Precisely patterned nanofibres made from extendable protein multiplexes

Neville P.  Bethel; Andrew J. Borst; Fabio Parmeggiani; Matthew J. Bick; T J Brunette; Hannah Nguyen; David  Baker; et al

doi:10.1038/s41557-023-01314-x

Precisely patterned nanofibres made from extendable protein multiplexes

Neville P. Bethel
, Andrew J. Borst
, Fabio Parmeggiani
, Matthew J. Bick
, T J Brunette
, Hannah Nguyen
, David Baker^*
, et al

^*Corresponding author for this work

School of Chemistry

Research output: Contribution to journal › Article (Academic Journal) › peer-review

26 Citations (Scopus)

Abstract

Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be readily lengthened or shortened by changing the length of the constituent monomers. Among proteins, alpha-helical coiled coils have such symmetric, extendable architectures, but are limited by the relatively fixed geometry and flexibility of the helical protomers. Here we describe a systematic approach to generating modular and rigid repeat protein oligomers with coincident C2 to C8 and superhelical symmetry axes that can be readily extended by repeat propagation. From these building blocks, we demonstrate that a wide range of unbounded fibres can be systematically designed by introducing hydrophilic surface patches that force staggering of the monomers; the geometry of such fibres can be precisely tuned by varying the number of repeat units in the monomer and the placement of the hydrophilic patches.

Original language	English
Pages (from-to)	1664-1671
Number of pages	8
Journal	Nature Chemistry
Volume	15
Issue number	12
Early online date	4 Sept 2023
DOIs	https://doi.org/10.1038/s41557-023-01314-x
Publication status	Published - 1 Dec 2023

Bibliographical note

Funding Information:
We thank T. Huddy, Y. Hsia, H. Pyles, H. Shen, A. Courbet, F. Praetorius and L. Stewart for helpful discussions. We also thank S. Dickinson and J. Quispe for training and operation of the electron microscopes at the Arnold & Mabel Beckman Center for Cryo-Electron Microscopy. We also thank A. Murray, P. Heine and S. Gerben for their work in expressing and purifying protein for crystal screens and N. Ennist for his help with circular dichroism experiments. We also thank the SIBYLS group for their work on the SAXS data collection at the Advanced Light Source (ALS) and at the Integrated Diffraction Analysis Technologies (IDAT) programme. The SIBYLS group is supported by the National Institutes of Health project ALS-ENABLE (P30 GM124169) and a High-End Instrumentation Grant (S10OD018483). This work was supported with funds provided by the Howard Hughes Medical Institute (D.B.), a Hanna Gray Postdoctoral Fellowship (GT11817; N.P.B.), the Institute for Protein Design Directors Fund (M.J.B.), the Donald and Jo Anne Petersen Endowment for Accelerating Advancements in Alzheimer’s Disease Research (T.B.) and the Audacious Project at the Institute for Protein (A.J.B., H.N., A.K., M.C.M., L.C., M.L., X.L., R.D.K. and D.B.). F.P. is the recipient of an Engineering and Physical Sciences Research Council (EPSRC) early career fellowship (EP/S017542/1) and was supported by the BrisSynBio grant BB/L01386X/1. This work was also supported, in whole or in part, by the Bill & Melinda Gates Foundation (grant no. INV-010680). Crystallographic data were collected at ALS and the Advanced Photon Source (APS). ALS is a national user facility operated by Lawrence Berkeley National Laboratory on behalf of the US Department of Energy (DOE), Office of Basic Energy Sciences, through the Integrated Diffraction Analysis Technologies (IDAT) programme, supported by the DOE Office of Biological and Environmental Research. APS is a DOE Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under contract no. DE-AC02-06CH11357. At APS, we used the Northeastern Collaborative Access Team beamlines, which are funded by the National Institute of General Medical Sciences from the National Institutes of Health (P30 GM124165). This work was also supported by grant DE-SC0018940 MOD03, funded by the DOE, Office of Science (D.B. and N.P.B.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

Publisher Copyright:
© 2023, The Author(s).

Research Groups and Themes

Bristol BioDesign Institute

Keywords

synthetic biology

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Cite this

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title = "Precisely patterned nanofibres made from extendable protein multiplexes",

abstract = "Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be readily lengthened or shortened by changing the length of the constituent monomers. Among proteins, alpha-helical coiled coils have such symmetric, extendable architectures, but are limited by the relatively fixed geometry and flexibility of the helical protomers. Here we describe a systematic approach to generating modular and rigid repeat protein oligomers with coincident C2 to C8 and superhelical symmetry axes that can be readily extended by repeat propagation. From these building blocks, we demonstrate that a wide range of unbounded fibres can be systematically designed by introducing hydrophilic surface patches that force staggering of the monomers; the geometry of such fibres can be precisely tuned by varying the number of repeat units in the monomer and the placement of the hydrophilic patches.",

keywords = "synthetic biology",

author = "Bethel, \{Neville P.\} and Borst, \{Andrew J.\} and Fabio Parmeggiani and Bick, \{Matthew J.\} and Brunette, \{T J\} and Hannah Nguyen and David Baker and et al",

note = "Funding Information: We thank T. Huddy, Y. Hsia, H. Pyles, H. Shen, A. Courbet, F. Praetorius and L. Stewart for helpful discussions. We also thank S. Dickinson and J. Quispe for training and operation of the electron microscopes at the Arnold \& Mabel Beckman Center for Cryo-Electron Microscopy. We also thank A. Murray, P. Heine and S. Gerben for their work in expressing and purifying protein for crystal screens and N. Ennist for his help with circular dichroism experiments. We also thank the SIBYLS group for their work on the SAXS data collection at the Advanced Light Source (ALS) and at the Integrated Diffraction Analysis Technologies (IDAT) programme. The SIBYLS group is supported by the National Institutes of Health project ALS-ENABLE (P30 GM124169) and a High-End Instrumentation Grant (S10OD018483). This work was supported with funds provided by the Howard Hughes Medical Institute (D.B.), a Hanna Gray Postdoctoral Fellowship (GT11817; N.P.B.), the Institute for Protein Design Directors Fund (M.J.B.), the Donald and Jo Anne Petersen Endowment for Accelerating Advancements in Alzheimer{\textquoteright}s Disease Research (T.B.) and the Audacious Project at the Institute for Protein (A.J.B., H.N., A.K., M.C.M., L.C., M.L., X.L., R.D.K. and D.B.). F.P. is the recipient of an Engineering and Physical Sciences Research Council (EPSRC) early career fellowship (EP/S017542/1) and was supported by the BrisSynBio grant BB/L01386X/1. This work was also supported, in whole or in part, by the Bill \& Melinda Gates Foundation (grant no. INV-010680). Crystallographic data were collected at ALS and the Advanced Photon Source (APS). ALS is a national user facility operated by Lawrence Berkeley National Laboratory on behalf of the US Department of Energy (DOE), Office of Basic Energy Sciences, through the Integrated Diffraction Analysis Technologies (IDAT) programme, supported by the DOE Office of Biological and Environmental Research. APS is a DOE Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under contract no. DE-AC02-06CH11357. At APS, we used the Northeastern Collaborative Access Team beamlines, which are funded by the National Institute of General Medical Sciences from the National Institutes of Health (P30 GM124165). This work was also supported by grant DE-SC0018940 MOD03, funded by the DOE, Office of Science (D.B. and N.P.B.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. Publisher Copyright: {\textcopyright} 2023, The Author(s).",

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doi = "10.1038/s41557-023-01314-x",

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T1 - Precisely patterned nanofibres made from extendable protein multiplexes

AU - Bethel, Neville P.

AU - Borst, Andrew J.

AU - Parmeggiani, Fabio

AU - Bick, Matthew J.

AU - Brunette, T J

AU - Nguyen, Hannah

AU - Baker, David

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N1 - Funding Information: We thank T. Huddy, Y. Hsia, H. Pyles, H. Shen, A. Courbet, F. Praetorius and L. Stewart for helpful discussions. We also thank S. Dickinson and J. Quispe for training and operation of the electron microscopes at the Arnold & Mabel Beckman Center for Cryo-Electron Microscopy. We also thank A. Murray, P. Heine and S. Gerben for their work in expressing and purifying protein for crystal screens and N. Ennist for his help with circular dichroism experiments. We also thank the SIBYLS group for their work on the SAXS data collection at the Advanced Light Source (ALS) and at the Integrated Diffraction Analysis Technologies (IDAT) programme. The SIBYLS group is supported by the National Institutes of Health project ALS-ENABLE (P30 GM124169) and a High-End Instrumentation Grant (S10OD018483). This work was supported with funds provided by the Howard Hughes Medical Institute (D.B.), a Hanna Gray Postdoctoral Fellowship (GT11817; N.P.B.), the Institute for Protein Design Directors Fund (M.J.B.), the Donald and Jo Anne Petersen Endowment for Accelerating Advancements in Alzheimer’s Disease Research (T.B.) and the Audacious Project at the Institute for Protein (A.J.B., H.N., A.K., M.C.M., L.C., M.L., X.L., R.D.K. and D.B.). F.P. is the recipient of an Engineering and Physical Sciences Research Council (EPSRC) early career fellowship (EP/S017542/1) and was supported by the BrisSynBio grant BB/L01386X/1. This work was also supported, in whole or in part, by the Bill & Melinda Gates Foundation (grant no. INV-010680). Crystallographic data were collected at ALS and the Advanced Photon Source (APS). ALS is a national user facility operated by Lawrence Berkeley National Laboratory on behalf of the US Department of Energy (DOE), Office of Basic Energy Sciences, through the Integrated Diffraction Analysis Technologies (IDAT) programme, supported by the DOE Office of Biological and Environmental Research. APS is a DOE Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under contract no. DE-AC02-06CH11357. At APS, we used the Northeastern Collaborative Access Team beamlines, which are funded by the National Institute of General Medical Sciences from the National Institutes of Health (P30 GM124165). This work was also supported by grant DE-SC0018940 MOD03, funded by the DOE, Office of Science (D.B. and N.P.B.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. Publisher Copyright: © 2023, The Author(s).

PY - 2023/12/1

Y1 - 2023/12/1

N2 - Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be readily lengthened or shortened by changing the length of the constituent monomers. Among proteins, alpha-helical coiled coils have such symmetric, extendable architectures, but are limited by the relatively fixed geometry and flexibility of the helical protomers. Here we describe a systematic approach to generating modular and rigid repeat protein oligomers with coincident C2 to C8 and superhelical symmetry axes that can be readily extended by repeat propagation. From these building blocks, we demonstrate that a wide range of unbounded fibres can be systematically designed by introducing hydrophilic surface patches that force staggering of the monomers; the geometry of such fibres can be precisely tuned by varying the number of repeat units in the monomer and the placement of the hydrophilic patches.

AB - Molecular systems with coincident cyclic and superhelical symmetry axes have considerable advantages for materials design as they can be readily lengthened or shortened by changing the length of the constituent monomers. Among proteins, alpha-helical coiled coils have such symmetric, extendable architectures, but are limited by the relatively fixed geometry and flexibility of the helical protomers. Here we describe a systematic approach to generating modular and rigid repeat protein oligomers with coincident C2 to C8 and superhelical symmetry axes that can be readily extended by repeat propagation. From these building blocks, we demonstrate that a wide range of unbounded fibres can be systematically designed by introducing hydrophilic surface patches that force staggering of the monomers; the geometry of such fibres can be precisely tuned by varying the number of repeat units in the monomer and the placement of the hydrophilic patches.

KW - synthetic biology

U2 - 10.1038/s41557-023-01314-x

DO - 10.1038/s41557-023-01314-x

M3 - Article (Academic Journal)

C2 - 37667012

SN - 1755-4330

VL - 15

SP - 1664

EP - 1671

JO - Nature Chemistry

JF - Nature Chemistry

IS - 12

ER -

Precisely patterned nanofibres made from extendable protein multiplexes

Abstract

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