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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]
+ Show Author Affiliations
  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. doi:10.7554/eLife.47839.
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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
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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.
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@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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https://doi.org/10.7554/eLife.47839
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Works referenced in this record:

Computational design of a homotrimeric metalloprotein with a trisbipyridyl core
journal, December 2016

  • Mills, Jeremy H.; Sheffler, William; Ener, Maraia E.
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 52
  • DOI: 10.1073/pnas.1600188113

Conditional Protein Alleles Using Knockin Mice and a Chemical Inducer of Dimerization
journal, December 2003

Molecular Dynamics Simulation Directed Rational Design of Inhibitors Targeting Drug-Resistant Mutants of Influenza A Virus M2
journal, August 2011

  • Wang, Jun; Ma, Chunlong; Fiorin, Giacomo
  • Journal of the American Chemical Society, Vol. 133, Issue 32
  • DOI: 10.1021/ja204969m

Manipulating signaling at will: chemically-inducible dimerization (CID) techniques resolve problems in cell biology
journal, January 2013

  • DeRose, Robert; Miyamoto, Takafumi; Inoue, Takanari
  • Pflügers Archiv - European Journal of Physiology, Vol. 465, Issue 3
  • DOI: 10.1007/s00424-012-1208-6

Two-Dimensional NMR Lineshape Analysis
journal, April 2016

  • Waudby, Christopher A.; Ramos, Andres; Cabrita, Lisa D.
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep24826

Rapid and orthogonal logic gating with a gibberellin-induced dimerization system
journal, March 2012

  • Miyamoto, Takafumi; DeRose, Robert; Suarez, Allison
  • Nature Chemical Biology, Vol. 8, Issue 5
  • DOI: 10.1038/nchembio.922

De Novo Design of a D 2 - Symmetrical Protein that Reproduces the Diheme Four-Helix Bundle in Cytochrome bc 1
journal, July 2004

  • Ghirlanda, Giovanna; Osyczka, Artur; Liu, Weixia
  • Journal of the American Chemical Society, Vol. 126, Issue 26
  • DOI: 10.1021/ja039935g

A nonnatural transcriptional coactivator
journal, December 1997

  • Nyanguile, O.; Uesugi, M.; Austin, D. J.
  • Proceedings of the National Academy of Sciences, Vol. 94, Issue 25
  • DOI: 10.1073/pnas.94.25.13402

Efficacy and safety of amantadine for the treatment of l-DOPA-induced dyskinesia
journal, March 2018

Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity
journal, September 2015

TM-align: a protein structure alignment algorithm based on the TM-score
journal, April 2005

Overview of the CCP 4 suite and current developments
journal, March 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4
  • DOI: 10.1107/S0907444910045749

NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy
journal, December 2014

Sampling and energy evaluation challenges in ligand binding protein design: Computational Protein Design
journal, October 2017

  • Dou, Jiayi; Doyle, Lindsey; Jr. Greisen, Per
  • Protein Science, Vol. 26, Issue 12
  • DOI: 10.1002/pro.3317

Coot model-building tools for molecular graphics
journal, November 2004

  • Emsley, Paul; Cowtan, Kevin
  • Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132
  • DOI: 10.1107/S0907444904019158

De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity
journal, May 2016

Accurate design of megadalton-scale two-component icosahedral protein complexes
journal, July 2016

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

De novo design of a hyperstable non-natural protein–ligand complex with sub-Å accuracy
journal, August 2017

  • Polizzi, Nicholas F.; Wu, Yibing; Lemmin, Thomas
  • Nature Chemistry, Vol. 9, Issue 12
  • DOI: 10.1038/nchem.2846

Chemically Controlled Protein Assembly: Techniques and Applications
journal, June 2010

  • Fegan, Adrian; White, Brian; Carlson, Jonathan C. T.
  • Chemical Reviews, Vol. 110, Issue 6
  • DOI: 10.1021/cr8002888

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
journal, May 2007

  • Davis, I. W.; Leaver-Fay, A.; Chen, V. B.
  • Nucleic Acids Research, Vol. 35, Issue Web Server
  • DOI: 10.1093/nar/gkm216

NMRPipe: A multidimensional spectral processing system based on UNIX pipes
journal, November 1995

  • Delaglio, Frank; Grzesiek, Stephan; Vuister, GeertenW.
  • Journal of Biomolecular NMR, Vol. 6, Issue 3
  • DOI: 10.1007/BF00197809

Design of a hyperstable 60-subunit protein icosahedron
journal, June 2016

  • Hsia, Yang; Bale, Jacob B.; Gonen, Shane
  • Nature, Vol. 535, Issue 7610
  • DOI: 10.1038/nature18010

Computational design of ligand-binding proteins with high affinity and selectivity
journal, September 2013

  • Tinberg, Christine E.; Khare, Sagar D.; Dou, Jiayi
  • Nature, Vol. 501, Issue 7466, p. 212-216
  • DOI: 10.1038/nature12443

Conditional cell ablation by tight control of caspase-3 dimerization in transgenic mice
journal, November 2002

  • Mallet, Vincent O.; Mitchell, Claudia; Guidotti, Jacques-Emmanuel
  • Nature Biotechnology, Vol. 20, Issue 12
  • DOI: 10.1038/nbt762

Sparse matrix sampling: a screening method for crystallization of proteins
journal, August 1991

Inhibitors of the M2 Proton Channel Engage and Disrupt Transmembrane Networks of Hydrogen-Bonded Waters
journal, August 2018

  • Thomaston, Jessica L.; Polizzi, Nicholas F.; Konstantinidi, Athina
  • Journal of the American Chemical Society, Vol. 140, Issue 45
  • DOI: 10.1021/jacs.8b06741

Joint X-ray and neutron refinement with phenix.refine
journal, October 2010

  • Afonine, Pavel V.; Mustyakimov, Marat; Grosse-Kunstleve, Ralf W.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 11
  • DOI: 10.1107/S0907444910026582

[20] Processing of X-ray diffraction data collected in oscillation mode
book, January 1997

Functional analysis of Fas signaling in vivo using synthetic inducers of dimerization
journal, July 1996

Delineation of the caspase-9 signaling cascade
journal, September 2007

Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206

De novo design of a fluorescence-activating β-barrel
journal, September 2018

Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation
journal, February 2021

Multi-functionality of a tryptophan residue conserved in substrate-binding groove of GH19 chitinases
journal, January 2021

Overview of the CCP4 suite and current developments.
text, January 2011

  • Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D.
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.52322

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
text, January 2007

  • B., Chen, Vincent; C., Richardson, David; S., Richardson, Jane
  • The University of North Carolina at Chapel Hill University Libraries
  • DOI: 10.17615/m2an-p252

PHENIX: a comprehensive Python-based system for macromolecular structure solution.
text, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Apollo - University of Cambridge Repository
  • DOI: 10.17863/cam.45787
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