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:
-
- 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.
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
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.
@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}
}
Web of Science
Figures / Tables:

Works referenced in this record:
Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design
journal, March 2018
- Maguire, Jack B.; Boyken, Scott E.; Baker, David
- Journal of Chemical Theory and Computation, Vol. 14, Issue 5
Elfin: An algorithm for the computational design of custom three-dimensional structures from modular repeat protein building blocks
journal, February 2018
- Yeh, Chun-Ting; Brunette, Tj; Baker, David
- Journal of Structural Biology, Vol. 201, Issue 2
A General Computational Approach for Repeat Protein Design
journal, January 2015
- Parmeggiani, Fabio; Huang, Po-Ssu; Vorobiev, Sergey
- Journal of Molecular Biology, Vol. 427, Issue 2
Super-Resolution in Solution X-Ray Scattering and Its Applications to Structural Systems Biology
journal, May 2013
- Rambo, Robert P.; Tainer, John A.
- Annual Review of Biophysics, Vol. 42, Issue 1
Exploring the repeat protein universe through computational protein design
journal, December 2015
- Brunette, Tj; Parmeggiani, Fabio; Huang, Po-Ssu
- Nature, Vol. 528, Issue 7583
Design of structurally distinct proteins using strategies inspired by evolution
journal, May 2016
- Jacobs, T. M.; Williams, B.; Williams, T.
- Science, Vol. 352, Issue 6286
Controlling protein assembly on inorganic crystals through designed protein interfaces
journal, July 2019
- Pyles, Harley; Zhang, Shuai; De Yoreo, James J.
- Nature, Vol. 571, Issue 7764
DNA Origami: Scaffolds for Creating Higher Order Structures
journal, June 2017
- Hong, Fan; Zhang, Fei; Liu, Yan
- Chemical Reviews, Vol. 117, Issue 20
Designing repeat proteins: a modular approach to protein design
journal, August 2017
- Parmeggiani, Fabio; Huang, Po-Ssu
- Current Opinion in Structural Biology, Vol. 45
Glycosidase and glycan polymorphism control hydrolytic release of immunogenic flagellin peptides
journal, April 2019
- Buscaill, Pierre; Chandrasekar, Balakumaran; Sanguankiattichai, Nattapong
- Science, Vol. 364, Issue 6436
Limb proportions show developmental plasticity in response to embryo movement
journal, February 2017
- Pollard, A. S.; Charlton, B. G.; Hutchinson, J. R.
- Scientific Reports, Vol. 7, Issue 1
Arabidopsis PROTEASOME REGULATOR1 is required for auxin-mediated suppression of proteasome activity and regulates auxin signalling
journal, April 2016
- Yang, Bao-Jun; Han, Xin-Xin; Yin, Lin-Lin
- Nature Communications, Vol. 7, Issue 1
Computational design of self-assembling cyclic protein homo-oligomers
journal, December 2016
- Fallas, Jorge A.; Ueda, George; Sheffler, William
- Nature Chemistry, Vol. 9, Issue 4
HU multimerization shift controls nucleoid compaction
journal, July 2016
- Hammel, Michal; Amlanjyoti, Dhar; Reyes, Francis E.
- Science Advances, Vol. 2, Issue 7
Extreme stability in de novo-designed repeat arrays is determined by unusually stable short-range interactions
journal, June 2018
- Geiger-Schuller, Kathryn; Sforza, Kevin; Yuhas, Max
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 29
De novo design of self-assembling helical protein filaments
journal, November 2018
- Shen, Hao; Fallas, Jorge A.; Lynch, Eric
- Science, Vol. 362, Issue 6415
Comprehensive macromolecular conformations mapped by quantitative SAXS analyses
journal, April 2013
- Hura, Greg L.; Budworth, Helen; Dyer, Kevin N.
- Nature Methods, Vol. 10, Issue 6
Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)
journal, July 2009
- Hura, Greg L.; Menon, Angeli L.; Hammel, Michal
- Nature Methods, Vol. 6, Issue 8
Bispecific antibodies: a mechanistic review of the pipeline
journal, June 2019
- Labrijn, Aran F.; Janmaat, Maarten L.; Reichert, Janice M.
- Nature Reviews Drug Discovery, Vol. 18, Issue 8
Multi-input chemical control of protein dimerization for programming graded cellular responses
journal, September 2019
- Foight, Glenna Wink; Wang, Zhizhi; Wei, Cindy T.
- Nature Biotechnology, Vol. 37, Issue 10
Geometrical assembly of ultrastable protein templates for nanomaterials
journal, June 2016
- Glover, Dominic J.; Giger, Lars; Kim, Steve S.
- Nature Communications, Vol. 7, Issue 1
Topological control of cytokine receptor signaling induces differential effects in hematopoiesis
journal, May 2019
- Mohan, Kritika; Ueda, George; Kim, Ah Ram
- Science, Vol. 364, Issue 6442
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
Recent advances in de novo protein design: Principles, methods, and applications
journal, January 2021
- Pan, Xingjie; Kortemme, Tanja
- Journal of Biological Chemistry, Vol. 296