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

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

doi:10.7554/eLife.47839

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

Journal Article · 19 December 2019 · eLife

DOI: https://doi.org/10.7554/eLife.47839 · OSTI ID:1598025

^[1]; Selvaraj, Brinda ^[2];

^[3];

^[4];

^[5]; Oberdorfer, Gustav ^[6]; DeGrado, William ^[7];

^[3];

^[8];

^[2];

^[9]

Univ. of Washington, Seattle, WA (United States); Sana Biotechnology, Inc., Seattle, WA (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Univ. of California, Santa Cruz, CA (United States)
Univ. of Washington, Seattle, WA (United States); Lyell Immunopharma, Inc., Seattle, WA (United States)
Univ. of Washington, Seattle, WA (United States); Univ. of California, Berkeley, CA (United States)
Graz University of Technology (Austria)
Univ. of California, San Francisco, CA (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); St. Jude Children’s Research Hospital, Memphis, TN (United States)
Univ. of Washington, Seattle, WA (United States)

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.

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Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: 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)

Grant/Contract Number:: AC02-06CH11357; 1R35GM125034-01; S10OD018455

OSTI ID:: 1598025

Journal Information:: eLife, Vol. 8, Issue 2019; ISSN 2050-084X

Publisher:: eLife Sciences Publications, Ltd.Copyright Statement

Country of Publication:: United States

Language:: ENGLISH

References (41)

Computational design of a homotrimeric metalloprotein with a trisbipyridyl core Mills, Jeremy H.; Sheffler, William; Ener, Maraia E. Proceedings of the National Academy of Sciences, Vol. 113, Issue 52 https://doi.org/10.1073/pnas.1600188113	journal	December 2016
Conditional Protein Alleles Using Knockin Mice and a Chemical Inducer of Dimerization Stankunas, Kryn; Bayle, J. Henri; Gestwicki, Jason E. Molecular Cell, Vol. 12, Issue 6 https://doi.org/10.1016/S1097-2765(03)00491-X	journal	December 2003
Molecular Dynamics Simulation Directed Rational Design of Inhibitors Targeting Drug-Resistant Mutants of Influenza A Virus M2 Wang, Jun; Ma, Chunlong; Fiorin, Giacomo Journal of the American Chemical Society, Vol. 133, Issue 32 https://doi.org/10.1021/ja204969m	journal	August 2011
Manipulating signaling at will: chemically-inducible dimerization (CID) techniques resolve problems in cell biology DeRose, Robert; Miyamoto, Takafumi; Inoue, Takanari Pflügers Archiv - European Journal of Physiology, Vol. 465, Issue 3 https://doi.org/10.1007/s00424-012-1208-6	journal	January 2013
LAUEGEN version 6.0 and INTLDM Campbell, J. W.; Hao, Q.; Harding, M. M. Journal of Applied Crystallography, Vol. 31, Issue 3 https://doi.org/10.1107/S0021889897016683	journal	June 1998
Two-Dimensional NMR Lineshape Analysis Waudby, Christopher A.; Ramos, Andres; Cabrita, Lisa D. Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep24826	journal	April 2016
Rapid and orthogonal logic gating with a gibberellin-induced dimerization system Miyamoto, Takafumi; DeRose, Robert; Suarez, Allison Nature Chemical Biology, Vol. 8, Issue 5 https://doi.org/10.1038/nchembio.922	journal	March 2012
De Novo Design of a D ₂ - Symmetrical Protein that Reproduces the Diheme Four-Helix Bundle in Cytochrome bc ₁ Ghirlanda, Giovanna; Osyczka, Artur; Liu, Weixia Journal of the American Chemical Society, Vol. 126, Issue 26 https://doi.org/10.1021/ja039935g	journal	July 2004
A nonnatural transcriptional coactivator Nyanguile, O.; Uesugi, M.; Austin, D. J. Proceedings of the National Academy of Sciences, Vol. 94, Issue 25 https://doi.org/10.1073/pnas.94.25.13402	journal	December 1997
Efficacy and safety of amantadine for the treatment of l-DOPA-induced dyskinesia Perez-Lloret, Santiago; Rascol, Olivier Journal of Neural Transmission, Vol. 125, Issue 8 https://doi.org/10.1007/s00702-018-1869-1	journal	March 2018
Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity Ollikainen, Noah; de Jong, René M.; Kortemme, Tanja PLOS Computational Biology, Vol. 11, Issue 9 https://doi.org/10.1371/journal.pcbi.1004335	journal	September 2015
TM-align: a protein structure alignment algorithm based on the TM-score Zhang, Y. Nucleic Acids Research, Vol. 33, Issue 7 https://doi.org/10.1093/nar/gki524	journal	April 2005
The IMAGINE instrument: first neutron protein structure and new capabilities for neutron macromolecular crystallography Meilleur, Flora; Munshi, Parthapratim; Robertson, Lee Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 10 https://doi.org/10.1107/S0907444913019604	journal	September 2013
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy Lee, Woonghee; Tonelli, Marco; Markley, John L. Bioinformatics, Vol. 31, Issue 8 https://doi.org/10.1093/bioinformatics/btu830	journal	December 2014
Sampling and energy evaluation challenges in ligand binding protein design: Computational Protein Design Dou, Jiayi; Doyle, Lindsey; Jr. Greisen, Per Protein Science, Vol. 26, Issue 12 https://doi.org/10.1002/pro.3317	journal	October 2017
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity Boyken, S. E.; Chen, Z.; Groves, B. Science, Vol. 352, Issue 6286 https://doi.org/10.1126/science.aad8865	journal	May 2016
Accurate design of megadalton-scale two-component icosahedral protein complexes Bale, J. B.; Gonen, S.; Liu, Y. Science, Vol. 353, Issue 6297 https://doi.org/10.1126/science.aaf8818	journal	July 2016
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
De novo design of a hyperstable non-natural protein–ligand complex with sub-Å accuracy Polizzi, Nicholas F.; Wu, Yibing; Lemmin, Thomas Nature Chemistry, Vol. 9, Issue 12 https://doi.org/10.1038/nchem.2846	journal	August 2017
Chemically Controlled Protein Assembly: Techniques and Applications Fegan, Adrian; White, Brian; Carlson, Jonathan C. T. Chemical Reviews, Vol. 110, Issue 6 https://doi.org/10.1021/cr8002888	journal	June 2010
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids Davis, I. W.; Leaver-Fay, A.; Chen, V. B. Nucleic Acids Research, Vol. 35, Issue Web Server https://doi.org/10.1093/nar/gkm216	journal	May 2007
NMRPipe: A multidimensional spectral processing system based on UNIX pipes Delaglio, Frank; Grzesiek, Stephan; Vuister, GeertenW. Journal of Biomolecular NMR, Vol. 6, Issue 3 https://doi.org/10.1007/BF00197809	journal	November 1995
Design of a hyperstable 60-subunit protein icosahedron Hsia, Yang; Bale, Jacob B.; Gonen, Shane Nature, Vol. 535, Issue 7610 https://doi.org/10.1038/nature18010	journal	June 2016
Computational design of ligand-binding proteins with high affinity and selectivity Tinberg, Christine E.; Khare, Sagar D.; Dou, Jiayi Nature, Vol. 501, Issue 7466, p. 212-216 https://doi.org/10.1038/nature12443	journal	September 2013
LSCALE – the new normalization, scaling and absorption correction program in the Daresbury Laue software suite Arzt, Steffi; Campbell, John W.; Harding, Marjorie M. Journal of Applied Crystallography, Vol. 32, Issue 3 https://doi.org/10.1107/S0021889898015350	journal	June 1999
Conditional cell ablation by tight control of caspase-3 dimerization in transgenic mice Mallet, Vincent O.; Mitchell, Claudia; Guidotti, Jacques-Emmanuel Nature Biotechnology, Vol. 20, Issue 12 https://doi.org/10.1038/nbt762	journal	November 2002
Sparse matrix sampling: a screening method for crystallization of proteins Jancarik, J.; Kim, S. H. Journal of Applied Crystallography, Vol. 24, Issue 4 https://doi.org/10.1107/S0021889891004430	journal	August 1991
Inhibitors of the M2 Proton Channel Engage and Disrupt Transmembrane Networks of Hydrogen-Bonded Waters Thomaston, Jessica L.; Polizzi, Nicholas F.; Konstantinidi, Athina Journal of the American Chemical Society, Vol. 140, Issue 45 https://doi.org/10.1021/jacs.8b06741	journal	August 2018
Joint X-ray and neutron refinement with phenix.refine Afonine, Pavel V.; Mustyakimov, Marat; Grosse-Kunstleve, Ralf W. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 11 https://doi.org/10.1107/S0907444910026582	journal	October 2010
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
Functional analysis of Fas signaling in vivo using synthetic inducers of dimerization Spencer, David M.; Belshaw, Peter J.; Chen, Lei Current Biology, Vol. 6, Issue 7 https://doi.org/10.1016/S0960-9822(02)00607-3	journal	July 1996
Delineation of the caspase-9 signaling cascade Guerrero, Alan D.; Chen, Min; Wang, Jin Apoptosis, Vol. 13, Issue 1 https://doi.org/10.1007/s10495-007-0139-8	journal	September 2007
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
De novo design of a fluorescence-activating β-barrel Dou, Jiayi; Vorobieva, Anastassia A.; Sheffler, William Nature, Vol. 561, Issue 7724 https://doi.org/10.1038/s41586-018-0509-0	journal	September 2018
Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation Tillu, Vikas A.; Rae, James; Gao, Ya Nature Communications, Vol. 12, Issue 1 https://doi.org/10.1038/s41467-021-21035-4	journal	February 2021
Multi-functionality of a tryptophan residue conserved in substrate-binding groove of GH19 chitinases Nagata, Takuya; Shinya, Shoko; Ohnuma, Takayuki Scientific Reports, Vol. 11, Issue 1 https://doi.org/10.1038/s41598-021-81903-3	journal	January 2021
Overview of the CCP4 suite and current developments. Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.52322	text	January 2011
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids B., Chen, Vincent; C., Richardson, David; S., Richardson, Jane The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/m2an-p252	text	January 2007
PHENIX: a comprehensive Python-based system for macromolecular structure solution. Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.45787	text	January 2010

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