, and its modulation by membrane voltage. While the existence of this powerful coupling was recognized many decades ago, its direct structural demonstration, and ties to the CNG channel inherent pore flexibility, is a recent achievement.
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Napolitano LMR, Marchesi A, Rodriguez A, De March M, Onesti S, Laio A, Torre V. The permeation mechanism of organic cations through a CNG mimic channel. PLoS Comput Biol 2018; 14:e1006295. [PMID: 30071012 PMCID: PMC6091977 DOI: 10.1371/journal.pcbi.1006295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 08/14/2018] [Accepted: 06/12/2018] [Indexed: 11/18/2022] Open
Abstract
Several channels, ranging from TRP receptors to Gap junctions, allow the exchange of small organic solute across cell membrane. However, very little is known about the molecular mechanism of their permeation. Cyclic Nucleotide Gated (CNG) channels, despite their homology with K+ channels and in contrast with them, allow the passage of larger methylated and ethylated ammonium ions like dimethylammonium (DMA) and ethylammonium (EA). We combined electrophysiology and molecular dynamics simulations to examine how DMA interacts with the pore and permeates through it. Due to the presence of hydrophobic groups, DMA enters easily in the channel and, unlike the alkali cations, does not need to cross any barrier. We also show that while the crystal structure is consistent with the presence of a single DMA ion at full occupancy, the channel is able to conduct a sizable current of DMA ions only when two ions are present inside the channel. Moreover, the second DMA ion dramatically changes the free energy landscape, destabilizing the crystallographic binding site and lowering by almost 25 kJ/mol the binding affinity between DMA and the channel. Based on the results of the simulation the experimental electron density maps can be re-interpreted with the presence of a second ion at lower occupancy. In this mechanism the flexibility of the channel plays a key role, extending the classical multi-ion permeation paradigm in which conductance is enhanced by the plain interaction between the ions.
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Affiliation(s)
- Luisa M. R. Napolitano
- International School for Advanced Studies (SISSA), Trieste, Italy
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Basovizza, Trieste, Italy
| | - Arin Marchesi
- INSERM U1006, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - Alex Rodriguez
- International School for Advanced Studies (SISSA), Trieste, Italy
| | - Matteo De March
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Basovizza, Trieste, Italy
| | - Silvia Onesti
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Basovizza, Trieste, Italy
| | - Alessandro Laio
- International School for Advanced Studies (SISSA), Trieste, Italy
- ICTP, International Centre for Theoretical Physics, Trieste, Italy
| | - Vincent Torre
- International School for Advanced Studies (SISSA), Trieste, Italy
- Cixi Institute of Biomedical Engineering (CNITECH), Nigbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Zhejiang, P.R. China
- Center of Systems Medicine, Chinese Academy of Medical Sciences, Suzhou Institute of Systems Medicine, Suzhou Industrial Park, Suzhou, Jiangsu, P.R. China
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8
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Mazzolini M, Arcangeletti M, Marchesi A, Napolitano LMR, Grosa D, Maity S, Anselmi C, Torre V. The gating mechanism in cyclic nucleotide-gated ion channels. Sci Rep 2018; 8:45. [PMID: 29311674 PMCID: PMC5758780 DOI: 10.1038/s41598-017-18499-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 12/04/2017] [Indexed: 11/09/2022] Open
Abstract
Cyclic nucleotide-gated (CNG) channels mediate transduction in several sensory neurons. These channels use the free energy of CNs' binding to open the pore, a process referred to as gating. CNG channels belong to the superfamily of voltage-gated channels, where the motion of the α-helix S6 controls gating in most of its members. To date, only the open, cGMP-bound, structure of a CNG channel has been determined at atomic resolution, which is inadequate to determine the molecular events underlying gating. By using electrophysiology, site-directed mutagenesis, chemical modification, and Single Molecule Force Spectroscopy, we demonstrate that opening of CNGA1 channels is initiated by the formation of salt bridges between residues in the C-linker and S5 helix. These events trigger conformational changes of the α-helix S5, transmitted to the P-helix and leading to channel opening. Therefore, the superfamily of voltage-gated channels shares a similar molecular architecture but has evolved divergent gating mechanisms.
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Affiliation(s)
- Monica Mazzolini
- International School for Advanced Studies, Trieste, 34136, Italy.
| | | | - Arin Marchesi
- INSERM U1006, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy, Marseille, 13009, France
| | - Luisa M R Napolitano
- International School for Advanced Studies, Trieste, 34136, Italy
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Basovizza, Trieste, 34149, Italy
| | - Debora Grosa
- International School for Advanced Studies, Trieste, 34136, Italy
| | - Sourav Maity
- International School for Advanced Studies, Trieste, 34136, Italy
| | - Claudio Anselmi
- National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Vincent Torre
- International School for Advanced Studies, Trieste, 34136, Italy.
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9
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Li M, Zhou X, Wang S, Michailidis I, Gong Y, Su D, Li H, Li X, Yang J. Structure of a eukaryotic cyclic-nucleotide-gated channel. Nature 2017; 542:60-65. [PMID: 28099415 DOI: 10.1038/nature20819] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Accepted: 11/23/2016] [Indexed: 12/11/2022]
Abstract
Cyclic-nucleotide-gated channels are essential for vision and olfaction. They belong to the voltage-gated ion channel superfamily but their activities are controlled by intracellular cyclic nucleotides instead of transmembrane voltage. Here we report a 3.5-Å-resolution single-particle electron cryo-microscopy structure of a cyclic-nucleotide-gated channel from Caenorhabditis elegans in the cyclic guanosine monophosphate (cGMP)-bound open state. The channel has an unusual voltage-sensor-like domain, accounting for its deficient voltage dependence. A carboxy-terminal linker connecting S6 and the cyclic-nucleotide-binding domain interacts directly with both the voltage-sensor-like domain and the pore domain, forming a gating ring that couples conformational changes triggered by cyclic nucleotide binding to the gate. The selectivity filter is lined by the carboxylate side chains of a functionally important glutamate and three rings of backbone carbonyls. This structure provides a new framework for understanding mechanisms of ion permeation, gating and channelopathy of cyclic-nucleotide-gated channels and cyclic nucleotide modulation of related channels.
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Affiliation(s)
- Minghui Li
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Xiaoyuan Zhou
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shu Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Chinese Academy of Sciences, Kunming 650223, China.,Key Laboratory of Bioactive Peptides of Yunnan Province, Chinese Academy of Sciences, Kunming 650223, China.,Ion Channel Research and Drug Development Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Ioannis Michailidis
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Ye Gong
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Chinese Academy of Sciences, Kunming 650223, China.,Key Laboratory of Bioactive Peptides of Yunnan Province, Chinese Academy of Sciences, Kunming 650223, China.,Ion Channel Research and Drug Development Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Deyuan Su
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Chinese Academy of Sciences, Kunming 650223, China.,Key Laboratory of Bioactive Peptides of Yunnan Province, Chinese Academy of Sciences, Kunming 650223, China.,Ion Channel Research and Drug Development Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Huan Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Chinese Academy of Sciences, Kunming 650223, China.,Key Laboratory of Bioactive Peptides of Yunnan Province, Chinese Academy of Sciences, Kunming 650223, China.,Ion Channel Research and Drug Development Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming 650204, China
| | - Xueming Li
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jian Yang
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA.,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, Chinese Academy of Sciences, Kunming 650223, China.,Key Laboratory of Bioactive Peptides of Yunnan Province, Chinese Academy of Sciences, Kunming 650223, China.,Ion Channel Research and Drug Development Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
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10
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Maity S, Marchesi A, Torre V, Mazzolini M. Structural Heterogeneity of CNGA1 Channels Revealed by Electrophysiology and Single-Molecule Force Spectroscopy. ACS OMEGA 2016; 1:1205-1219. [PMID: 31457189 PMCID: PMC6640748 DOI: 10.1021/acsomega.6b00202] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/14/2016] [Indexed: 06/10/2023]
Abstract
The determination at atomic resolution of the three-dimensional molecular structure of membrane proteins such as receptors and several ion channels has been a major breakthrough in structural biology. The molecular structure of several members of the superfamily of voltage-gated ionic channels such as K+ and Na+ is now available. However, despite several attempts, the molecular structure at atomic resolution of the full cyclic nucleotide-gated (CNG) ion channel, although a member of the same superfamily of voltage-gated ion channels, has not been obtained yet, neither by X-ray crystallography nor by electron cryomicroscopy (cryo-EM). It is possible that CNG channels have a high structural heterogeneity, making difficult crystallization and single-particle analysis. To address this issue, we have combined single-molecule force spectroscopy (SMFS) and electrophysiological experiments to characterize the structural heterogeneity of CNGA1 channels expressed in Xenopus laevis oocytes. The unfolding of the cytoplasmic domain had force peaks, occurring with a probability from 0.2 to 0.96. Force peaks during the unfolding of the transmembrane domain had a probability close to 1, but the distribution of the increase in contour length between two successive force peaks had multiple maxima differing by tens of nanometers. Concomitant electrophysiological experiments showed that the rundown in mutant channels S399C is highly variable and that the effect of thiol reagents when specific residues were mutated was consistent with a dynamic structural heterogeneity. These results show that CNGA1 channels have a wide spectrum of native conformations that are difficult to detect with X-ray crystallography and cryo-EM.
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11
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Napolitano LMR, Bisha I, De March M, Marchesi A, Arcangeletti M, Demitri N, Mazzolini M, Rodriguez A, Magistrato A, Onesti S, Laio A, Torre V. A structural, functional, and computational analysis suggests pore flexibility as the base for the poor selectivity of CNG channels. Proc Natl Acad Sci U S A 2015; 112:E3619-28. [PMID: 26100907 PMCID: PMC4500290 DOI: 10.1073/pnas.1503334112] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Cyclic nucleotide-gated (CNG) ion channels, despite a significant homology with the highly selective K(+) channels, do not discriminate among monovalent alkali cations and are permeable also to several organic cations. We combined electrophysiology, molecular dynamics (MD) simulations, and X-ray crystallography to demonstrate that the pore of CNG channels is highly flexible. When a CNG mimic is crystallized in the presence of a variety of monovalent cations, including Na(+), Cs(+), and dimethylammonium (DMA(+)), the side chain of Glu66 in the selectivity filter shows multiple conformations and the diameter of the pore changes significantly. MD simulations indicate that Glu66 and the prolines in the outer vestibule undergo large fluctuations, which are modulated by the ionic species and the voltage. This flexibility underlies the coupling between gating and permeation and the poor ionic selectivity of CNG channels.
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Affiliation(s)
| | - Ina Bisha
- International School for Advanced Studies, Trieste 34136, Italy
| | - Matteo De March
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Basovizza, Trieste 34149, Italy
| | - Arin Marchesi
- International School for Advanced Studies, Trieste 34136, Italy
| | | | - Nicola Demitri
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Basovizza, Trieste 34149, Italy
| | | | - Alex Rodriguez
- International School for Advanced Studies, Trieste 34136, Italy
| | - Alessandra Magistrato
- International School for Advanced Studies, Trieste 34136, Italy; National Research Council-Institute of Materials (CNR-IOM)-Democritos National Simulation Center c/o International School for Advanced Studies, Trieste 34136, Italy
| | - Silvia Onesti
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste S.C.p.A., Basovizza, Trieste 34149, Italy;
| | - Alessandro Laio
- International School for Advanced Studies, Trieste 34136, Italy;
| | - Vincent Torre
- International School for Advanced Studies, Trieste 34136, Italy;
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