Constructing ion channels from water-soluble α-helical barrels.
Journal
Nature chemistry
ISSN: 1755-4349
Titre abrégé: Nat Chem
Pays: England
ID NLM: 101499734
Informations de publication
Date de publication:
07 2021
07 2021
Historique:
received:
28
05
2020
accepted:
05
03
2021
pubmed:
12
5
2021
medline:
2
10
2021
entrez:
11
5
2021
Statut:
ppublish
Résumé
The design of peptides that assemble in membranes to form functional ion channels is challenging. Specifically, hydrophobic interactions must be designed between the peptides and at the peptide-lipid interfaces simultaneously. Here, we take a multi-step approach towards this problem. First, we use rational de novo design to generate water-soluble α-helical barrels with polar interiors, and confirm their structures using high-resolution X-ray crystallography. These α-helical barrels have water-filled lumens like those of transmembrane channels. Next, we modify the sequences to facilitate their insertion into lipid bilayers. Single-channel electrical recordings and fluorescent imaging of the peptides in membranes show monodisperse, cation-selective channels of unitary conductance. Surprisingly, however, an X-ray structure solved from the lipidic cubic phase for one peptide reveals an alternative state with tightly packed helices and a constricted channel. To reconcile these observations, we perform computational analyses to compare the properties of possible different states of the peptide.
Identifiants
pubmed: 33972753
doi: 10.1038/s41557-021-00688-0
pii: 10.1038/s41557-021-00688-0
pmc: PMC7611114
mid: EMS118809
doi:
Substances chimiques
Ion Channels
0
Lipid Bilayers
0
Peptides
0
Water
059QF0KO0R
Banques de données
figshare
['10.6084/m9.figshare.14406419']
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
643-650Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/R001790/1
Pays : United Kingdom
Organisme : NIGMS NIH HHS
ID : F32 GM125217
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM008284
Pays : United States
Organisme : NIGMS NIH HHS
ID : P30 GM124169
Pays : United States
Organisme : Howard Hughes Medical Institute (HHMI)
ID : NA
Organisme : NIGMS NIH HHS
ID : R35 GM122603
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01 GM124149
Pays : United States
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/J009784/1
Pays : United Kingdom
Organisme : European Research Council
ID : 340764
Pays : International
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/L01386X/1
Pays : United Kingdom
Commentaires et corrections
Type : CommentIn
Références
Huang, P. S., Boyken, S. E. & Baker, D. The coming of age of de novo protein design. Nature 537, 320–327 (2016).
pubmed: 27629638
doi: 10.1038/nature19946
Korendovych, I. V. & DeGrado, W. F. De novo protein design, a retrospective. Q. Rev. Biophys. 53, e3 (2020).
pubmed: 32041676
pmcid: 7243446
doi: 10.1017/S0033583519000131
Lu, P. L. et al. Accurate computational design of multipass transmembrane proteins. Science 359, 1042–1046 (2018).
pubmed: 29496880
pmcid: 7328376
doi: 10.1126/science.aaq1739
Mravic, M. et al. Packing of apolar side chains enables accurate design of highly stable membrane proteins. Science 363, 1418–1423 (2019).
pubmed: 30923216
pmcid: 7380683
doi: 10.1126/science.aav7541
Joh, N. H. et al. De novo design of a transmembrane Zn
pubmed: 25525248
pmcid: 4400864
doi: 10.1126/science.1261172
Davey, J. A., Damry, A. M., Goto, N. K. & Chica, R. A. Rational design of proteins that exchange on functional timescales. Nat. Chem. Biol. 13, 1280–1285 (2017).
pubmed: 29058725
doi: 10.1038/nchembio.2503
Chen, K.-Y. M., Keri, D. & Barth, P. Computational design of G Protein-Coupled Receptor allosteric signal transductions. Nat. Chem. Biol. 16, 77–86 (2020).
pubmed: 31792443
doi: 10.1038/s41589-019-0407-2
Woolfson, D. N. Coiled-coil design: updated and upgraded. Subcell. Biochem. 82, 35–61 (2017).
pubmed: 28101858
doi: 10.1007/978-3-319-49674-0_2
Lear, J. D., Wasserman, Z. R. & Degrado, W. F. Synthetic amphiphilic peptide models for protein ion channels. Science 240, 1177–1181 (1988).
pubmed: 2453923
doi: 10.1126/science.2453923
Mahendran, K. R. et al. A monodisperse transmembrane α-helical peptide barrel. Nat. Chem. 9, 411–419 (2017).
pubmed: 28430192
doi: 10.1038/nchem.2647
Bowie, J. U. Helix packing in membrane proteins. J. Mol. Biol. 272, 780–789 (1997).
pubmed: 9368657
doi: 10.1006/jmbi.1997.1279
Hong, H. Toward understanding driving forces in membrane protein folding. Arch. Biochem. Biophys. 564, 297–313 (2014).
pubmed: 25107533
doi: 10.1016/j.abb.2014.07.031
Liu, J. et al. A seven-helix coiled coil. Proc. Natl Acad. Sci. USA 103, 15457–15462 (2006).
pubmed: 17030805
pmcid: 1622844
doi: 10.1073/pnas.0604871103
Zaccai, N. R. et al. A de novo peptide hexamer with a mutable channel. Nat. Chem. Biol. 7, 935–941 (2011).
pubmed: 22037471
pmcid: 3223406
doi: 10.1038/nchembio.692
Thomson, A. R. et al. Computational design of water-soluble α-helical barrels. Science 346, 485–488 (2014).
pubmed: 25342807
doi: 10.1126/science.1257452
Rhys, G. G. et al. Maintaining and breaking symmetry in homomeric coiled-coil assemblies. Nat. Commun. 9, 4132 (2018).
pubmed: 30297707
pmcid: 6175849
doi: 10.1038/s41467-018-06391-y
Wood, C. W. & Woolfson, D. N. CCBuilder 2.0: powerful and accessible coiled-coil modeling. Protein Sci. 27, 103–111 (2018).
pubmed: 28836317
doi: 10.1002/pro.3279
Walshaw, J. & Woolfson, D. N. SOCKET: a program for identifying and analysing coiled-coil motifs within protein structures. J. Mol. Biol. 307, 1427–1450 (2001).
pubmed: 11292353
doi: 10.1006/jmbi.2001.4545
Klesse, G., Rao, S. L., 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
Aryal, P., Sansom, M. S. P. & Tucker, S. J. Hydrophobic gating in ion channels. J. Mol. Biol. 427, 121–130 (2015).
pubmed: 25106689
doi: 10.1016/j.jmb.2014.07.030
Carugo, O. Statistical survey of the buried waters in the Protein Data Bank. Amino Acids 48, 193–202 (2016).
pubmed: 26315961
doi: 10.1007/s00726-015-2064-4
Dawson, J. P., Weinger, J. S. & Engelman, D. M. Motifs of serine and threonine can drive association of transmembrane helices. J. Mol. Biol. 316, 799–805 (2002).
pubmed: 11866532
doi: 10.1006/jmbi.2001.5353
Hessa, T. et al. Molecular code for transmembrane-helix recognition by the Sec61 translocon. Nature 450, 1026–1030 (2007).
pubmed: 18075582
doi: 10.1038/nature06387
Harriss, L. M., Cronin, B., Thompson, J. R. & Wallace, M. I. Imaging multiple conductance states in an alamethicin pore. J. Am. Chem. Soc. 133, 14507–14509 (2011).
pubmed: 21848341
doi: 10.1021/ja204275t
Landau, E. M. & Rosenbusch, J. P. Lipidic cubic phases: a novel concept for the crystallization of membrane proteins. Proc. Natl Acad. Sci. USA 93, 14532–14535 (1996).
pubmed: 8962086
pmcid: 26167
doi: 10.1073/pnas.93.25.14532
Gernert, K. M., Surles, M. C., Labean, T. H., Richardson, J. S. & Richardson, D. C. The Alacoil: a very tight, antiparallel coiled-coil of helices. Protein Sci. 4, 2252–2260 (1995).
pubmed: 8563621
pmcid: 2143020
doi: 10.1002/pro.5560041102
Adamian, L. & Liang, J. Interhelical hydrogen bonds and spatial motifs in membrane proteins: polar clamps and serine zippers. Proteins 47, 209–218 (2002).
pubmed: 11933067
doi: 10.1002/prot.10071
Zhang, S. Q. et al. The membrane- and soluble-protein helix-helix Interactome: similar geometry via different interactions. Structure 23, 527–541 (2015).
pubmed: 25703378
pmcid: 4351763
doi: 10.1016/j.str.2015.01.009
Rhys, G. G. et al. Navigating the structural landscape of de novo α-helical bundles. J. Am. Chem. Soc. 141, 8787–8797 (2019).
pubmed: 31066556
doi: 10.1021/jacs.8b13354
Song, C. et al. Crystal structure and functional mechanism of a human antimicrobial membrane channel. Proc. Natl Acad. Sci. USA 110, 4586–4591 (2013).
pubmed: 23426625
pmcid: 3607029
doi: 10.1073/pnas.1214739110
Hayouka, Z. et al. Quasiracemate crystal structures of magainin 2 derivatives support the functional significance of the phenylalanine zipper motif. J. Am. Chem. Soc. 137, 11884–11887 (2015).
pubmed: 26369301
pmcid: 4831726
doi: 10.1021/jacs.5b07206
Kurgan, K. W. et al. Retention of native quaternary structure in racemic melittin crystals. J. Am. Chem. Soc. 141, 7704–7708 (2019).
pubmed: 31059253
pmcid: 6520119
doi: 10.1021/jacs.9b02691
Sansom, M. S. The biophysics of peptide models of ion channels. Prog. Biophys. Mol. Biol. 55, 139–235 (1991).
pubmed: 1715999
doi: 10.1016/0079-6107(91)90004-C
Hille, B. Ionic Channels of Excitable Membranes (Oxford Univ. Press, 2001).
Kienker, P. K., DeGrado, W. F. & Lear, J. D. A helical-dipole model describes the single-channel current rectification of an uncharged peptide ion channel. Proc. Natl Acad. Sci. USA 91, 4859–4863 (1994).
pubmed: 7515180
pmcid: 43888
doi: 10.1073/pnas.91.11.4859
Noskov, S. Y., Im, W. & Roux, B. Ion permeation through the α-hemolysin channel: theoretical studies based on Brownian dynamics and Poisson-Nernst-Plank electrodiffusion theory. Biophys. J. 87, 2299–2309 (2004).
pubmed: 15454431
pmcid: 1304654
doi: 10.1529/biophysj.104.044008
Wang, S. Q., Song, L. S., Lakatta, E. G. & Cheng, H. P. Ca
pubmed: 11279498
doi: 10.1038/35069083
Heron, A. J., Thompson, J. R., Cronin, B., Bayley, H. & Wallace, M. I. Simultaneous measurement of ionic current and fluorescence from single protein pores. J. Am. Chem. Soc. 131, 1652–1653 (2009).
pubmed: 19146373
doi: 10.1021/ja808128s
Leptihn, S. et al. Constructing droplet interface bilayers from the contact of aqueous droplets in oil. Nat. Protoc. 8, 1048–1057 (2013).
pubmed: 23640169
doi: 10.1038/nprot.2013.061
Ramadurai, S., Duurkens, R., Krasnikov, V. V. & Poolman, B. Lateral diffusion of membrane proteins: consequences of hydrophobic mismatch and lipid composition. Biophys. J. 99, 1482–1489 (2010).
pubmed: 20816060
pmcid: 2931744
doi: 10.1016/j.bpj.2010.06.036
Saffman, P. G. & Delbrück, M. Brownian motion in biological membranes. Proc. Natl Acad. Sci. USA 72, 3111–3113 (1975).
pubmed: 1059096
pmcid: 432930
doi: 10.1073/pnas.72.8.3111
Callenberg, K. M. et al. APBSmem: a graphical interface for electrostatic calculations at the membrane. PLoS One 5, e12722 (2010).
pubmed: 20949122
pmcid: 2947494
doi: 10.1371/journal.pone.0012722
Roux, B., Allen, T., Berneche, S. & Im, W. Theoretical and computational models of biological ion channels. Q. Rev. Biophys. 37, 15–103 (2004).
pubmed: 17390604
doi: 10.1017/S0033583504003968
Krishnan, R. S. et al. Autonomously assembled synthetic transmembrane peptide pore. J. Am. Chem. Soc. 141, 2949–2959 (2019).
doi: 10.1021/jacs.8b09973
Spruijt, E., Tusk, S. E. & Bayley, H. DNA scaffolds support stable and uniform peptide nanopores. Nat. Nanotechnol. 13, 739–745 (2018).
pubmed: 29808001
doi: 10.1038/s41565-018-0139-6
Grigoryan, G., Reinke, A. W. & Keating, A. E. Design of protein-interaction specificity gives selective bZIP-binding peptides. Nature 458, 859–864 (2009).
pubmed: 19370028
pmcid: 2748673
doi: 10.1038/nature07885
Peraro, M. D. & van der Goot, F. G. Pore-forming toxins: ancient, but never really out of fashion. Nat. Rev. Microbiol. 14, 77–92 (2016).
doi: 10.1038/nrmicro.2015.3
Niitsu, A., Heal, J. W., Fauland, K., Thomson, A. R. & Woolfson, D. N. Membrane-spanning α-helical barrels as tractable protein-design targets. Philos. Trans. Royal Soc. B 372, 20160213 (2017).
doi: 10.1098/rstb.2016.0213
Xu, C. et al. Computational design of transmembrane pores. Nature 585, 129–134 (2020).
pubmed: 32848250
pmcid: 7483984
doi: 10.1038/s41586-020-2646-5
Howorka, S. Building membrane nanopores. Nat. Nanotechnol. 12, 619–630 (2017).
pubmed: 28681859
doi: 10.1038/nnano.2017.99
Dou, J. Y. et al. De novo design of a fluorescence-activating β-barrel. Nature 561, 485–491 (2018).
pubmed: 30209393
pmcid: 6275156
doi: 10.1038/s41586-018-0509-0
Schuck, P. Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and Lamm equation modeling. Biophys. J. 78, 1606–1619 (2000).
pubmed: 10692345
pmcid: 1300758
doi: 10.1016/S0006-3495(00)76713-0
Battye, T. G. G., Kontogiannis, L., Johnson, O., Powell, H. R. & Leslie, A. G. W. iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM. Acta Crystallogr. D 67, 271–281 (2011).
pubmed: 21460445
pmcid: 3069742
doi: 10.1107/S0907444910048675
Evans, P. Scaling and assessment of data quality. Acta Crystallogr. D 62, 72–82 (2006).
pubmed: 16369096
doi: 10.1107/S0907444905036693
Evans, P. R. & Murshudov, G. N. How good are my data and what is the resolution? Acta Crystallogr. D 69, 1204–1214 (2013).
pubmed: 23793146
pmcid: 3689523
doi: 10.1107/S0907444913000061
Evans, P. R. An introduction to data reduction: space-group determination, scaling and intensity statistics. Acta Crystallogr. D 67, 282–292 (2011).
pubmed: 21460446
pmcid: 3069743
doi: 10.1107/S090744491003982X
Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D 75, 861–877 (2019).
doi: 10.1107/S2059798319011471
Joosten, R. P., Long, F., Murshudov, G. N. & Perrakis, A. The PDB_REDO server for macromolecular structure model optimization. IUCrJ 1, 213–220 (2014).
pubmed: 25075342
pmcid: 4107921
doi: 10.1107/S2052252514009324
Caffrey, M. & Cherezov, V. Crystallizing membrane proteins using lipidic mesophases. Nat. Protoc. 4, 706–731 (2009).
pubmed: 19390528
pmcid: 2732203
doi: 10.1038/nprot.2009.31
Kabsch, W. XDS. Acta Crystallogr. D 66, 125–132 (2010).
pubmed: 20124692
pmcid: 2815665
doi: 10.1107/S0907444909047337
Sammito, M. et al. ARCIMBOLDO_LITE: single-workstation implementation and use. Acta Crystallogr. D 71, 1921–1930 (2015).
pubmed: 26327382
doi: 10.1107/S1399004715010846
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).
pubmed: 20383002
pmcid: 2852313
doi: 10.1107/S0907444910007493
Maglia, G., Heron, A. J., Stoddart, D., Japrung, D. & Bayley, H. Analysis of single nucleic acid molecules with protein nanopores. Methods Enzymol. 475, 591–623 (2010).
pubmed: 20627172
pmcid: 3137938
doi: 10.1016/S0076-6879(10)75022-9
Montal, M. & Mueller, P. Formation of bimolecular membranes from lipid monolayers and a study of their electrical properties. Proc. Natl Acad. Sci. USA 69, 3561–3566 (1972).
pubmed: 4509315
pmcid: 389821
doi: 10.1073/pnas.69.12.3561
Gu, L. Q. et al. Reversal of charge selectivity in transmembrane protein pores by using noncovalent molecular adapters. Proc. Natl Acad. Sci. USA 97, 3959–3964 (2000).
pubmed: 10760267
pmcid: 18124
doi: 10.1073/pnas.97.8.3959
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
pubmed: 22743772
doi: 10.1038/nmeth.2019
Tinevez, J. Y. et al. TrackMate: an open and extensible platform for single-particle tracking. Methods 115, 80–90 (2017).
pubmed: 27713081
doi: 10.1016/j.ymeth.2016.09.016
Ramadurai, S. et al. Lateral diffusion of membrane proteins. J. Am. Chem. Soc. 131, 12650–12656 (2009).
pubmed: 19673517
doi: 10.1021/ja902853g
Kučerka, N., Nieh, M.-P. & Katsaras, J. Fluid phase lipid areas and bilayer thicknesses of commonly used phosphatidylcholines as a function of temperature. Biochim. Biophys. Acta Biomembr. 1808, 2761–2771 (2011).
doi: 10.1016/j.bbamem.2011.07.022