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Title: De novo design of a fluorescence-activating β-barrel

Abstract

The regular arrangements of β-strands around a central axis in β-barrels and of α-helices in coiled coils contrast with the irregular tertiary structures of most globular proteins, and have fascinated structural biologists since they were first discovered. Simple parametric models have been used to design a wide range of α-helical coiled-coil structures, but to date there has been no success with β-barrels. Here we show that accurate de novo design of β-barrels requires considerable symmetry-breaking to achieve continuous hydrogen-bond connectivity and eliminate backbone strain. We then build ensembles of β-barrel backbone models with cavity shapes that match the fluorogenic compound DFHBI, and use a hierarchical grid-based search method to simultaneously optimize the rigid-body placement of DFHBI in these cavities and the identities of the surrounding amino acids to achieve high shape and chemical complementarity. The designs have high structural accuracy and bind and fluorescently activate DFHBI in vitro and in Escherichia coli, yeast and mammalian cells. Finally, this de novo design of small-molecule binding activity, using backbones custom-built to bind the ligand, should enable the design of increasingly sophisticated ligand-binding proteins, sensors and catalysts that are not limited by the backbone geometries available in known protein structures.

Authors:
 [1];  [1];  [1];  [2];  [1];  [1];  [3];  [3];  [3];  [3];  [1];  [4];  [1];  [1];  [1];  [3];  [2];  [5]
  1. Univ. of Washington, Seattle, WA (United States). Inst. for Protein Design
  2. Fred Hutchinson Cancer Research Center, Seattle, WA (United States)
  3. Univ. of Washington, Seattle, WA (United States)
  4. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  5. Univ. of Washington, Seattle, WA (United States). Inst. for Protein Design, and Howard Hughes Medical Inst.
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); Fulbright Commission for Belgium and Luxembourg; National Institutes of Health (NIH)
OSTI Identifier:
1601813
Grant/Contract Number:  
[AC02-05CH11231; R01 GM115545]
Resource Type:
Accepted Manuscript
Journal Name:
Nature (London)
Additional Journal Information:
[Journal Name: Nature (London); Journal Volume: 561; Journal Issue: 7724]; Journal ID: ISSN 0028-0836
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Dou, Jiayi, Vorobieva, Anastassia A., Sheffler, William, Doyle, Lindsey A., Park, Hahnbeom, Bick, Matthew J., Mao, Binchen, Foight, Glenna W., Lee, Min Yen, Gagnon, Lauren A., Carter, Lauren, Sankaran, Banumathi, Ovchinnikov, Sergey, Marcos, Enrique, Huang, Po-Ssu, Vaughan, Joshua C., Stoddard, Barry L., and Baker, David. De novo design of a fluorescence-activating β-barrel. United States: N. p., 2018. Web. doi:10.1038/s41586-018-0509-0.
Dou, Jiayi, Vorobieva, Anastassia A., Sheffler, William, Doyle, Lindsey A., Park, Hahnbeom, Bick, Matthew J., Mao, Binchen, Foight, Glenna W., Lee, Min Yen, Gagnon, Lauren A., Carter, Lauren, Sankaran, Banumathi, Ovchinnikov, Sergey, Marcos, Enrique, Huang, Po-Ssu, Vaughan, Joshua C., Stoddard, Barry L., & Baker, David. De novo design of a fluorescence-activating β-barrel. United States. doi:10.1038/s41586-018-0509-0.
Dou, Jiayi, Vorobieva, Anastassia A., Sheffler, William, Doyle, Lindsey A., Park, Hahnbeom, Bick, Matthew J., Mao, Binchen, Foight, Glenna W., Lee, Min Yen, Gagnon, Lauren A., Carter, Lauren, Sankaran, Banumathi, Ovchinnikov, Sergey, Marcos, Enrique, Huang, Po-Ssu, Vaughan, Joshua C., Stoddard, Barry L., and Baker, David. Wed . "De novo design of a fluorescence-activating β-barrel". United States. doi:10.1038/s41586-018-0509-0. https://www.osti.gov/servlets/purl/1601813.
@article{osti_1601813,
title = {De novo design of a fluorescence-activating β-barrel},
author = {Dou, Jiayi and Vorobieva, Anastassia A. and Sheffler, William and Doyle, Lindsey A. and Park, Hahnbeom and Bick, Matthew J. and Mao, Binchen and Foight, Glenna W. and Lee, Min Yen and Gagnon, Lauren A. and Carter, Lauren and Sankaran, Banumathi and Ovchinnikov, Sergey and Marcos, Enrique and Huang, Po-Ssu and Vaughan, Joshua C. and Stoddard, Barry L. and Baker, David},
abstractNote = {The regular arrangements of β-strands around a central axis in β-barrels and of α-helices in coiled coils contrast with the irregular tertiary structures of most globular proteins, and have fascinated structural biologists since they were first discovered. Simple parametric models have been used to design a wide range of α-helical coiled-coil structures, but to date there has been no success with β-barrels. Here we show that accurate de novo design of β-barrels requires considerable symmetry-breaking to achieve continuous hydrogen-bond connectivity and eliminate backbone strain. We then build ensembles of β-barrel backbone models with cavity shapes that match the fluorogenic compound DFHBI, and use a hierarchical grid-based search method to simultaneously optimize the rigid-body placement of DFHBI in these cavities and the identities of the surrounding amino acids to achieve high shape and chemical complementarity. The designs have high structural accuracy and bind and fluorescently activate DFHBI in vitro and in Escherichia coli, yeast and mammalian cells. Finally, this de novo design of small-molecule binding activity, using backbones custom-built to bind the ligand, should enable the design of increasingly sophisticated ligand-binding proteins, sensors and catalysts that are not limited by the backbone geometries available in known protein structures.},
doi = {10.1038/s41586-018-0509-0},
journal = {Nature (London)},
number = [7724],
volume = [561],
place = {United States},
year = {2018},
month = {9}
}

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