دورية أكاديمية
De novo design of pH-responsive self-assembling helical protein filaments.
| العنوان: | De novo design of pH-responsive self-assembling helical protein filaments. |
|---|---|
| المؤلفون: | Shen H; Department of Biochemistry, University of Washington, Seattle, WA, USA. shenh2@uw.edu.; Institute for Protein Design, University of Washington, Seattle, WA, USA. shenh2@uw.edu., Lynch EM; Department of Biochemistry, University of Washington, Seattle, WA, USA., Akkineni S; Department of Materials Science and Engineering, University of Washington, Seattle, WA, USA.; Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA., Watson JL; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA.; MRC Laboratory of Molecular Biology, Cambridge, UK., Decarreau J; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Bethel NP; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Benna I; Institute for Protein Design, University of Washington, Seattle, WA, USA.; Department of Bioengineering, University of Washington, Seattle, WA, USA., Sheffler W; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Farrell D; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., DiMaio F; Department of Biochemistry, University of Washington, Seattle, WA, USA.; Institute for Protein Design, University of Washington, Seattle, WA, USA., Derivery E; MRC Laboratory of Molecular Biology, Cambridge, UK., De Yoreo JJ; Department of Materials Science and Engineering, University of Washington, Seattle, WA, USA.; Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA., Kollman J; Department of Biochemistry, University of Washington, Seattle, WA, USA., Baker D; Department of Biochemistry, University of Washington, Seattle, WA, USA. dabaker@uw.edu.; Institute for Protein Design, University of Washington, Seattle, WA, USA. dabaker@uw.edu.; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA. dabaker@uw.edu. |
| المصدر: | Nature nanotechnology [Nat Nanotechnol] 2024 Jul; Vol. 19 (7), pp. 1016-1021. Date of Electronic Publication: 2024 Apr 03. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Nature Pub. Group Country of Publication: England NLM ID: 101283273 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1748-3395 (Electronic) Linking ISSN: 17483387 NLM ISO Abbreviation: Nat Nanotechnol Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: London : Nature Pub. Group, 2006- |
| مواضيع طبية MeSH: | Histidine*/chemistry, Hydrogen-Ion Concentration ; Proteins/chemistry ; Nanostructures/chemistry ; Models, Molecular ; Hydrogen Bonding ; Cryoelectron Microscopy |
| مستخلص: | Biological evolution has led to precise and dynamic nanostructures that reconfigure in response to pH and other environmental conditions. However, designing micrometre-scale protein nanostructures that are environmentally responsive remains a challenge. Here we describe the de novo design of pH-responsive protein filaments built from subunits containing six or nine buried histidine residues that assemble into micrometre-scale, well-ordered fibres at neutral pH. The cryogenic electron microscopy structure of an optimized design is nearly identical to the computational design model for both the subunit internal geometry and the subunit packing into the fibre. Electron, fluorescent and atomic force microscopy characterization reveal a sharp and reversible transition from assembled to disassembled fibres over 0.3 pH units, and rapid fibre disassembly in less than 1 s following a drop in pH. The midpoint of the transition can be tuned by modulating buried histidine-containing hydrogen bond networks. Computational protein design thus provides a route to creating unbound nanomaterials that rapidly respond to small pH changes. (© 2024. The Author(s).) |
| References: | Askarieh, G. et al. Self-assembly of spider silk proteins is controlled by a pH-sensitive relay. Nature 465, 236–238 (2010). (PMID: 10.1038/nature0896220463740) Hansen, J. M. et al. Cryo-EM structures of CTP synthase filaments reveal mechanism of pH-sensitive assembly during budding yeast starvation. eLife 10, e73368 (2021). (PMID: 10.7554/eLife.73368347348018641951) Polka, J. K. & Silver, P. A. A tunable protein piston that breaks membranes to release encapsulated cargo. ACS Synth. Biol. 5, 303–311 (2016). (PMID: 10.1021/acssynbio.5b0023726814170) Beun, L. H. et al. From micelles to fibers: balancing self-assembling and random coiling domains in pH-responsive silk-collagen-like protein-based polymers. Biomacromolecules 15, 3349–3357 (2014). (PMID: 10.1021/bm500826y251339904260859) Zimenkov, Y. et al. Rational design of a reversible pH-responsive switch for peptide self-assembly. J. Am. Chem. Soc. 128, 6770–6771 (2006). (PMID: 10.1021/ja060597416719440) Boyken, S. E. et al. De novo design of tunable, pH-driven conformational changes. Science 364, 658–664 (2019). Shen, H. et al. De novo design of self-assembling helical protein filaments. Science 362, 705–709 (2018). (PMID: 10.1126/science.aau3775304098856637945) 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). (PMID: 10.1038/nmeth.416928165473) Carpenter, A. E. et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol. 7, R100 (2006). (PMID: 10.1186/gb-2006-7-10-r100170768951794559) Akkineni, S. et al. Amyloid-like amelogenin nanoribbons template mineralization via a low-energy interface of ion binding sites. Proc. Natl Acad. Sci. USA 119, e2106965119 (2022). (PMID: 10.1073/pnas.2106965119355227099172371) Kohse, S., Neubauer, A., Pazidis, A., Lochbrunner, S. & Kragl, U. Photoswitching of enzyme activity by laser-induced pH-jump. J. Am. Chem. Soc. 135, 9407–9411 (2013). (PMID: 10.1021/ja400700x23688056) Watson, J. L. et al. De novo design of protein structure and function with RFdiffusion. Nature 620, 1089–1100 (2023). (PMID: 10.1038/s41586-023-06415-83743332710468394) Dauparas, J. et al. Robust deep learning–based protein sequence design using ProteinMPNN. Science 378, 49–56 (2022). (PMID: 10.1126/science.add2187361080509997061) Boyken, S. E. et al. De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity. Science 352, 680–687 (2016). (PMID: 10.1126/science.aad8865271518625497568) Liu, P., Agrafiotis, D. K. & Theobald, D. L. Fast determination of the optimal rotational matrix for macromolecular superpositions. J. Comput. Chem. 31, 1561–1563 (2010). (PMID: 10.1002/jcc.2143920017124) Studier, F. W. Protein production by auto-induction in high density shaking cultures. Protein Expr. Purif. 41, 207–234 (2005). (PMID: 10.1016/j.pep.2005.01.01615915565) Nannenga, B. L., Iadanza, M. G., Vollmar, B. S. & Gonen, T. Overview of electron crystallography of membrane proteins: crystallization and screening strategies using negative stain electron microscopy. Curr. Protoc. Protein Sci. 72, 17.15.1–17.15.11 (2013). (PMID: 10.1002/0471140864.ps1715s72) Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012). (PMID: 10.1038/nmeth.201922743772) Suloway, C. et al. Automated molecular microscopy: the new Leginon system. J. Struct. Biol. 151, 41–60 (2005). (PMID: 10.1016/j.jsb.2005.03.01015890530) Terwilliger, T. C., Ludtke, S. J., Read, R. J., Adams, P. D. & Afonine, P. V. Improvement of cryo-EM maps by density modification. Nat. Methods 17, 923–927 (2020). (PMID: 10.1038/s41592-020-0914-9328079577484085) Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010). (PMID: 10.1107/S0907444909052925201247022815670) Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. D 74, 519–530 (2018). (PMID: 10.1107/S2059798318002425) Wang, R. Y.-R. et al. De novo protein structure determination from near-atomic-resolution cryo-EM maps. Nat. Methods 12, 335–338 (2015). (PMID: 10.1038/nmeth.3287257070294435692) Song, Y. et al. High-resolution comparative modeling with RosettaCM. Structure 21, 1735–1742 (2013). (PMID: 10.1016/j.str.2013.08.00524035711) McQuin, C. et al. CellProfiler 3.0: next-generation image processing for biology. PLoS Biol. 16, e2005970 (2018). (PMID: 10.1371/journal.pbio.2005970299694506029841) Choi, J., Hirota, N. & Terazima, M. A pH-jump reaction studied by the transient grating method: photodissociation of o-nitrobenzaldehyde. J. Phys. Chem. A 105, 12–18 (2001). (PMID: 10.1021/jp0014162) Shen, H. Fiber_design. GitHub https://github.com/shenh2/fiber_design (2024). |
| معلومات مُعتمدة: | Graduate Research Fellowship award 1762114 and 2140004 National Science Foundation (NSF); DE-SC0019288 U.S. Department of Energy (DOE); R35 GM149542 United States GM NIGMS NIH HHS; Award FWP 72448 U.S. Department of Energy (DOE); R35GM149542, R01GM118396 and S10 OD032290 U.S. Department of Health & Human Services | National Institutes of Health (NIH); Hanna Gray Fellowship via GT11817 Howard Hughes Medical Institute (HHMI); MC_UP_1201/13 RCUK | Medical Research Council (MRC); G-2021-16899 Alfred P. Sloan Foundation; RGP0061 Human Frontier Science Program (HFSP); Biostasis W911NF1920017 United States Department of Defense | Defense Advanced Research Projects Agency (DARPA); Career Development Award CDA00034/2017 Human Frontier Science Program (HFSP); R01 GM118396 United States GM NIGMS NIH HHS |
| المشرفين على المادة: | 4QD397987E (Histidine) 0 (Proteins) |
| تواريخ الأحداث: | Date Created: 20240403 Date Completed: 20240729 Latest Revision: 20240814 |
| رمز التحديث: | 20240815 |
| مُعرف محوري في PubMed: | PMC11286511 |
| DOI: | 10.1038/s41565-024-01641-1 |
| PMID: | 38570702 |
| قاعدة البيانات: | MEDLINE |
Find this article in full text from Springer Verlag. 
Full Text Finder | تدمد: | 1748-3395 |
|---|---|
| DOI: | 10.1038/s41565-024-01641-1 |