De novo design of a reversible phosphorylation-dependent switch for membrane targeting.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
05 03 2021
05 03 2021
Historique:
received:
18
05
2020
accepted:
03
02
2021
entrez:
6
3
2021
pubmed:
7
3
2021
medline:
20
3
2021
Statut:
epublish
Résumé
Modules that switch protein-protein interactions on and off are essential to develop synthetic biology; for example, to construct orthogonal signaling pathways, to control artificial protein structures dynamically, and for protein localization in cells or protocells. In nature, the E. coli MinCDE system couples nucleotide-dependent switching of MinD dimerization to membrane targeting to trigger spatiotemporal pattern formation. Here we present a de novo peptide-based molecular switch that toggles reversibly between monomer and dimer in response to phosphorylation and dephosphorylation. In combination with other modules, we construct fusion proteins that couple switching to lipid-membrane targeting by: (i) tethering a 'cargo' molecule reversibly to a permanent membrane 'anchor'; and (ii) creating a 'membrane-avidity switch' that mimics the MinD system but operates by reversible phosphorylation. These minimal, de novo molecular switches have potential applications for introducing dynamic processes into designed and engineered proteins to augment functions in living cells and add functionality to protocells.
Identifiants
pubmed: 33674566
doi: 10.1038/s41467-021-21622-5
pii: 10.1038/s41467-021-21622-5
pmc: PMC7935970
doi:
Substances chimiques
Peptides
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
1472Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/L01386X1
Pays : United Kingdom
Références
Alberts, B. et al. Molecular Biology of the Cell (W.W. Norton & Company, 2014).
Ambroggio, X. I. & Kuhlman, B. Design of protein conformational switches. Curr. Opin. Struct. Biol. 16, 525–530 (2006).
pubmed: 16765587
doi: 10.1016/j.sbi.2006.05.014
Ha, J.-H. & Loh, S. N. Protein conformational switches: from nature to design. Chemistry 18, 7984–7999 (2012).
pubmed: 22688954
pmcid: 3404493
doi: 10.1002/chem.201200348
Stein, V. & Alexandrov, K. Synthetic protein switches: design principles and applications. Trends Biotechnol. 33, 101–110 (2014).
pubmed: 25535088
doi: 10.1016/j.tibtech.2014.11.010
Rollins, C. T. et al. A ligand-reversible dimerization system for controlling protein-protein interactions. Proc. Natl Acad. Sci. USA 97, 7096–7101 (2000).
pubmed: 10852943
doi: 10.1073/pnas.100101997
Fegan, A., White, B., Carlson, J. C. T. & Wagner, C. R. Chemically controlled protein assembly: techniques and applications. Chem. Rev. 110, 3315–3336 (2010).
pubmed: 20353181
doi: 10.1021/cr8002888
Miyamoto, T. et al. Rapid and orthogonal logic gating with a gibberellin-induced dimerization system. Nat. Chem. Biol. 8, 465–470 (2012).
pubmed: 22446836
pmcid: 3368803
doi: 10.1038/nchembio.922
Zhang, K. & Cui, B. Optogenetic control of intracellular signaling pathways. Trends Biotechnol. 33, 92–100 (2014).
pubmed: 25529484
pmcid: 4308517
doi: 10.1016/j.tibtech.2014.11.007
Guntas, G. et al. Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins. Proc. Natl Acad. Sci. USA 112, 112–117 (2015).
pubmed: 25535392
doi: 10.1073/pnas.1417910112
Strickland, D. et al. TULIPs: tunable, light-controlled interacting protein tags for cell biology. Nat. Methods 9, 379–384 (2012).
pubmed: 22388287
pmcid: 3444151
doi: 10.1038/nmeth.1904
Wang, H. et al. LOVTRAP: an optogenetic system for photoinduced protein dissociation. Nat. Methods 13, 755–758 (2016).
pubmed: 27427858
pmcid: 5137947
doi: 10.1038/nmeth.3926
Goryachev, A. B. & Pokhilko, A. V. Dynamics of Cdc42 network embodies a Turing-type mechanism of yeast cell polarity. FEBS Lett. 582, 1437–1443 (2008).
pubmed: 18381072
doi: 10.1016/j.febslet.2008.03.029
Jahnke, K. et al. Programmable Functionalization of Surfactant‐Stabilized Microfluidic Droplets via DNA‐Tags. Adv. Funct. Mater. 29, 1808647 (2019).
Lee, M. J. et al. Engineered synthetic scaffolds for organizing proteins within the bacterial cytoplasm. Nat. Chem. Biol. 14, 142–147 (2018).
pubmed: 29227472
doi: 10.1038/nchembio.2535
Ramm, B., Heermann, T. & Schwille, P. The E. coli MinCDE system in the regulation of protein patterns and gradients. Cell. Mol. Life Sci. 25, 1–29 (2019).
Loose, M., Fischer-Friedrich, E., Ries, J., Kruse, K. & Schwille, P. Spatial regulators for bacterial cell division self-organize into surface waves in vitro. Science 320, 789–792 (2008).
pubmed: 18467587
doi: 10.1126/science.1154413
Johnson, J. M., Jin, M. & Lew, D. J. Symmetry breaking and the establishment of cell polarity in budding yeast. Curr. Opin. Genet. Dev. 21, 740–746 (2011).
pubmed: 21955794
pmcid: 3224179
doi: 10.1016/j.gde.2011.09.007
Szeto, T. H., Rowland, S. L., Rothfield, L. I. & King, G. F. Membrane localization of MinD is mediated by a C-terminal motif that is conserved across eubacteria, archaea, and chloroplasts. Proc. Natl Acad. Sci. USA 99, 15693–15698 (2002).
pubmed: 12424340
doi: 10.1073/pnas.232590599
Szeto, T. H., Rowland, S. L., Habrukowich, C. L. & King, G. F. The MinD membrane targeting sequence is a transplantable lipid-binding helix. J. Biol. Chem. 278, 40050–40056 (2003).
pubmed: 12882967
doi: 10.1074/jbc.M306876200
Lemmon, M. A. & Schlessinger, J. Cell signaling by receptor tyrosine kinases. Cell 141, 1117–1134 (2010).
pubmed: 20602996
pmcid: 2914105
doi: 10.1016/j.cell.2010.06.011
Zondlo, S. C., Gao, F. & Zondlo, N. J. Design of an encodable tyrosine kinase-inducible domain: detection of tyrosine kinase activity by terbium luminescence. J. Am. Chem. Soc. 132, 5619–5621 (2010).
pubmed: 20361796
doi: 10.1021/ja100862u
Gao, F., Thornley, B. S., Tressler, C. M., Naduthambi, D. & Zondlo, N. J. Phosphorylation-dependent protein design: design of a minimal protein kinase-inducible domain. Org. Biomol. Chem. 17, 3984–3995 (2019).
pubmed: 30942803
pmcid: 6668337
doi: 10.1039/C9OB00502A
Shi, J., Fichman, G. & Schneider, J. P. Enzymatic Control of the Conformational Landscape of Self-Assembling Peptides. Angew. Chem. Int. Ed. Engl. 57, 11188–11192 (2018).
pubmed: 29969177
pmcid: 6294317
doi: 10.1002/anie.201803983
Signarvic, R. S. & DeGrado, W. F. De novo design of a molecular switch: phosphorylation-dependent association of designed peptides. J. Mol. Biol. 334, 1–12 (2003).
pubmed: 14596795
doi: 10.1016/j.jmb.2003.09.041
Szilák, L., Moitra, J. & Vinson, C. Design of a leucine zipper coiled coil stabilized 1.4 kcal mol-1 by phosphorylation of a serine in the e position. Protein Sci. 6, 1273–1283 (1997).
pubmed: 9194187
pmcid: 2143729
doi: 10.1002/pro.5560060615
Szilák, L., Moitra, J., Krylov, D. & Vinson, C. Phosphorylation destabilizes alpha-helices. Nat. Struct. Biol. 4, 112–114 (1997).
pubmed: 9033589
doi: 10.1038/nsb0297-112
Ciani, B., Hutchinson, E. G., Sessions, R. B. & Woolfson, D. N. A designed system for assessing how sequence affects alpha to beta conformational transitions in proteins. J. Biol. Chem. 277, 10150–10155 (2002).
pubmed: 11751929
doi: 10.1074/jbc.M107663200
Pandya, M. J. et al. Sequence and structural duality: designing peptides to adopt two stable conformations. J. Am. Chem. Soc. 126, 17016–17024 (2004).
pubmed: 15612740
doi: 10.1021/ja045568c
Cerasoli, E., Sharpe, B. K. & Woolfson, D. N. ZiCo: a peptide designed to switch folded state upon binding zinc. J. Am. Chem. Soc. 127, 15008–15009 (2005).
pubmed: 16248623
doi: 10.1021/ja0543604
Ambroggio, X. I. & Kuhlman, B. Computational design of a single amino acid sequence that can switch between two distinct protein folds. J. Am. Chem. Soc. 128, 1154–1161 (2006).
pubmed: 16433531
doi: 10.1021/ja054718w
Lizatović, R. et al. A de novo designed coiled-coil peptide with a reversible pH-induced oligomerization switch. Structure 24, 946–955 (2016).
pubmed: 27161978
doi: 10.1016/j.str.2016.03.027
Boyken, S. E. et al. De novo design of tunable, pH-driven conformational changes. Science 364, 658–664 (2019).
pubmed: 31097662
pmcid: 7072037
doi: 10.1126/science.aav7897
Thomas, F., Boyle, A. L., Burton, A. J. & Woolfson, D. N. A set of de novo designed parallel heterodimeric coiled coils with quantified dissociation constants in the micromolar to sub-nanomolar regime. J. Am. Chem. Soc. 135, 5161–5166 (2013).
pubmed: 23477407
doi: 10.1021/ja312310g
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
Woolfson, D. N. The design of coiled-coil structures and assemblies. Adv. Protein Chem. 70, 79–112 (2005).
pubmed: 15837514
doi: 10.1016/S0065-3233(05)70004-8
Hussey, B. J. & McMillen, D. R. Programmable T7-based synthetic transcription factors. Nucleic Acids Res. 46, 9842–9854 (2018).
pubmed: 30169636
pmcid: 6182181
doi: 10.1093/nar/gky785
Smith, A. J., Thomas, F., Shoemark, D., Woolfson, D. N. & Savery, N. J. Guiding biomolecular interactions in cells using de novo protein-protein interfaces. ACS Synth. Biol. 8, 1284–1293 (2019).
pubmed: 31059644
doi: 10.1021/acssynbio.8b00501
Edgell, C. L., Smith, A. J., Beesley, J. L., Savery, N. J. & Woolfson, D. N. De novo designed protein-interaction modules for in-cell applications. ACS Synth. Biol. 9, 427–436 (2020).
Fink, T. et al. Design of fast proteolysis-based signaling and logic circuits in mammalian cells. Nat. Chem. Biol. 15, 115–122 (2019).
pubmed: 30531965
doi: 10.1038/s41589-018-0181-6
Gordley, R. M., Bugaj, L. J. & Lim, W. A. Modular engineering of cellular signaling proteins and networks. Curr. Opin. Struct. Biol. 39, 106–114 (2016).
pubmed: 27423114
pmcid: 5127285
doi: 10.1016/j.sbi.2016.06.012
Woolfson, D. N. & Alber, T. Predicting oligomerization states of coiled coils. Protein Sci. 4, 1596–1607 (1995).
pubmed: 8520486
pmcid: 2143200
doi: 10.1002/pro.5560040818
Acharya, A., Rishi, V. & Vinson, C. Stability of 100 homo and heterotypic coiled-coil a-a’ pairs for ten amino acids (A, L, I, V, N, K, S, T, E, and R). Biochemistry 45, 11324–11332 (2006).
pubmed: 16981692
doi: 10.1021/bi060822u
Nye, J. A. & Groves, J. T. Kinetic control of histidine-tagged protein surface density on supported lipid bilayers. Langmuir 24, 4145–4149 (2008).
pubmed: 18303929
doi: 10.1021/la703788h
Buchkovich, N. J., Henne, W. M., Tang, S. & Emr, S. D. Essential N-terminal insertion motif anchors the ESCRT-III filament during MVB vesicle formation. Dev. Cell 27, 201–214 (2013).
pubmed: 24139821
doi: 10.1016/j.devcel.2013.09.009
Behrendorff, J. B. Y. H., Borràs-Gas, G. & Pribil, M. Synthetic protein scaffolding at biological membranes. Trends Biotechnol. 38, 432–446 (2019).
Lee, M. J. et al. Engineered synthetic scaffolds for organizing proteins within the bacterial cytoplasm. Nat. Chem. Biol. 14, 142–147 (2018).
pubmed: 29227472
doi: 10.1038/nchembio.2535
Kurokawa, C. et al. DNA cytoskeleton for stabilizing artificial cells. Proc. Natl Acad. Sci. USA 114, 7228–7233 (2017).
pubmed: 28652345
doi: 10.1073/pnas.1702208114
Nautiyal, S., Woolfson, D. N., King, D. S. & Alber, T. A designed heterotrimeric coiled coil. Biochemistry 34, 11645–11651 (1995).
pubmed: 7547896
doi: 10.1021/bi00037a001
Fletcher, J. M. et al. A basis set of de novo coiled-coil peptide oligomers for rational protein design and synthetic biology. ACS Synth. Biol. 1, 240–250 (2012).
pubmed: 23651206
doi: 10.1021/sb300028q
Leopold, A. V., Chernov, K. G. & Verkhusha, V. V. Optogenetically controlled protein kinases for regulation of cellular signaling. Chem. Soc. Rev. 47, 2454–2484 (2018).
pubmed: 29498733
pmcid: 5882534
doi: 10.1039/C7CS00404D
Gao, X. J., Chong, L. S., Kim, M. S. & Elowitz, M. B. Programmable protein circuits in living cells. Science 361, 1252–1258 (2018).
pubmed: 30237357
pmcid: 7176481
doi: 10.1126/science.aat5062
Langan, R. A. et al. De novo design of bioactive protein switches. Nature 537, 320 (2019).
Ng, A. H. et al. Modular and tunable biological feedback control using a de novo protein switch. Nature 352, 680 (2019).
Ptashne, M. & Gann, A. Transcriptional activation by recruitment. Nature 386, 569–577 (1997).
doi: 10.1038/386569a0
Thompson, K. E., Bashor, C. J., Lim, W. A. & Keating, A. E. SYNZIP protein interaction toolbox: in vitro and in vivo specifications of heterospecific coiled-coil interaction domains. ACS Synth. Biol. 1, 118–129 (2012).
pubmed: 22558529
pmcid: 3339576
doi: 10.1021/sb200015u
Edgell, C. L., Smith, A. J., Beesley, J. L., Savery, N. J. & Woolfson, D. N. De novo designed protein-interaction modules for in-cell applications. ACS Synth. Biol. 9, 427–436 (2020).
pubmed: 31977192
doi: 10.1021/acssynbio.9b00453
Fletcher, J. M. et al. Self-assembling cages from coiled-coil peptide modules. Science 340, 595–599 (2013).
pubmed: 23579496
pmcid: 6485442
doi: 10.1126/science.1233936
Ljubetič, A. et al. Design of coiled-coil protein-origami cages that self-assemble in vitro and in vivo. Nat. Biotechnol. 35, 1094–1101 (2017).
pubmed: 29035374
doi: 10.1038/nbt.3994
Jones, D. H. & Howard, B. H. A rapid method for recombination and site-specific mutagenesis by placing homologous ends on DNA using polymerase chain reaction. BioTechniques 10, 62–66 (1991).
pubmed: 2003926
Bubeck, P., Winkler, M. & Bautsch, W. Rapid cloning by homologous recombination in vivo. Nucleic Acids Res. 21, 3601–3602 (1993).
pubmed: 8346047
pmcid: 331480
doi: 10.1093/nar/21.15.3601
Harrington, L., Cheley, S., Alexander, L. T., Knapp, S. & Bayley, H. Stochastic detection of Pim protein kinases reveals electrostatically enhanced association of a peptide substrate. Proc. Natl Acad. Sci. USA 110, E4417–E4426 (2013).
pubmed: 24194548
doi: 10.1073/pnas.1312739110
Walker, B., Krishnasastry, M., Zorn, L., Kasianowicz, J. & Bayley, H. Functional expression of the alpha-hemolysin of Staphylococcus aureus in intact Escherichia coli and in cell lysates. Deletion of five C-terminal amino acids selectively impairs hemolytic activity. J. Biol. Chem. 267, 10902–10909 (1992).
pubmed: 1587866
doi: 10.1016/S0021-9258(19)50103-X
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
doi: 10.1038/nmeth.2019