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Title: De novo design of a homo-trimeric amantadine-binding protein

Abstract

The computational design of a symmetric protein homo-oligomer that binds a symmetry-matched small molecule larger than a metal ion has not yet been achieved. We used de novo protein design to create a homo-trimeric protein that binds the C3 symmetric small molecule drug amantadine with each protein monomer making identical interactions with each face of the small molecule. Solution NMR data show that the protein has regular three-fold symmetry and undergoes localized structural changes upon ligand binding. A high-resolution X-ray structure reveals a close overall match to the design model with the exception of water molecules in the amantadine binding site not included in the Rosetta design calculations, and a neutron structure provides experimental validation of the computationally designed hydrogen-bond networks. Exploration of approaches to generate a small molecule inducible homo-trimerization system based on the design highlight challenges that must be overcome to computationally design such systems.

Authors:
ORCiD logo [1];  [2]; ORCiD logo [3]; ORCiD logo [4]; ORCiD logo [5];  [6];  [7]; ORCiD logo [3]; ORCiD logo [8]; ORCiD logo [2]; ORCiD logo [9]
  1. Univ. of Washington, Seattle, WA (United States); Sana Biotechnology, Inc., Seattle, WA (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  3. Univ. of California, Santa Cruz, CA (United States)
  4. Univ. of Washington, Seattle, WA (United States); Lyell Immunopharma, Inc., Seattle, WA (United States)
  5. Univ. of Washington, Seattle, WA (United States); Univ. of California, Berkeley, CA (United States)
  6. Graz University of Technology (Austria)
  7. Univ. of California, San Francisco, CA (United States)
  8. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); St. Jude Children’s Research Hospital, Memphis, TN (United States)
  9. Univ. of Washington, Seattle, WA (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); Washington Research Foundation; National Inst. of General Medical Sciences; Burroughs Wellcome Fund; Howard Hughes Medical Inst.; National Institutes of Health (NIH)
OSTI Identifier:
1598025
Grant/Contract Number:  
AC02-06CH11357; 1R35GM125034-01; S10OD018455
Resource Type:
Accepted Manuscript
Journal Name:
eLife
Additional Journal Information:
Journal Volume: 8; Journal Issue: 2019; Journal ID: ISSN 2050-084X
Publisher:
eLife Sciences Publications, Ltd.
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Park, Jooyoung, Selvaraj, Brinda, McShan, Andrew C., Boyken, Scott E., Wei, Kathy Y., Oberdorfer, Gustav, DeGrado, William, Sgourakis, Nikolaos G., Cuneo, Matthew J., Myles, Dean A. A., and Baker, David. De novo design of a homo-trimeric amantadine-binding protein. United States: N. p., 2019. Web. https://doi.org/10.7554/eLife.47839.
Park, Jooyoung, Selvaraj, Brinda, McShan, Andrew C., Boyken, Scott E., Wei, Kathy Y., Oberdorfer, Gustav, DeGrado, William, Sgourakis, Nikolaos G., Cuneo, Matthew J., Myles, Dean A. A., & Baker, David. De novo design of a homo-trimeric amantadine-binding protein. United States. https://doi.org/10.7554/eLife.47839
Park, Jooyoung, Selvaraj, Brinda, McShan, Andrew C., Boyken, Scott E., Wei, Kathy Y., Oberdorfer, Gustav, DeGrado, William, Sgourakis, Nikolaos G., Cuneo, Matthew J., Myles, Dean A. A., and Baker, David. Thu . "De novo design of a homo-trimeric amantadine-binding protein". United States. https://doi.org/10.7554/eLife.47839. https://www.osti.gov/servlets/purl/1598025.
@article{osti_1598025,
title = {De novo design of a homo-trimeric amantadine-binding protein},
author = {Park, Jooyoung and Selvaraj, Brinda and McShan, Andrew C. and Boyken, Scott E. and Wei, Kathy Y. and Oberdorfer, Gustav and DeGrado, William and Sgourakis, Nikolaos G. and Cuneo, Matthew J. and Myles, Dean A. A. and Baker, David},
abstractNote = {The computational design of a symmetric protein homo-oligomer that binds a symmetry-matched small molecule larger than a metal ion has not yet been achieved. We used de novo protein design to create a homo-trimeric protein that binds the C3 symmetric small molecule drug amantadine with each protein monomer making identical interactions with each face of the small molecule. Solution NMR data show that the protein has regular three-fold symmetry and undergoes localized structural changes upon ligand binding. A high-resolution X-ray structure reveals a close overall match to the design model with the exception of water molecules in the amantadine binding site not included in the Rosetta design calculations, and a neutron structure provides experimental validation of the computationally designed hydrogen-bond networks. Exploration of approaches to generate a small molecule inducible homo-trimerization system based on the design highlight challenges that must be overcome to computationally design such systems.},
doi = {10.7554/eLife.47839},
journal = {eLife},
number = 2019,
volume = 8,
place = {United States},
year = {2019},
month = {12}
}

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