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Title: Modular repeat protein sculpting using rigid helical junctions

Abstract

The ability to precisely design large proteins with diverse shapes would enable applications ranging from the design of protein binders that wrap around their target to the positioning of multiple functional sites in specified orientations. We describe a protein backbone design method for generating a wide range of rigid fusions between helix-containing proteins and use it to design 75,000 structurally unique junctions between monomeric and homo-oligomeric de novo designed and ankyrin repeat proteins (RPs). Of the junction designs that were experimentally characterized, 82% have circular dichroism and solution small-angle X-ray scattering profiles consistent with the design models and are stable at 95 °C. Crystal structures of four designed junctions were in close agreement with the design models with rmsds ranging from 0.9 to 1.6 Å. Electron microscopic images of extended tetrameric structures and ~10-nm-diameter “L” and “V” shapes generated using the junctions are close to the design models, demonstrating the control the rigid junctions provide for protein shape sculpting over multiple nanometer length scales.

Authors:
ORCiD logo [1]; ORCiD logo [1];  [1];  [1];  [1]; ORCiD logo [1]
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  1. Univ. of Washington, Seattle, WA (United States)
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
NIGMS; USDOE
OSTI Identifier:
1630336
Resource Type:
Accepted Manuscript
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 117; Journal Issue: 16; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Brunette, TJ, Bick, Matthew J., Hansen, Jesse M., Chow, Cameron M., Kollman, Justin M., and Baker, David. Modular repeat protein sculpting using rigid helical junctions. United States: N. p., 2020. Web. doi:10.1073/pnas.1908768117.
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Brunette, TJ, Bick, Matthew J., Hansen, Jesse M., Chow, Cameron M., Kollman, Justin M., & Baker, David. Modular repeat protein sculpting using rigid helical junctions. United States. https://doi.org/10.1073/pnas.1908768117
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Brunette, TJ, Bick, Matthew J., Hansen, Jesse M., Chow, Cameron M., Kollman, Justin M., and Baker, David. Fri . "Modular repeat protein sculpting using rigid helical junctions". United States. https://doi.org/10.1073/pnas.1908768117. https://www.osti.gov/servlets/purl/1630336.
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@article{osti_1630336,
title = {Modular repeat protein sculpting using rigid helical junctions},
author = {Brunette, TJ and Bick, Matthew J. and Hansen, Jesse M. and Chow, Cameron M. and Kollman, Justin M. and Baker, David},
abstractNote = {The ability to precisely design large proteins with diverse shapes would enable applications ranging from the design of protein binders that wrap around their target to the positioning of multiple functional sites in specified orientations. We describe a protein backbone design method for generating a wide range of rigid fusions between helix-containing proteins and use it to design 75,000 structurally unique junctions between monomeric and homo-oligomeric de novo designed and ankyrin repeat proteins (RPs). Of the junction designs that were experimentally characterized, 82% have circular dichroism and solution small-angle X-ray scattering profiles consistent with the design models and are stable at 95 °C. Crystal structures of four designed junctions were in close agreement with the design models with rmsds ranging from 0.9 to 1.6 Å. Electron microscopic images of extended tetrameric structures and ~10-nm-diameter “L” and “V” shapes generated using the junctions are close to the design models, demonstrating the control the rigid junctions provide for protein shape sculpting over multiple nanometer length scales.},
doi = {10.1073/pnas.1908768117},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 16,
volume = 117,
place = {United States},
year = {2020},
month = {4}
}
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Journal Article:
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Publisher's Version of Record
https://doi.org/10.1073/pnas.1908768117
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Citation Metrics:
Cited by: 21 works
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Figures / Tables:

Fig. 1 Fig. 1: A general method to create arbitrary protein shapes using a library of designed junctions. (A) Building blocks: (Left, with different numbers of repeat units indicated in parentheses) DHRs, (Middle) homo-oligomers made from DHRs (9), and (Right) an ankyrin. (B) Junctions can be made by superimposing helices by overlappingmore » six residues (red) in terminal repeats (gray). The nearby residues are then redesigned (red sticks). (C) Junctions can also be made by building additional protein backbone (gold) as a contiguous chain with Rosetta fragment assembly. Following removal of a helix (gray) and/or one to four terminal helix residues (black), the sequence near the interface is redesigned (red sticks). (D) Designs from both fusion methods are filtered to ensure they are lower in energy than other conformations in the energy landscape, contain two or more helices in contact throughout the junction, and there are no buried unsatisfied residues. To check that the design is the lowest energy we used either Rosetta@home to model the energy landscape or a machine-learning approximation to the Rosetta@home simulation (SI Appendix, Discussion S2). (E) The junction library is then used to sculpt proteins into various shapes. In this case, a repeat protein shown in dark blue is connected first to a repeat protein in cyan followed by a repeat protein in light blue. Junctions are shown in gold. REU, Rosetta energy units.« less
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    Works referencing / citing this record:

    Protein sequence design by conformational landscape optimization
    journal, March 2021

    • Norn, Christoffer; Wicky, Basile I. M.; Juergens, David
    • Proceedings of the National Academy of Sciences, Vol. 118, Issue 11
    • DOI: 10.1073/pnas.2017228118

    Recent advances in de novo protein design: Principles, methods, and applications
    journal, January 2021

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