Catalytic peptide-based coacervates for enhanced function through structural organization and substrate specificity.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
30 Oct 2024
30 Oct 2024
Historique:
received:
07
07
2023
accepted:
15
10
2024
medline:
31
10
2024
pubmed:
31
10
2024
entrez:
31
10
2024
Statut:
epublish
Résumé
Liquid-liquid phase separation (LLPS) in living cells provides innovative pathways for synthetic compartmentalized catalytic systems. While LLPS has been explored for enhancing enzyme catalysis, its potential application to catalytic peptides remains unexplored. Here, we demonstrate the use of coacervation, a key LLPS feature, to constrain the conformational flexibility of catalytic peptides, resulting in structured domains that enhance peptide catalysis. Using the flexible catalytic peptide P7 as a model, we induce reversible biomolecular coacervates with structured peptide domains proficient in hydrolyzing phosphate ester molecules and selectively sequestering phosphorylated proteins. Remarkably, these coacervate-based microreactors exhibit a 15,000-fold increase in catalytic efficiency compared to soluble peptides. Our findings highlight the potential of a single peptide to induce coacervate formation, selectively recruit substrates, and mediate catalysis, enabling a simple design for low-complexity, single peptide-based compartments with broad implications. Moreover, LLPS emerges as a fundamental mechanism in the evolution of chemical functions, effectively managing conformational heterogeneity in short peptides and providing valuable insights into the evolution of enzyme activity and catalysis in prebiotic chemistry.
Identifiants
pubmed: 39477955
doi: 10.1038/s41467-024-53699-z
pii: 10.1038/s41467-024-53699-z
doi:
Substances chimiques
Peptides
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
9368Informations de copyright
© 2024. The Author(s).
Références
Mann, S. Life as a nanoscale phenomenon. Angew. Chem. Int. Ed. 47, 5306–5320 (2008).
doi: 10.1002/anie.200705538
Schrum, J. P., Zhu, T. F. & Szostak, J. W. The origins of cellular life. Cold Spring Harb. Perspect. Biol. 2, a002212 (2010).
Szostak, J. W., Bartel, D. P. & Luisi, P. L. Synthesizing life. Nature 409, 387–390 (2001).
pubmed: 11201752
doi: 10.1038/35053176
Rumyantsev, A. M., Jackson, N. E. & de Pablo, J. J. Polyelectrolyte complex coacervates: recent developments and new frontiers. Ann. Rev. Condens. Matter Phys. 12, 155–176 (2021).
doi: 10.1146/annurev-conmatphys-042020-113457
Banani, S. F., Lee, H. O., Hyman, A. A. & Rosen, M. K. Biomolecular condensates: organizers of cellular Biochem. Nat. Rev. Mol. Cell Biol. 18, 285–298 (2017).
pubmed: 28225081
doi: 10.1038/nrm.2017.7
Boeynaems, S. et al. Protein phase separation: a new phase in cell biology. Trends Cell Biol. 28, 420–435 (2018).
pubmed: 29602697
doi: 10.1016/j.tcb.2018.02.004
Bracha, D., Walls, M. T. & Brangwynne, C. P. Probing and engineering liquid-phase organelles. Nat. Biotechnol. 37, 1435–1445 (2019).
pubmed: 31792412
doi: 10.1038/s41587-019-0341-6
Li, P. et al. Phase transitions in the assembly of multivalent signalling proteins. Nature 483, 336–340 (2012).
pubmed: 22398450
doi: 10.1038/nature10879
Su, X. et al. Phase separation of signaling molecules promotes T cell receptor signal transduction. Science 352, 595–599 (2016).
pubmed: 27056844
doi: 10.1126/science.aad9964
Wang, H. et al. Rubisco condensate formation by CcmM in β-carboxysome biogenesis. Nature 566, 131–135 (2019).
pubmed: 30675061
doi: 10.1038/s41586-019-0880-5
Peeples, W. & Rosen, M. K. Mechanistic dissection of increased enzymatic rate in a phase-separated compartment. Nat. Chem. Biol. 17, 693–702 (2021).
pubmed: 34035521
doi: 10.1038/s41589-021-00801-x
Wang, Y. et al. Phase-separated multienzyme compartmentalization for terpene biosynthesis in a prokaryote. Angew. Chem. Int. Ed. 61, e202203909 (2022).
doi: 10.1002/anie.202203909
Song, S. et al. Engineering transient dynamics of artificial cells by stochastic distribution of enzymes. Nat. Commun. 12, 6897 (2021).
pubmed: 34824231
doi: 10.1038/s41467-021-27229-0
Abbas, M., Lipiński, W. P., Nakashima, K. K., Huck, W. T. S. & Spruijt, E. A short peptide synthon for liquid–liquid phase separation. Nat. Chem. 13, 1046–1054 (2021).
pubmed: 34645986
doi: 10.1038/s41557-021-00788-x
Metrano, A. J. & Miller, S. J. Peptide-based catalysts reach the outer sphere through remote desymmetrization and atroposelectivity. Acc. Chem. Res. 52, 199–215 (2019).
pubmed: 30525436
doi: 10.1021/acs.accounts.8b00473
Carvalho, S., Peralta Reis, D. Q., Pereira, S. V., Kalafatovic, D. & Pina, A. S. Catalytic peptides: the challenge between simplicity and functionality. Isr. J. Chem. 62, e202200029 (2022).
doi: 10.1002/ijch.202200029
Abbas, M., Lipiński, W. P., Wang, J. & Spruijt, E. Peptide-based coacervates as biomimetic protocells. Chem. Soc. Rev. 50, 3690–3705 (2021).
pubmed: 33616129
doi: 10.1039/D0CS00307G
Adamala, K. & Szostak, J. W. Competition between model protocells driven by an encapsulated catalyst. Nat. Chem. 5, 495–501 (2013).
pubmed: 23695631
doi: 10.1038/nchem.1650
Sun, Y. et al. Phase-separating peptides for direct cytosolic delivery and redox-activated release of macromolecular therapeutics. Nat. Chem. 14, 274–283 (2022).
pubmed: 35115657
doi: 10.1038/s41557-021-00854-4
Baruch Leshem, A. et al. Biomolecular condensates formed by designer minimalistic peptides. Nat. Commun. 14, 421 (2023).
pubmed: 36702825
doi: 10.1038/s41467-023-36060-8
Tang, Y. et al. Prediction and characterization of liquid-liquid phase separation of minimalistic peptides. Cell Rep. Phys. Sci. 2, 100579 (2021).
doi: 10.1016/j.xcrp.2021.100579
Fisher, R. S. & Elbaum-Garfinkle, S. Tunable multiphase dynamics of arginine and lysine liquid condensates. Nat. Commun. 11, 4628 (2020).
pubmed: 32934220
doi: 10.1038/s41467-020-18224-y
Sementa, D. et al. Sequence-tunable phase behavior and intrinsic fluorescence in dynamically interacting peptides. Angew. Chem. Int. Ed. 62, e202311479 (2023).
doi: 10.1002/anie.202311479
Dai, Y. et al. Programmable synthetic biomolecular condensates for cellular control. Nat. Chem. Biol. 19, 518–528 (2023).
pubmed: 36747054
doi: 10.1038/s41589-022-01252-8
Pina, A. S. et al. Discovery of phosphotyrosine-binding oligopeptides with supramolecular target selectivity. Chem. Sci. 13, 210–217 (2022).
doi: 10.1039/D1SC04420F
Krainer, G. et al. Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions. Nat. Commun. 12, 1085 (2021).
pubmed: 33597515
doi: 10.1038/s41467-021-21181-9
Bagińska, K., Makowska, J., Wiczk, W., Kasprzykowski, F. & ChmurzyńSKI, L. Conformational studies of alanine-rich peptide using CD and FTIR spectroscopy. J. Pept. Sci. 14, 283–289 (2008).
pubmed: 17918765
doi: 10.1002/psc.923
Barreto, M. S. C., Elzinga, E. J. & Alleoni, L. R. F. The molecular insights into protein adsorption on hematite surface disclosed by in-situ ATR-FTIR/2D-COS study. Sci. Rep. 10, 13441 (2020).
pubmed: 32778712
doi: 10.1038/s41598-020-70201-z
Booth, R., Qiao, Y., Li, M. & Mann, S. Spatial positioning and chemical coupling in coacervate-in-proteinosome protocells. Angew. Chem. Int. Ed. 58, 9120–9124 (2019).
doi: 10.1002/anie.201903756
Küchler, A., Yoshimoto, M., Luginbühl, S., Mavelli, F. & Walde, P. Enzymatic reactions in confined environments. Nat. Nanotechnol. 11, 409–420 (2016).
pubmed: 27146955
doi: 10.1038/nnano.2016.54
Schoonen, L. & van Hest, J. C. M. Compartmentalization approaches in soft matter science: from nanoreactor development to organelle mimics. Adv. Mater. 28, 1109–1128 (2016).
pubmed: 26509964
doi: 10.1002/adma.201502389
Love, C. et al. Reversible pH-responsive coacervate formation in lipid vesicles activates dormant enzymatic reactions. Angew. Chem. Int. Ed. 59, 5950–5957 (2020).
doi: 10.1002/anie.201914893
Garenne, D. et al. Sequestration of proteins by fatty acid coacervates for their encapsulation within vesicles. Angew. Chem. Int. Ed. 55, 13475–13479 (2016).
doi: 10.1002/anie.201607117
Hammes, G. G. & Wu, C.-W. Kinetics of allosteric enzymes. Ann. Rev. Biophys. Bioeng. 3, 1–33 (1974).
doi: 10.1146/annurev.bb.03.060174.000245
Cakmak, F. P., Choi, S., Meyer, M. O., Bevilacqua, P. C. & Keating, C. D. Prebiotically-relevant low polyion multivalency can improve functionality of membraneless compartments. Nat. Commun. 11, 5949 (2020).
pubmed: 33230101
pmcid: 7683531
doi: 10.1038/s41467-020-19775-w
Choi, S., Knoerdel, A. R., Sing, C. E. & Keating, C. D. Effect of polypeptide complex coacervate microenvironment on protonation of a guest molecule. J. Phys. Chem. B 127, 5978–5991 (2023).
pubmed: 37350455
doi: 10.1021/acs.jpcb.3c02098
Freitas, C. et al. A protein phosphorylation module patterns the Bacillus subtilis spore outer coat. Mol. Microbiol. 114, 934–951 (2020).
pubmed: 32592201
pmcid: 7821199
doi: 10.1111/mmi.14562
Hansson, O. Biomarkers for neurodegenerative diseases. Nat. Med. 27, 954–963 (2021).
pubmed: 34083813
doi: 10.1038/s41591-021-01382-x
van Veldhuisen, T. W. et al. Enzymatic regulation of protein–protein interactions in artificial cells. Adv. Mater. 35, 2300947 (2023).
doi: 10.1002/adma.202300947
Pabis, A., Duarte, F. & Kamerlin, S. C. L. Promiscuity in the enzymatic catalysis of phosphate and sulfate transfer. Biochem 55, 3061–3081 (2016).
doi: 10.1021/acs.biochem.6b00297
Gao, N. & Mann, S. Membranized coacervate microdroplets: from versatile protocell models to cytomimetic materials. Acc. Chem. Res. 56, 297–307 (2023).
pubmed: 36625520
doi: 10.1021/acs.accounts.2c00696
Frenkel-Pinter, M., Samanta, M., Ashkenasy, G. & Leman, L. J. Prebiotic peptides: molecular hubs in the origin of life. Chem. Rev. 120, 4707–4765 (2020).
pubmed: 32101414
doi: 10.1021/acs.chemrev.9b00664
Koga, S., Williams, D. S., Perriman, A. W. & Mann, S. Peptide–nucleotide microdroplets as a step towards a membrane-free protocell model. Nat. Chem. 3, 720–724 (2011).
pubmed: 21860462
doi: 10.1038/nchem.1110
Crowe, C. D. & Keating, C. D. Liquid–liquid phase separation in artificial cells. Interface Focus 8, 20180032 (2018).
pubmed: 30443328
doi: 10.1098/rsfs.2018.0032
Keating, C. D. Aqueous phase separation as a possible route to compartmentalization of biological molecules. Acc. Chem. Res. 45, 2114–2124 (2012).
pubmed: 22330132
doi: 10.1021/ar200294y
Nakashima, K. K., André, A. A. M. & Spruijt, E. in Methods in Enzymology Vol. 646 (ed Christine D. Keating) 353–389 (Academic Press, 2021).
Pereira, P. M., Almada, P. & Henriques, R. in Methods Cell Biol, Vol. 125 (ed Ewa K. Paluch) 95−117 (Academic Press, 2015).
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
Greenfield, N. J. Using circular dichroism spectra to estimate protein secondary structure. Nat. Protoc. 1, 2876–2890 (2006).
pubmed: 17406547
doi: 10.1038/nprot.2006.202
Shaka, A. J., Lee, C. J. & Pines, A. Iterative schemes for bilinear operators; application to spin decoupling. J. Magn. Reson. 77, 274–293 (1988).
Hwang, T. L. & Shaka, A. J. Water suppression that works. Excitation sculpting using arbitrary wave-forms and pulsed-field gradients. J. Magn. Reson. Ser. A 112, 275–279 (1995).
doi: 10.1006/jmra.1995.1047
Bax, A. & Davis, D. G. Practical aspects of two-dimensional transverse NOE spectroscopy. J. Magn. Reson. 63, 207–213 (1985).
Palmer, A. G., Cavanagh, J., Wright, P. E. & Rance, M. Sensitivity improvement in proton-detected two-dimensional heteronuclear correlation NMR spectroscopy. J. Magn. Reson. 93, 151–170 (1991).
Schleucher, J. et al. A general enhancement scheme in heteronuclear multidimensional NMR employing pulsed field gradients. J. Biomol. NMR 4, 301–306 (1994).
pubmed: 8019138
doi: 10.1007/BF00175254
Kay, L. E., Keifer, P. & Saarinen, T. Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity. J. Am. Chem. Soc. 114, 10663–10665 (1992).
doi: 10.1021/ja00052a088
Lee, W., Rahimi, M., Lee, Y. & Chiu, A. POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules. Bioinformatics 37, 3041–3042 (2021).
pubmed: 33715003
doi: 10.1093/bioinformatics/btab180
Pierattelli, R., Banci, L. & Turner, D. L. Indirect determination of magnetic susceptibility tensors in peroxidases: a novel approach to structure elucidation by NMR. JBIC J. Biol. Inorg. Chem. 1, 320–329 (1996).
doi: 10.1007/s007750050060
Wishart, D. S. et al. 1H, 13C and 15N chemical shift referencing in biomolecular NMR. J. Biomol. NMR 6, 135–140 (1995).
pubmed: 8589602
doi: 10.1007/BF00211777
Hafsa, N. E., Arndt, D. & Wishart, D. S. CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts. Nucleic Acids Res. 43, W370–W377 (2015).
pubmed: 25979265
doi: 10.1093/nar/gkv494
Rino, J., Martin, R. M., Carvalho, T. & Carmo-Fonseca, M. Imaging dynamic interactions between spliceosomal proteins and pre-mRNA in living cells. Methods 65, 359–366, (2014).
pubmed: 23969316
doi: 10.1016/j.ymeth.2013.08.010