Cryo-EM structures of prokaryotic ligand-gated ion channel GLIC provide insights into gating in a lipid environment.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
05 Apr 2024
05 Apr 2024
Historique:
received:
22
02
2023
accepted:
28
03
2024
medline:
6
4
2024
pubmed:
6
4
2024
entrez:
5
4
2024
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 38580666
doi: 10.1038/s41467-024-47370-w
pii: 10.1038/s41467-024-47370-w
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
2967Subventions
Organisme : National Research Foundation Singapore (National Research Foundation-Prime Minister's office, Republic of Singapore)
ID : NRF-NRFF14-2022-0007
Informations de copyright
© 2024. The Author(s).
Références
Menny, A. et al. Identification of a pre-active conformation of a pentameric channel receptor. eLife 6, e23955 (2017).
pubmed: 28294942
pmcid: 5398890
doi: 10.7554/eLife.23955
Ruan, Y. et al. Structural titration of receptor ion channel GLIC gating by HS-AFM. Proc. Natl Acad. Sci. 115, 10333–10338 (2018).
pubmed: 30181288
pmcid: 6187180
doi: 10.1073/pnas.1805621115
Gielen, M. & Corringer, P.-J. The dual-gate model for pentameric ligand-gated ion channels activation and desensitization. J. Physiol. 596, 1873–1902 (2018).
pubmed: 29484660
pmcid: 5978336
doi: 10.1113/JP275100
Rodríguez Cruz, P. M., Palace, J. & Beeson, D. The neuromuscular junction and wide heterogeneity of congenital myasthenic syndromes. Int. J. Mol. Sci. 19, 1677 (2018).
pubmed: 29874875
pmcid: 6032286
doi: 10.3390/ijms19061677
Lemoine, D. et al. Ligand-gated ion channels: new insights into neurological disorders and ligand recognition. Chem. Rev. 112, 6285–6318 (2012).
pubmed: 22988962
doi: 10.1021/cr3000829
Dineley, K. T., Pandya, A. A. & Yakel, J. L. Nicotinic ACh receptors as therapeutic targets in CNS disorders. Trends Pharmacol. Sci. 36, 96–108 (2015).
pubmed: 25639674
pmcid: 4324614
doi: 10.1016/j.tips.2014.12.002
Bocquet, N. et al. X-ray structure of a pentameric ligand-gated ion channel in an apparently open conformation. Nature 457, 111–114 (2009).
pubmed: 18987633
doi: 10.1038/nature07462
Sauguet, L. et al. Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels. EMBO J. 32, 728–741 (2013).
pubmed: 23403925
pmcid: 3590989
doi: 10.1038/emboj.2013.17
Sauguet, L. et al. Crystal structures of a pentameric ligand-gated ion channel provide a mechanism for activation. Proc. Natl Acad. Sci. USA 111, 966–971 (2014).
pubmed: 24367074
doi: 10.1073/pnas.1314997111
Basak, S., Schmandt, N., Gicheru, Y. & Chakrapani, S. Crystal structure and dynamics of a lipid-induced potential desensitized-state of a pentameric ligand-gated channel. eLife 6, e23886 (2017).
pubmed: 28262093
pmcid: 5378477
doi: 10.7554/eLife.23886
Hilf, R. J. & Dutzler, R. X-ray structure of a prokaryotic pentameric ligand-gated ion channel. Nature 452, 375–379 (2008).
pubmed: 18322461
doi: 10.1038/nature06717
Kumar, P., Cymes, G. D. & Grosman, C. Structure and function at the lipid–protein interface of a pentameric ligand-gated ion channel. Proc. Natl Acad. Sci. USA 118, e2100164118 (2021).
pubmed: 34083441
pmcid: 8201805
doi: 10.1073/pnas.2100164118
Petroff, J. T. et al. Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation. Nat. Commun. 13, 7017 (2022).
pubmed: 36385237
pmcid: 9668969
doi: 10.1038/s41467-022-34813-5
Basak, S., Gicheru, Y., Rao, S., Sansom, M. S. P. & Chakrapani, S. Cryo-EM reveals two distinct serotonin-bound conformations of full-length 5-HT3A receptor. Nature 563, 270–274 (2018).
pubmed: 30401837
pmcid: 6237196
doi: 10.1038/s41586-018-0660-7
Basak, S. et al. Cryo-EM structure of 5-HT3A receptor in its resting conformation. Nat. Commun. 9, 514 (2018).
pubmed: 29410406
pmcid: 5802770
doi: 10.1038/s41467-018-02997-4
Polovinkin, L. et al. Conformational transitions of the serotonin 5-HT3 receptor. Nature 563, 275–279 (2018).
pubmed: 30401839
pmcid: 6614044
doi: 10.1038/s41586-018-0672-3
Hassaine, G. et al. X-ray structure of the mouse serotonin 5-HT3 receptor. Nature 512, 276–281 (2014).
pubmed: 25119048
doi: 10.1038/nature13552
Zhang, Y. et al. Asymmetric opening of the homopentameric 5-HT3A serotonin receptor in lipid bilayers. Nat. Commun. 12, 1074 (2021).
pubmed: 33594077
pmcid: 7887223
doi: 10.1038/s41467-021-21016-7
Miller, P. S. & Aricescu, A. R. Crystal structure of a human GABAA receptor. Nature 512, 270–275 (2014).
pubmed: 24909990
pmcid: 4167603
doi: 10.1038/nature13293
Du, J., Lü, W., Wu, S., Cheng, Y. & Gouaux, E. Glycine receptor mechanism elucidated by electron cryo-microscopy. Nature 526, 224–229 (2015).
pubmed: 26344198
pmcid: 4659708
doi: 10.1038/nature14853
Noviello, C. M. et al. Structure and gating mechanism of the α7 nicotinic acetylcholine receptor. Cell 184, 2121–2134.e13 (2021).
pubmed: 33735609
pmcid: 8135066
doi: 10.1016/j.cell.2021.02.049
Masiulis, S. et al. GABAA receptor signalling mechanisms revealed by structural pharmacology. Nature 565, 454–459 (2019).
pubmed: 30602790
pmcid: 6370056
doi: 10.1038/s41586-018-0832-5
Kasaragod, V. B. et al. Mechanisms of inhibition and activation of extrasynaptic αβ GABAA receptors. Nature 602, 529–533 (2022).
pubmed: 35140402
pmcid: 8850191
doi: 10.1038/s41586-022-04402-z
Zarkadas, E. et al. Conformational transitions and ligand-binding to a muscle-type nicotinic acetylcholine receptor. Neuron 110, 1358–1370.e5 (2022).
pubmed: 35139364
doi: 10.1016/j.neuron.2022.01.013
Rahman, M. M. et al. Structural mechanism of muscle nicotinic receptor desensitization and block by curare. Nat. Struct. Mol. Biol. 29, 386–394 (2022).
pubmed: 35301478
pmcid: 9531584
doi: 10.1038/s41594-022-00737-3
Yu, J. et al. Mechanism of gating and partial agonist action in the glycine receptor. Cell 184, 957–968.e21 (2021).
pubmed: 33567265
pmcid: 8115384
doi: 10.1016/j.cell.2021.01.026
Kumar, A. et al. Mechanisms of activation and desensitization of full-length glycine receptor in lipid nanodiscs. Nat. Commun. 11, 3752 (2020).
pubmed: 32719334
pmcid: 7385131
doi: 10.1038/s41467-020-17364-5
Dellisanti, C. D. et al. Site-directed spin labeling reveals pentameric ligand-gated ion channel gating motions. PLoS Biol. 11, e1001714 (2013).
pubmed: 24260024
pmcid: 3833874
doi: 10.1371/journal.pbio.1001714
Popot, J.-L., Cartaud, J. & Changeux, J.-P. Reconstitution of a functional acetylcholine receptor. Eur. J. Biochem. 118, 203–214 (1981).
pubmed: 7285917
doi: 10.1111/j.1432-1033.1981.tb06388.x
Fong, T. M. & McNamee, M. G. Correlation between acetylcholine receptor function and structural properties of membranes. Biochemistry 25, 830–840 (1986).
pubmed: 3008814
doi: 10.1021/bi00352a015
Criado, M., Eibl, H. & Barrantes, F. J. Effects of lipids on acetylcholine receptor. Essential need of cholesterol for maintenance of agonist-induced state transitions in lipid vesicles. Biochemistry 21, 3622–3629 (1982).
pubmed: 7115688
doi: 10.1021/bi00258a015
Tol, M. B. et al. Thermal unfolding of a mammalian pentameric ligand-gated ion channel proceeds at consecutive, distinct steps. J. Biol. Chem. 288, 5756–5769 (2013).
pubmed: 23275379
doi: 10.1074/jbc.M112.422287
Nothdurfter, C. et al. Impact of lipid raft integrity on 5-HT3 receptor function and its modulation by antidepressants. Neuropsychopharmacology 35, 1510–1519 (2010).
pubmed: 20200506
pmcid: 3055465
doi: 10.1038/npp.2010.20
Hammond, J. R. & Martin, I. L. Solubilization of the benzodiazepine/γ-aminobutyric acid receptor complex: comparison of the detergents octylglucopyranoside and 3-[(3-cholamidopropyl)-dimethylammonio] 1-propanesulfonate (CHAPS). J. Neurochem. 47, 1161–1171 (1986).
pubmed: 3018163
doi: 10.1111/j.1471-4159.1986.tb00735.x
Dunn, S. M. J., Shelman, R. A. & Agey, M. W. Fluorescence measurements of anion transport by the GABAA receptor in reconstituted membrane preparations. Biochemistry 28, 2551–2557 (1989).
pubmed: 2543444
doi: 10.1021/bi00432a031
Hammond, J. R. & Martin, I. L. Modulation of [3H]flunitrazepam binding to rat cerebellar benzodiazepine receptors by phosphatidylserine. Eur. J. Pharmacol. 137, 49–58 (1987).
pubmed: 3038577
doi: 10.1016/0014-2999(87)90181-6
Hu, H. et al. Electrostatics, proton sensor, and networks governing the gating transition in GLIC, a proton-gated pentameric ion channel. Proc. Natl Acad. Sci. USA 115, E12172–E12181 (2018).
pubmed: 30541892
pmcid: 6310827
doi: 10.1073/pnas.1813378116
Nemecz, Á. et al. 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. 15, e2004470 (2017).
pubmed: 29281623
pmcid: 5760087
doi: 10.1371/journal.pbio.2004470
Velisetty, P. & Chakrapani, S. Desensitization mechanism in prokaryotic ligand-gated ion channel. J. Biol. Chem. 287, 18467–18477 (2012).
pubmed: 22474322
pmcid: 3365738
doi: 10.1074/jbc.M112.348045
Rienzo, M., Lummis, S. C. & Dougherty, D. A. Structural requirements in the transmembrane domain of GLIC revealed by incorporation of noncanonical histidine analogs. Chem. Biol. 21, 1700–1706 (2014).
pubmed: 25525989
pmcid: 4291181
doi: 10.1016/j.chembiol.2014.10.019
Bocquet, N. et al. A prokaryotic proton-gated ion channel from the nicotinic acetylcholine receptor family. Nature 445, 116–119 (2007).
pubmed: 17167423
doi: 10.1038/nature05371
Nury, H. et al. X-ray structures of general anaesthetics bound to a pentameric ligand-gated ion channel. Nature 469, 428–431 (2011).
pubmed: 21248852
doi: 10.1038/nature09647
Hilf, R. J. C. et al. Structural basis of open channel block in a prokaryotic pentameric ligand-gated ion channel. Nat. Struct. Mol. Biol. 17, 1330–1336 (2010).
pubmed: 21037567
doi: 10.1038/nsmb.1933
Sauguet, L. et al. Structural basis for potentiation by alcohols and anaesthetics in a ligand-gated ion channel. Nat. Commun. 4, 1697 (2013).
pubmed: 23591864
doi: 10.1038/ncomms2682
Zabara, A. et al. Design of ultra-swollen lipidic mesophases for the crystallization of membrane proteins with large extracellular domains. Nat. Commun. 9, 544 (2018).
pubmed: 29416037
pmcid: 5803273
doi: 10.1038/s41467-018-02996-5
Rovsnik, U. et al. Dynamic closed states of a ligand-gated ion channel captured by cryo-EM and simulations. Life Sci. Alliance 4, e202101011 (2021).
pubmed: 34210687
pmcid: 8326787
doi: 10.26508/lsa.202101011
Bergh, C., Rovšnik, U., Howard, R. J. & Lindahl, E. Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM. eLife 12, RP86016 (2023).
doi: 10.7554/eLife.86016
Dämgen, M. A. & Biggin, P. C. State-dependent protein-lipid interactions of a pentameric ligand-gated ion channel in a neuronal membrane. PLoS Comput. Biol. 17, e1007856 (2021).
pubmed: 33571182
pmcid: 7904231
doi: 10.1371/journal.pcbi.1007856
Hilf, R. J. & Dutzler, R. Structure of a potentially open state of a proton-activated pentameric ligand-gated ion channel. Nature 457, 115–118 (2009).
pubmed: 18987630
doi: 10.1038/nature07461
Fourati, Z. et al. Structural basis for a bimodal allosteric mechanism of general anesthetic modulation in pentameric ligand-gated ion channels. Cell Rep. 23, 993–1004 (2018).
pubmed: 29694907
doi: 10.1016/j.celrep.2018.03.108
Howard, R. J. Elephants in the dark: insights and incongruities in pentameric ligand-gated ion channel models. J. Mol. Biol. 433, 167128 (2021).
pubmed: 34224751
doi: 10.1016/j.jmb.2021.167128
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. 76, 668–675 (2020).
pubmed: 32627739
pmcid: 7336382
doi: 10.1107/S205979832000772X
Lev, B. et al. String method solution of the gating pathways for a pentameric ligand-gated ion channel. Proc. Natl Acad. Sci. USA 114, E4158–E4167 (2017).
pubmed: 28487483
pmcid: 5448215
doi: 10.1073/pnas.1617567114
Calimet, N. et al. A gating mechanism of pentameric ligand-gated ion channels. Proc. Natl Acad. Sci. USA 110, E3987–E3996 (2013).
pubmed: 24043807
pmcid: 3801054
doi: 10.1073/pnas.1313785110
Jackson, M. B. Spontaneous openings of the acetylcholine receptor channel. Proc. Natl Acad. Sci. USA 81, 3901–3904 (1984).
pubmed: 6328531
pmcid: 345330
doi: 10.1073/pnas.81.12.3901
Purohit, P. & Auerbach, A. Unliganded gating of acetylcholine receptor channels. Proc. Natl Acad. Sci. USA 106, 115–120 (2009).
pubmed: 19114650
doi: 10.1073/pnas.0809272106
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
Kimanius, D., Dong, L., Sharov, G., Nakane, T. & Scheres, S. H. W. New tools for automated cryo-EM single-particle analysis in RELION-4.0. Biochem. J. 478, 4169–4185 (2021).
pubmed: 34783343
doi: 10.1042/BCJ20210708
Bertozzi, C., Zimmermann, I., Engeler, S., Hilf, R. J. C. & Dutzler, R. Signal transduction at the domain interface of prokaryotic pentameric ligand-gated ion channels. PLoS Biol. 14, e1002393 (2016).
pubmed: 26943937
pmcid: 4778918
doi: 10.1371/journal.pbio.1002393
Bergh, C., Heusser, S. A., Howard, R. & Lindahl, E. Markov state models of proton- and pore-dependent activation in a pentameric ligand-gated ion channel. eLife 10, e68369 (2021).
pubmed: 34652272
pmcid: 8635979
doi: 10.7554/eLife.68369
Marcus, Y. Ionic radii in aqueous solutions. Chem. Rev. 88, 1475–1498 (1988).
doi: 10.1021/cr00090a003
Gharpure, A. et al. Agonist selectivity and ion permeation in the α3β4 ganglionic nicotinic receptor. Neuron 104, 501–511.e6 (2019).
pubmed: 31488329
pmcid: 6842111
doi: 10.1016/j.neuron.2019.07.030
Thompson, M. J. & Baenziger, J. E. Structural basis for the modulation of pentameric ligand-gated ion channel function by lipids. Biochim. Biophys. Acta 1862, 183304 (2020).
doi: 10.1016/j.bbamem.2020.183304
Dalal, V. et al. Lipid nanodisc scaffold and size alter the structure of a pentameric ligand-gated ion channel. Nat. Commun. 15, 25 (2024).
pubmed: 38167383
pmcid: 10762164
doi: 10.1038/s41467-023-44366-w
Bayburt, T. H. & Sligar, S. G. Membrane protein assembly into Nanodiscs. FEBS Lett. 584, 1721–1727 (2010).
pubmed: 19836392
doi: 10.1016/j.febslet.2009.10.024
Ritchie, T. K. et al. in Methods in Enzymology (ed. Düzgünes, N.) Ch. 11 (Academic Press, 2009).
Jha, A., Cadugan, D. J., Purohit, P. & Auerbach, A. Acetylcholine receptor gating at extracellular transmembrane domain interface: the cys-loop and M2–M3 linker. J. Gen. Physiol. 130, 547–558 (2007).
pubmed: 18040057
pmcid: 2151658
doi: 10.1085/jgp.200709856
Lee, W. Y. & Sine, S. M. Principal pathway coupling agonist binding to channel gating in nicotinic receptors. Nature 438, 243–247 (2005).
pubmed: 16281039
doi: 10.1038/nature04156
Lummis, S. C. R. et al. Cis–trans isomerization at a proline opens the pore of a neurotransmitter-gated ion channel. Nature 438, 248–252 (2005).
pubmed: 16281040
doi: 10.1038/nature04130
Gonzalez-Gutierrez, G. & Grosman, C. Bridging the gap between structural models of nicotinic receptor superfamily ion channels and their corresponding functional states. J. Mol. Biol. 403, 693–705 (2010).
pubmed: 20863833
pmcid: 2966540
doi: 10.1016/j.jmb.2010.09.026
Parikh, R. B., Bali, M. & Akabas, M. H. Structure of the M2 transmembrane segment of GLIC, a prokaryotic Cys loop receptor homologue from Gloeobacter violaceus, probed by substituted cysteine accessibility. J. Biol. Chem. 286, 14098–14109 (2011).
pubmed: 21362624
pmcid: 3077611
doi: 10.1074/jbc.M111.221895
Gielen, M., Thomas, P. & Smart, T. G. The desensitization gate of inhibitory Cys-loop receptors. Nat. Commun. 6, 6829 (2015).
pubmed: 25891813
doi: 10.1038/ncomms7829
Carswell, C. L., Sun, J. & Baenziger, J. E. Intramembrane aromatic interactions influence the lipid sensitivities of pentameric ligand-gated ion channels. J. Biol. Chem. 290, 2496–2507 (2015).
pubmed: 25519904
doi: 10.1074/jbc.M114.624395
Cheng, W. W. L. et al. Mapping two neurosteroid-modulatory sites in the prototypic pentameric ligand-gated ion channel GLIC. J. Biol. Chem. 293, 3013–3027 (2018).
pubmed: 29301936
pmcid: 5827446
doi: 10.1074/jbc.RA117.000359
Prevost, M. S. et al. A locally closed conformation of a bacterial pentameric proton-gated ion channel. Nat. Struct. Mol. Biol. 19, 642–649 (2012).
pubmed: 22580559
doi: 10.1038/nsmb.2307
Bode, A. & Lynch, J. W. The impact of human hyperekplexia mutations on glycine receptor structure and function. Mol. Brain 7, 2 (2014).
pubmed: 24405574
pmcid: 3895786
doi: 10.1186/1756-6606-7-2
Lynagh, T., Kunz, A. & Laube, B. Propofol modulation of α1 glycine receptors does not require a structural transition at adjacent subunits that is crucial to agonist-induced activation. ACS Chem. Neurosci. 4, 1469–1478 (2013).
pubmed: 23992940
pmcid: 3837372
doi: 10.1021/cn400134p
Kaczor, P. T., Michałowski, M. A. & Mozrzymas, J. W. α1 proline 277 residues regulate GABAAR gating through M2-M3 loop interaction in the interface region. ACS Chem. Neurosci. 13, 3044–3056 (2022).
pubmed: 36219829
doi: 10.1021/acschemneuro.2c00401
Hibbs, R. E. & Gouaux, E. Principles of activation and permeation in an anion-selective Cys-loop receptor. Nature 474, 54–60 (2011).
pubmed: 21572436
pmcid: 3160419
doi: 10.1038/nature10139
Gibbs, E. et al. Conformational transitions and allosteric modulation in a heteromeric glycine receptor. Nat. Commun. 14, 1363 (2023).
pubmed: 36914669
pmcid: 10011588
doi: 10.1038/s41467-023-37106-7
Van Renterghem, C., Nemecz, Á., Delarue-Cochin, S., Joseph, D. & Corringer, P.-J. Fumarate as positive modulator of allosteric transitions in the pentameric ligand-gated ion channel GLIC: requirement of an intact vestibular pocket. J. Physiol. 601, 2447–2472 (2023).
pubmed: 37026398
doi: 10.1113/JP283765
Denisov, I. G., Baas, B. J., Grinkova, Y. V. & Sligar, S. G. Cooperativity in cytochrome P450 3A4: linkages in substrate binding, spin state, uncoupling, and product formation. J. Biol. Chem. 282, 7066–7076 (2007).
pubmed: 17213193
doi: 10.1074/jbc.M609589200
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
Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).
pubmed: 26278980
pmcid: 6760662
doi: 10.1016/j.jsb.2015.08.008
Bepler, T. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat. Methods 16, 1153–1160 (2019).
pubmed: 31591578
pmcid: 6858545
doi: 10.1038/s41592-019-0575-8
Punjani, A., Zhang, H. & Fleet, D. J. Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction. Nat. Methods 17, 1214–1221 (2020).
pubmed: 33257830
doi: 10.1038/s41592-020-00990-8
Kucukelbir, A., Sigworth, F. J. & Tagare, H. D. Quantifying the local resolution of cryo-EM density maps. Nat. Methods 11, 63–65 (2014).
pubmed: 24213166
doi: 10.1038/nmeth.2727
Pettersen, E. F. et al. UCSF chimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).
pubmed: 32881101
doi: 10.1002/pro.3943
Tang, G. et al. EMAN2: an extensible image processing suite for electron microscopy. J. Struct. Biol. 157, 38–46 (2007).
pubmed: 16859925
doi: 10.1016/j.jsb.2006.05.009
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).
pubmed: 20383002
pmcid: 2852313
doi: 10.1107/S0907444910007493
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
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
Potterton, L. et al. CCP4i2: the new graphical user interface to the CCP4 program suite. Acta Crystallogr. D Struct. Biol. 74, 68–84 (2018).
pubmed: 29533233
pmcid: 5947771
doi: 10.1107/S2059798317016035
Smart, O. S., Neduvelil, J. G., Wang, X., Wallace, B. A. & Sansom, M. S. P. HOLE: a program for the analysis of the pore dimensions of ion channel structural models. J. Mol. Graph. 14, 354–360 (1996).
pubmed: 9195488
doi: 10.1016/S0263-7855(97)00009-X
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
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
Wu, E. L. et al. CHARMM-GUI membrane builder toward realistic biological membrane simulations. J. Comput. Chem. 35, 1997–2004 (2014).
pubmed: 25130509
pmcid: 4165794
doi: 10.1002/jcc.23702
Abraham, M. J. et al. GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1, 19–25 (2015).
doi: 10.1016/j.softx.2015.06.001
Hess, B., Bekker, H., Berendsen, H. J. C. & Fraaije, J. G. E. M. LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 18, 1463–1472 (1997).
doi: 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
Essmann, U. et al. A smooth particle mesh Ewald method. J. Chem. Phys. 103, 8577–8593 (1995).
doi: 10.1063/1.470117
Bussi, G., Donadio, D. & Parrinello, M. Canonical sampling through velocity rescaling. J. Chem. Phys. 126, 014101 (2007).
pubmed: 17212484
doi: 10.1063/1.2408420
Parrinello, M. & Rahman, A. Polymorphic transitions in single crystals: a new molecular dynamics method. J. Appl. Phys. 52, 7182–7190 (1981).
doi: 10.1063/1.328693
Dämgen, M. A. & Biggin, P. C. A refined open state of the glycine receptor obtained via molecular dynamics simulations. Structure 28, 130–139.e2 (2020).
pubmed: 31753620
pmcid: 6945115
doi: 10.1016/j.str.2019.10.019
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