Einzeltreffer — DigiBib

A wooden house frame consists of many different lumber pieces, but because of the regularity of these building blocks, the structure can be designed using straightforward geometrical principles. The design of multicomponent protein assemblies, in comparison, has been much more complex, largely owing to the irregular shapes of protein structures 1 . Here we describe extendable linear, curved and angled protein building blocks, as well as inter-block interactions, that conform to specified geometric standards; assemblies designed using these blocks inherit their extendability and regular interaction surfaces, enabling them to be expanded or contracted by varying the number of modules, and reinforced with secondary struts. Using X-ray crystallography and electron microscopy, we validate nanomaterial designs ranging from simple polygonal and circular oligomers that can be concentrically nested, up to large polyhedral nanocages and unbounded straight 'train track' assemblies with reconfigurable sizes and geometries that can be readily blueprinted. Because of the complexity of protein structures and sequence-structure relationships, it has not previously been possible to build up large protein assemblies by deliberate placement of protein backbones onto a blank three-dimensional canvas; the simplicity and geometric regularity of our design platform now enables construction of protein nanomaterials according to 'back of an envelope' architectural blueprints.

Titel:	Blueprinting extendable nanomaterials with standardized protein blocks.
Autor/in / Beteiligte Person:	Huddy, TF ; Hsia, Y ; Kibler, RD ; Xu, J ; Bethel, N ; Nagarajan, D ; Redler, R ; Leung, PJY ; Weidle, C ; Courbet, A ; Yang, EC ; Bera, AK ; Coudray, N ; Calise, SJ ; Davila-Hernandez, FA ; Han, HL ; Carr, KD ; Li, Z ; McHugh, R ; Reggiano, G ; Kang, A ; Sankaran, B ; Dickinson, MS ; Coventry, B ; Brunette, TJ ; Liu, Y ; Dauparas, J ; Borst, AJ ; Ekiert, D ; Kollman, JM ; Bhabha, G ; Baker, D
Link:	View record at Springer (Volltext)
Zeitschrift:	Nature, Jg. 627 (2024-03-01), Heft 8005, S. 898-904
Veröffentlichung:	Basingstoke : Nature Publishing Group ; <i>Original Publication</i>: London, Macmillan Journals ltd., 2024
Medientyp:	academicJournal
ISSN:	1476-4687 (electronic)
DOI:	10.1038/s41586-024-07188-4
Schlagwort:	Crystallography, X-Ray Microscopy, Electron Reproducibility of Results Nanostructures chemistry Proteins chemistry Proteins metabolism
Sonstiges:	Nachgewiesen in: MEDLINE Sprachen: English Publication Type: Journal Article Language: English [Nature] 2024 Mar; Vol. 627 (8005), pp. 898-904. <i>Date of Electronic Publication: </i>2024 Mar 13. MeSH Terms: Nanostructures* / chemistry ; Proteins* / chemistry ; Proteins* / metabolism ; Crystallography, X-Ray ; Microscopy, Electron ; Reproducibility of Results Comments: Update of: bioRxiv. 2023 Jun 09;:. (PMID: 37333359) References: Berman, H. M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235–242 (2000). (PMID: 10.1093/nar/28.1.23510592235102472) ; Thomson, A. R. et al. Computational design of water-soluble α-helical barrels. Science 346, 485–488 (2014). (PMID: 10.1126/science.125745225342807) ; Wicky, B. I. M. et al. Hallucinating symmetric protein assemblies. Science 378, 56–61 (2022). (PMID: 10.1126/science.add1964361080489724707) ; Fallas, J. A. et al. Computational design of self-assembling cyclic protein homo-oligomers. Nat. Chem. 9, 353–360 (2017). (PMID: 10.1038/nchem.267328338692) ; 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). (PMID: 10.1038/nbt.399429035374) ; Hsia, Y. et al. Design of multi-scale protein complexes by hierarchical building block fusion. Nat. Commun. 12, 2294 (2021). (PMID: 10.1038/s41467-021-22276-z338638898052403) ; King, N. P. et al. Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science 336, 1171–1174 (2012). (PMID: 10.1126/science.1219364226540604138882) ; Sheffler, W. et al. Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock. PLoS Comput. Biol. 19, e1010680 (2023). (PMID: 10.1371/journal.pcbi.10106803721634310237659) ; Bethel, N. P. et al. Precisely patterned nanofibres made from extendable protein multiplexes. Nat. Chem. 15, 1664–1671 (2023). ; Brodin, J. D. et al. Metal-directed, chemically tunable assembly of one-, two- and three-dimensional crystalline protein arrays. Nat. Chem. 4, 375–382 (2012). (PMID: 10.1038/nchem.1290225222573335442) ; Sinclair, J. C., Davies, K. M., Vénien-Bryan, C. & Noble, M. E. M. Generation of protein lattices by fusing proteins with matching rotational symmetry. Nat. Nanotechnol. 6, 558–562 (2011). (PMID: 10.1038/nnano.2011.12221804552) ; Ben-Sasson, A.J. et al. Design of biologically active binary protein 2D materials. Nature 589, 468–473 (2021). (PMID: 10.1038/s41586-020-03120-8334084087855610) ; Li, Z. et al. Accurate computational design of three-dimensional protein crystals. Nat. Mater. 22, 1556–1563 (2023). ; Padilla, J. E., Colovos, C. & Yeates, T. O. Nanohedra: using symmetry to design self assembling protein cages, layers, crystals, and filaments. Proc. Natl Acad. Sci. USA 98, 2217–2221 (2001). (PMID: 10.1073/pnas.0416149981122621930118) ; Woolfson, D. N. Understanding a protein fold: the physics, chemistry, and biology of α-helical coiled coils. J. Biol. Chem. 299, 104579 (2023). (PMID: 10.1016/j.jbc.2023.1045793687175810124910) ; Grigoryan, G. & Degrado, W. F. Probing designability via a generalized model of helical bundle geometry. J. Mol. Biol. 405, 1079–1100 (2011). (PMID: 10.1016/j.jmb.2010.08.05820932976) ; Brunette, T. J. et al. Exploring the repeat protein universe through computational protein design. Nature 528, 580–584 (2015). (PMID: 10.1038/nature16162266757294845728) ; Huang, P.-S. et al. High thermodynamic stability of parametrically designed helical bundles. Science 346, 481–485 (2014). (PMID: 10.1126/science.1257481253428064612401) ; Alford, R. F. et al. The Rosetta all-atom energy function for macromolecular modeling and design. J. Chem. Theory Comput. 13, 3031–3048 (2017). (PMID: 10.1021/acs.jctc.7b00125284304265717763) ; Dauparas, J. et al. Robust deep learning–based protein sequence design using ProteinMPNN. Science 378, 49–56 (2022). (PMID: 10.1126/science.add2187361080509997061) ; Correnti, C. E. et al. Engineering and functionalization of large circular tandem repeat protein nanoparticles. Nat. Struct. Mol. Biol. 27, 342–350 (2020). (PMID: 10.1038/s41594-020-0397-5322034917336869) ; Coxeter, H. S. M. Regular Polytopes (Courier Corp., 1973). ; Yeates, T. O. Geometric principles for designing highly symmetric self-assembling protein nanomaterials. Annu. Rev. Biophys. 46, 23–42 (2017). (PMID: 10.1146/annurev-biophys-070816-03392828301774) ; Walshaw, J. & Woolfson, D. N. Extended knobs-into-holes packing in classical and complex coiled-coil assemblies. J. Struct. Biol. 144, 349–361 (2003). (PMID: 10.1016/j.jsb.2003.10.01414643203) ; Pédelacq, J.-D., Cabantous, S., Tran, T., Terwilliger, T. C. & Waldo, G. S. Engineering and characterization of a superfolder green fluorescent protein. Nat. Biotechnol. 24, 79–88 (2005). (PMID: 10.1038/nbt117216369541) ; Bindels, D. S. et al. mScarlet: a bright monomeric red fluorescent protein for cellular imaging. Nat. Methods 14, 53–56 (2016). (PMID: 10.1038/nmeth.407427869816) ; Kendrew, J. C. et al. A three-dimensional model of the myoglobin molecule obtained by X-ray analysis. Nature 181, 662–666 (1958). (PMID: 10.1038/181662a013517261) ; Pyles, H., Zhang, S., De Yoreo, J. J. & Baker, D. Controlling protein assembly on inorganic crystals through designed protein interfaces. Nature 571, 251–256 (2019). (PMID: 10.1038/s41586-019-1361-6312925596948101) ; Davila-Hernandez, F. A. et al. Directing polymorph specific calcium carbonate formation with de novo protein templates. Nat. Commun. 14, 8191 (2023). (PMID: 10.1038/s41467-023-43608-13809754410721895) ; Kibler, R. D. et al. Stepwise design of pseudosymmetric protein hetero-oligomers. Preprint at bioRxiv https://doi.org/10.1101/2023.04.07.535760 (2023). ; Wintersinger, C. M. et al. Multi-micron crisscross structures grown from DNA-origami slats. Nat. Nanotechnol. 18, 281–289 (2023). (PMID: 10.1038/s41565-022-01283-136543881) ; Bohlin, J., Turberfield, A. J., Louis, A. A. & Šulc, P. Designing the self-assembly of arbitrary shapes using minimal complexity building blocks. ACS Nano 17, 5387–5398 (2023). (PMID: 10.1021/acsnano.2c0967736763807) ; Petersen, P., Tikhomirov, G. & Qian, L. Information-based autonomous reconfiguration in systems of interacting DNA nanostructures. Nat. Commun. 9, 5362 (2018). (PMID: 10.1038/s41467-018-07805-7305608656299139) ; Sigl, C. et al. Programmable icosahedral shell system for virus trapping. Nat. Mater. 20, 1281–1289 (2021). (PMID: 10.1038/s41563-021-01020-4341278227611604) ; Wagenbauer, K. F., Sigl, C. & Dietz, H. Gigadalton-scale shape-programmable DNA assemblies. Nature 552, 78–83 (2017). (PMID: 10.1038/nature2465129219966) Grant Information: P41 GM103310 United States GM NIGMS NIH HHS; S10 OD023476 United States OD NIH HHS; U24 GM129539 United States GM NIGMS NIH HHS Substance Nomenclature: 0 (Proteins) Entry Date(s): Date Created: 20240314 Date Completed: 20240329 Latest Revision: 20240412 Update Code: 20240413 PubMed Central ID: PMC10972742

Klicken Sie ein Format an und speichern Sie dann die Daten oder geben Sie eine Empfänger-Adresse ein und lassen Sie sich per Email zusenden.

BibTeX Citavi, JabRef, u.a.
(Literaturverwaltung)

PDF kein Volltext!
(Merkzettel, Notizen)

RIS Endnote, Citavi u.a.
(Literaturverwaltung)

MODS
(XML zur Weiterverarbeitung)

oder

Wählen Sie das für Sie passende Zitationsformat und kopieren Sie es dann in die Zwischenablage, lassen es sich per Mail zusenden oder speichern es als PDF-Datei.

Gewünschter Zitations-Stil:

oder

Bitte prüfen Sie, ob die Zitation formal korrekt ist, bevor Sie sie in einer Arbeit verwenden. Benutzen Sie gegebenenfalls den "Exportieren"-Dialog, wenn Sie ein Literaturverwaltungsprogramm verwenden und die Zitat-Angaben selbst formatieren wollen.

Blueprinting extendable nanomaterials with standardized protein blocks.