Mechanism of ligand activation of a eukaryotic cyclic nucleotide-gated channel.
Journal
Nature structural & molecular biology
ISSN: 1545-9985
Titre abrégé: Nat Struct Mol Biol
Pays: United States
ID NLM: 101186374
Informations de publication
Date de publication:
07 2020
07 2020
Historique:
received:
13
01
2020
accepted:
10
04
2020
pubmed:
3
6
2020
medline:
21
10
2020
entrez:
3
6
2020
Statut:
ppublish
Résumé
Cyclic nucleotide-gated (CNG) channels convert cyclic nucleotide (CN) binding and unbinding into electrical signals in sensory receptors and neurons. The molecular conformational changes underpinning ligand activation are largely undefined. We report both closed- and open-state atomic cryo-EM structures of a full-length Caenorhabditis elegans cyclic GMP-activated channel TAX-4, reconstituted in lipid nanodiscs. These structures, together with computational and functional analyses and a mutant channel structure, reveal a double-barrier hydrophobic gate formed by two S6 amino acids in the central cavity. cGMP binding produces global conformational changes that open the cavity gate located ~52 Å away but do not alter the structure of the selectivity filter-the commonly presumed activation gate. Our work provides mechanistic insights into the allosteric gating and regulation of CN-gated and nucleotide-modulated channels and CNG channel-related channelopathies.
Identifiants
pubmed: 32483338
doi: 10.1038/s41594-020-0433-5
pii: 10.1038/s41594-020-0433-5
pmc: PMC7354226
mid: NIHMS1583976
doi:
Substances chimiques
Caenorhabditis elegans Proteins
0
Ion Channels
0
Ligands
0
Lipids
0
tax-4 protein, C elegans
0
Cyclic GMP
H2D2X058MU
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
625-634Subventions
Organisme : NIGMS NIH HHS
ID : P41 GM103310
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM055440
Pays : United States
Organisme : NCRR NIH HHS
ID : P41 RR001209
Pays : United States
Organisme : NEI NIH HHS
ID : R01 EY027800
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM085234
Pays : United States
Organisme : NIGMS NIH HHS
ID : U24 GM129539
Pays : United States
Organisme : NIH HHS
ID : S10 OD019994
Pays : United States
Références
Kaupp, U. B. & Seifert, R. Cyclic nucleotide-gated ion channels. Physiol. Rev. 82, 769–824 (2002).
pubmed: 12087135
doi: 10.1152/physrev.00008.2002
Zagotta, W. N. & Siegelbaum, S. A. Structure and function of cyclic nucleotide–gated channels. Annu. Rev. Neurosci. 19, 235–263 (1996).
pubmed: 8833443
doi: 10.1146/annurev.ne.19.030196.001315
Varnum, M. D. & Dai, G. in The Hankbook of Ion Channels (eds J. Zheng & M.C. Trudeau) 361−382 (CRC Press, 2015).
Michalakis, S., Becirovic, E. & Biel, M. Retinal cyclic nucleotide-gated channels: from pathophysiology to therapy. Int. J. Mol. Sci. 19, 749 (2018).
pmcid: 5877610
doi: 10.3390/ijms19030749
Fesenko, E. E., Kolesnikov, S. S. & Lyubarsky, A. L. Induction by cyclic GMP of cationic conductance in plasma membrane of retinal rod outer segment. Nature 313, 310–313 (1985).
pubmed: 2578616
doi: 10.1038/313310a0
Nakamura, T. & Gold, G. H. A cyclic nucleotide-gated conductance in olfactory receptor cilia. Nature 325, 442–444 (1987).
pubmed: 3027574
doi: 10.1038/325442a0
Kaupp, U. B. et al. Primary structure and functional expression from complementary DNA of the rod photoreceptor cyclic GMP-gated channel. Nature 342, 762–766 (1989).
pubmed: 2481236
doi: 10.1038/342762a0
Dhallan, R. S., Yau, K. W., Schrader, K. A. & Reed, R. R. Primary structure and functional expression of a cyclic nucleotide-activated channel from olfactory neurons. Nature 347, 184−187 (1990).
Goulding, E. H., Tibbs, G. R., Liu, D. & Siegelbaum, S. A. Role of H5 domain in determining pore diameter and ion permeation through cyclic nucleotide-gated channels. Nature 364, 61−64 (1993).
Li, M. et al. Structure of a eukaryotic cyclic-nucleotide-gated channel. Nature 542, 60–65 (2017).
pubmed: 28099415
pmcid: 5783306
doi: 10.1038/nature20819
Gordon, S. E. & Zagotta, W. N. A histidine residue associated with the gate of the cyclic nucleotide-activated channels in rod photoreceptors. Neuron 14, 177–183 (1995).
pubmed: 7530019
doi: 10.1016/0896-6273(95)90252-X
Gordon, S. E. & Zagotta, W. N. Localization of regions affecting an allosteric transition in cyclic nucleotide-activated channels. Neuron 14, 857–864 (1995).
pubmed: 7536427
doi: 10.1016/0896-6273(95)90229-5
Brown, R. L., Snow, S. D. & Haley, T. L. Movement of gating machinery during the activation of rod cyclic nucleotide-gated channels. Biophys. J. 75, 825–833 (1998).
pubmed: 9675183
pmcid: 1299756
doi: 10.1016/S0006-3495(98)77571-X
Zong, X., Zucker, H., Hofmann, F. & Biel, M. Three amino acids in the C-linker are major determinants of gating in cyclic nucleotide-gated channels. EMBO J. 17, 353−362 (1998).
Zhou, L., Olivier, N. B., Yao, H., Young, E. C. & Siegelbaum, S. A. A conserved tripeptide in CNG and HCN channels regulates ligand gating by controlling C-terminal oligomerization. Neuron 44, 823−834 (2004).
Paoletti, P., Young, E. C. & Siegelbaum, S. A. C-linker of cyclic nucleotide–gated channels controls coupling of ligand binding to channel gating. J. Gen. Physiol. 113, 17–34 (1999).
pubmed: 9874685
pmcid: 2222991
doi: 10.1085/jgp.113.1.17
Flynn, G. E. & Zagotta, W. N. Conformational changes in S6 coupled to the opening of cyclic nucleotide-gated channels. Neuron 30, 689–698 (2001).
pubmed: 11430803
doi: 10.1016/S0896-6273(01)00324-5
Contreras, J. E. & Holmgren, M. Access of quaternary ammonium blockers to the internal pore of cyclic nucleotide-gated channels: implications for the location of the gate. J. Gen. Physiol. 127, 481−494 (2006).
Contreras, J. E., Srikumar, D. & Holmgren, M. Gating at the selectivity filter in cyclic nucleotide-gated channels. Proc. Natl Acad. Sci. USA 105, 3310−3314 (2008).
Sun, Z. P., Akabas, M. H., Goulding, E. H., Karlin, A. & Siegelbaum, S. A. Exposure of residues in the cyclic nucleotide–gated channel pore: P region structure and function in gating. Neuron 16, 141–149 (1996).
pubmed: 8562078
doi: 10.1016/S0896-6273(00)80031-8
Becchetti, A. & Roncaglia, P. Cyclic nucleotide-gated channels: intra- and extracellular accessibility to Cd
James, Z. M. & Zagotta, W. N. Structural insights into the mechanisms of CNBD channel function. J. Gen. Physiol. 150, 225−244 (2018).
Flynn, G. E., Johnson, J. P., Jr. & Zagotta, W. N. Cyclic nucleotide-gated channels: shedding light on the opening of a channel pore. Nat Rev Neurosci. 2, 643−651 (2001).
Cukkemane, A., Seifert, R. & Kaupp, U. B. Cooperative and uncooperative cyclic-nucleotide-gated ion channels. Trends Biochem. Sci. 36, 55−64 (2011).
Clayton, G. M., Altieri, S., Heginbotham, L., Unger, V. M. & Morais-Cabral, J. H. Structure of the transmembrane regions of a bacterial cyclic nucleotide-regulated channel. Proc. Natl Acad. Sci. USA 105, 1511−1515 (2008).
James, Z. M. et al. CryoEM structure of a prokaryotic cyclic nucleotide-gated ion channel. Proc. Natl Acad. Sci. USA 114, 4430–4435 (2017).
pubmed: 28396445
doi: 10.1073/pnas.1700248114
pmcid: 5410850
Rheinberger, J., Gao, X., Schmidpeter, P. A. & Nimigean, C. M. Ligand discrimination and gating in cyclic nucleotide-gated ion channels from apo and partial agonist-bound cryo-EM structures. Elife 7, e39775 (2018).
pubmed: 30028291
pmcid: 6093708
doi: 10.7554/eLife.39775
Komatsu, H., Mori, I., Rhee, J. S., Akaike, N. & Ohshima, Y. Mutations in a cyclic nucleotide–gated channel lead to abnormal thermosensation and chemosensation in C. elegans. Neuron 17, 707–718 (1996).
pubmed: 8893027
doi: 10.1016/S0896-6273(00)80202-0
Komatsu, H. et al. Functional reconstitution of a heteromeric cyclic nucleotide-gated channel of Caenorhabditis elegans in cultured cells. Brain Res. 821, 160–168 (1999).
pubmed: 10064800
doi: 10.1016/S0006-8993(99)01111-7
Klesse, G., Rao, S., Sansom, M. S. P. & Tucker, S. J. CHAP: a versatile tool for the structural and functional annotation of ion channel pores. J. Mol. Biol. 431, 3353–3365 (2019).
pubmed: 31220459
pmcid: 6699600
doi: 10.1016/j.jmb.2019.06.003
Rao, S., Klesse, G., Stansfeld, P. J., Tucker, S. J. & Sansom, M. S. P. A heuristic derived from analysis of the ion channel structural proteome permits the rapid identification of hydrophobic gates. Proc. Natl Acad. Sci. USA 116, 13989−13995 (2019).
Trick, J. L. et al. Functional annotation of ion channel structures by molecular simulation. Structure 24, 2207–2216 (2016).
pubmed: 27866853
pmcid: 5145807
doi: 10.1016/j.str.2016.10.005
Doyle, D. A. et al. The structure of the potassium channel: molecular basis of K
pubmed: 9525859
doi: 10.1126/science.280.5360.69
Cao, E., Liao, M., Cheng, Y. & Julius, D. TRPV1 structures in distinct conformations reveal activation mechanisms. Nature 504, 113−118 (2013).
Lee, C. H. & MacKinnon, R. Structures of the human HCN1 hyperpolarization-activated channel. Cell 168, 111–120.e11 (2017).
pubmed: 28086084
pmcid: 5496774
doi: 10.1016/j.cell.2016.12.023
Flynn, G. E. & Zagotta, W. N. A cysteine scan of the inner vestibule of cyclic nucleotide-gated channels reveals architecture and rearrangement of the pore. J. Gen. Physiol. 121, 563−582 (2003).
Zagotta, W. N. et al. Structural basis for modulation and agonist specificity of HCN pacemaker channels. Nature 425, 200–205 (2003).
pubmed: 12968185
doi: 10.1038/nature01922
Saponaro, A. et al. Structural basis for the mutual antagonism of cAMP and TRIP8b in regulating HCN channel function. Proc. Natl Acad. Sci. USA 111, 14577–14582 (2014).
pubmed: 25197093
doi: 10.1073/pnas.1410389111
pmcid: 4210022
Xu, X., Vysotskaya, Z. V., Liu, Q. & Zhou, L. Structural basis for the cAMP-dependent gating in the human HCN4 channel. J. Biol. Chem. 285, 37082−37091 (2010).
Lolicato, M. et al. Tetramerization dynamics of C-terminal domain underlies isoform-specific cAMP gating in hyperpolarization-activated cyclic nucleotide-gated channels. J. Biol. Chem. 286, 44811–44820 (2011).
pubmed: 22006928
pmcid: 3247997
doi: 10.1074/jbc.M111.297606
Taraska, J. W., Puljung, M. C., Olivier, N. B., Flynn, G. E. & Zagotta, W. N. Mapping the structure and conformational movements of proteins with transition metal ion FRET. Nat. Methods 6, 532−537 (2009).
Altieri, S. L. et al. Structural and energetic analysis of activation by a cyclic nucleotide binding domain. J. Mol. Biol. 381, 655–669 (2008).
pubmed: 18619611
pmcid: 2555981
doi: 10.1016/j.jmb.2008.06.011
Goldschen-Ohm, M. P. et al. Structure and dynamics underlying elementary ligand binding events in human pacemaking channels. Elife 5, e20797 (2016).
pubmed: 27858593
pmcid: 5115869
doi: 10.7554/eLife.20797
Kowal, J. et al. Ligand-induced structural changes in the cyclic nucleotide-modulated potassium channel MloK1. Nat. Commun. 5, 3106 (2014).
pubmed: 24469021
doi: 10.1038/ncomms4106
Marchesi, A. et al. An iris diaphragm mechanism to gate a cyclic nucleotide-gated ion channel. Nat. Commun. 9, 3978 (2018).
pubmed: 30266906
pmcid: 6162275
doi: 10.1038/s41467-018-06414-8
Kim, D. M. & Nimigean, C. M. Voltage-gated potassium channels: a structural examination of selectivity and gating. Cold Spring Harb. Perspect. Biol. 8, a029231 (2016).
pubmed: 27141052
pmcid: 4852806
doi: 10.1101/cshperspect.a029231
Zhou, X. et al. Cryo-EM structures of the human endolysosomal TRPML3 channel in three distinct states. Nat. Struct. Mol. Biol. 24, 1146–1154 (2017).
pubmed: 29106414
pmcid: 5747366
doi: 10.1038/nsmb.3502
Fodor, A. A., Black, K. D. & Zagotta, W. N. Tetracaine reports a conformational change in the pore of cyclic nucleotide-gated channels. J. Gen. Physiol. 110, 591–600 (1997).
pubmed: 9348330
pmcid: 2229390
doi: 10.1085/jgp.110.5.591
Fodor, A. A., Gordon, S. E. & Zagotta, W. N. Mechanism of tetracaine block of cyclic nucleotide-gated channels. J. Gen. Physiol. 109, 3–14 (1997).
pubmed: 8997661
pmcid: 2217055
doi: 10.1085/jgp.109.1.3
Craven, K. B., Olivier, N. B. & Zagotta, W. N. C-terminal movement during gating in cyclic nucleotide-modulated channels. J. Biol. Chem. 283, 14728–14738 (2008).
pubmed: 18367452
pmcid: 2386932
doi: 10.1074/jbc.M710463200
Craven, K. B. & Zagotta, W. N. Salt bridges and gating in the COOH-terminal region of HCN2 and CNGA1 channels. J. Gen. Physiol. 124, 663–677 (2004).
pubmed: 15572346
pmcid: 2234033
doi: 10.1085/jgp.200409178
Mazzolini, M. et al. The gating mechanism in cyclic nucleotide-gated ion channels. Sci. Reports 8, 45 (2018).
Martinez-Francois, J. R., Xu, Y. & Lu, Z. Mutations reveal voltage gating of CNGA1 channels in saturating cGMP. J. Gen. Physiol. 134, 151−164 (2009).
Mazzolini, M., Anselmi, C. & Torre, V. The analysis of desensitizing CNGA1 channels reveals molecular interactions essential for normal gating. J. Gen. Physiol. 133, 375−386 (2009).
Crary, J. I., Dean, D. M., Nguitragool, W., Kurshan, P. T. & Zimmerman, A. L. Mechanism of inhibition of cyclic nucleotide–gated ion channels by diacylglycerol. J. Gen. Physiol. 116, 755–768 (2000).
pubmed: 11099345
pmcid: 2231817
doi: 10.1085/jgp.116.6.755
Womack, K. B. et al. Do phosphatidylinositides modulate vertebrate phototransduction? J. Neurosci. 20, 2792–2799 (2000).
pubmed: 10751430
pmcid: 6772201
doi: 10.1523/JNEUROSCI.20-08-02792.2000
Bright, S. R., Rich, E. D. & Varnum, M. D. Regulation of human cone cyclic nucleotide-gated channels by endogenous phospholipids and exogenously applied phosphatidylinositol 3,4,5-trisphosphate. Mol. Pharmacol. 71, 176−183 (2007).
Spehr, M., Wetzel, C. H., Hatt, H. & Ache, B. W. 3-phosphoinositides modulate cyclic nucleotide signaling in olfactory receptor neurons. Neuron 33, 731–739 (2002).
pubmed: 11879650
doi: 10.1016/S0896-6273(02)00610-4
Zhainazarov, A. B., Spehr, M., Wetzel, C. H., Hatt, H. & Ache, B. W. Modulation of the olfactory CNG channel by Ptdlns(3,4,5)P
pubmed: 15635812
doi: 10.1007/s00232-004-0707-4
Gordon, S. E., Downing-Park, J., Tam, B. & Zimmerman, A. L. Diacylglycerol analogs inhibit the rod cGMP-gated channel by a phosphorylation-independent mechanism. Biophys. J. 69, 409−417 (1995).
Dai, G., Peng, C., Liu, C. & Varnum, M. D. Two structural components in CNGA3 support regulation of cone CNG channels by phosphoinositides. J. Gen. Physiol. 141, 413−430 (2013).
Ritchie, T. K. et al. Chapter 11 — Reconstitution of membrane proteins in phospholipid bilayer nanodiscs. Methods Enzymol. 464, 211–231 (2009).
pubmed: 19903557
pmcid: 4196316
doi: 10.1016/S0076-6879(09)64011-8
Suloway, C. et al. Automated molecular microscopy: the new Leginon system. J. Struct. Biol. 151, 41–60 (2005).
pubmed: 15890530
doi: 10.1016/j.jsb.2005.03.010
Feng, X. et al. A fast and effective microfluidic spraying-plunging method for high-resolution single-particle cryo-EM. Structure 25, 663–670.e3 (2017).
pubmed: 28286002
pmcid: 5382802
doi: 10.1016/j.str.2017.02.005
Rice, W. J. et al. Routine determination of ice thickness for cryo-EM grids. J. Struct. Biol. 204, 38–44 (2018).
pubmed: 29981485
pmcid: 6119488
doi: 10.1016/j.jsb.2018.06.007
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
pubmed: 28250466
pmcid: 5494038
doi: 10.1038/nmeth.4193
Zhang, K. Gctf: real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016).
pubmed: 26592709
pmcid: 4711343
doi: 10.1016/j.jsb.2015.11.003
Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. Elife 7, e42166 (2018).
pubmed: 30412051
pmcid: 6250425
doi: 10.7554/eLife.42166
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
pubmed: 28165473
doi: 10.1038/nmeth.4169
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
pubmed: 15264254
doi: 10.1002/jcc.20084
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta. Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).
pubmed: 15572765
doi: 10.1107/S0907444904019158
Afonine, P. V. et al. Real-space refinement in PHENIX for cryo-EM and crystallography. Acta. Crystallogr. D Struct. Biol. 74, 531–544 (2018).
pubmed: 29872004
pmcid: 6096492
doi: 10.1107/S2059798318006551
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta. Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).
pubmed: 20124702
pmcid: 2815670
doi: 10.1107/S0907444909052925
Amunts, A. et al. Structure of the yeast mitochondrial large ribosomal subunit. Science 343, 1485–1489 (2014).
pubmed: 24675956
pmcid: 4046073
doi: 10.1126/science.1249410
Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta. Crystallogr. D Biol. Crystallogr. 66, 12–21 (2010).
pubmed: 20057044
doi: 10.1107/S0907444909042073
Jo, S., Kim, T., Iyer, V. G. & Im, W. CHARMM-GUI: a web-based graphical user interface for CHARMM. J. Comput. Chem. 29, 1859–1865 (2008).
pubmed: 18351591
doi: 10.1002/jcc.20945
Quick, M. & Javitch, J. A. Monitoring the function of membrane transport proteins in detergent-solubilized form. Proc. Natl Acad. Sci. USA 104, 3603–3608 (2007).
pubmed: 17360689
doi: 10.1073/pnas.0609573104
pmcid: 1805550