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Title: Computational design of closely related proteins that adopt two well-defined but structurally divergent folds

Abstract

The plasticity of naturally occurring protein structures, which can change shape considerably in response to changes in environmental conditions, is critical to biological function. While computational methods have been used for de novo design of proteins that fold to a single state with a deep free-energy minimum [P.-S. Huang, S. E. Boyken, D. Baker, Nature 537, 320–327 (2016)], and to reengineer natural proteins to alter their dynamics [J. A. Davey, A. M. Damry, N. K. Goto, R. A. Chica, Nat. Chem. Biol.13, 1280–1285 (2017)] or fold [P. A. Alexander, Y. He, Y. Chen, J. Orban, P. N. Bryan, Proc. Natl. Acad. Sci. U.S.A. 106, 21149–21154 (2009)], the de novo design of closely related sequences which adopt well-defined but structurally divergent structures remains an outstanding challenge. We designed closely related sequences (over 94% identity) that can adopt two very different homotrimeric helical bundle conformations—one short (~66 Å height) and the other long (~100 Å height)—reminiscent of the conformational transition of viral fusion proteins. Crystallographic and NMR spectroscopic characterization shows that both the short- and long-state sequences fold as designed. We sought to design bistable sequences for which both states are accessible, and obtained a single designed protein sequence that populates eithermore » the short state or the long state depending on the measurement conditions. The design of sequences which are poised to adopt two very different conformations sets the stage for creating large-scale conformational switches between structurally divergent forms.« less

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [2]; ORCiD logo [2];  [2]; ORCiD logo [4]; ORCiD logo [5]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [3]
  1. Univ. of Washington, Seattle, WA (United States); Univ. of California, Berkeley, CA (United States)
  2. Univ. of California, Santa Cruz, CA (United States)
  3. Univ. of Washington, Seattle, WA (United States)
  4. Stanford Univ., CA (United States)
  5. Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institute of Health
OSTI Identifier:
1625056
Alternate Identifier(s):
OSTI ID: 1646850
Grant/Contract Number:  
AC02-05CH11231
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: 13; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Science & Technology - Other Topics

Citation Formats

Wei, Kathy Y., Moschidi, Danai, Bick, Matthew J., Nerli, Santrupti, McShan, Andrew C., Carter, Lauren P., Huang, Po-Ssu, Fletcher, Daniel A., Sgourakis, Nikolaos G., Boyken, Scott E., and Baker, David. Computational design of closely related proteins that adopt two well-defined but structurally divergent folds. United States: N. p., 2020. Web. https://doi.org/10.1073/pnas.1914808117.
Wei, Kathy Y., Moschidi, Danai, Bick, Matthew J., Nerli, Santrupti, McShan, Andrew C., Carter, Lauren P., Huang, Po-Ssu, Fletcher, Daniel A., Sgourakis, Nikolaos G., Boyken, Scott E., & Baker, David. Computational design of closely related proteins that adopt two well-defined but structurally divergent folds. United States. https://doi.org/10.1073/pnas.1914808117
Wei, Kathy Y., Moschidi, Danai, Bick, Matthew J., Nerli, Santrupti, McShan, Andrew C., Carter, Lauren P., Huang, Po-Ssu, Fletcher, Daniel A., Sgourakis, Nikolaos G., Boyken, Scott E., and Baker, David. Wed . "Computational design of closely related proteins that adopt two well-defined but structurally divergent folds". United States. https://doi.org/10.1073/pnas.1914808117. https://www.osti.gov/servlets/purl/1625056.
@article{osti_1625056,
title = {Computational design of closely related proteins that adopt two well-defined but structurally divergent folds},
author = {Wei, Kathy Y. and Moschidi, Danai and Bick, Matthew J. and Nerli, Santrupti and McShan, Andrew C. and Carter, Lauren P. and Huang, Po-Ssu and Fletcher, Daniel A. and Sgourakis, Nikolaos G. and Boyken, Scott E. and Baker, David},
abstractNote = {The plasticity of naturally occurring protein structures, which can change shape considerably in response to changes in environmental conditions, is critical to biological function. While computational methods have been used for de novo design of proteins that fold to a single state with a deep free-energy minimum [P.-S. Huang, S. E. Boyken, D. Baker, Nature 537, 320–327 (2016)], and to reengineer natural proteins to alter their dynamics [J. A. Davey, A. M. Damry, N. K. Goto, R. A. Chica, Nat. Chem. Biol.13, 1280–1285 (2017)] or fold [P. A. Alexander, Y. He, Y. Chen, J. Orban, P. N. Bryan, Proc. Natl. Acad. Sci. U.S.A. 106, 21149–21154 (2009)], the de novo design of closely related sequences which adopt well-defined but structurally divergent structures remains an outstanding challenge. We designed closely related sequences (over 94% identity) that can adopt two very different homotrimeric helical bundle conformations—one short (~66 Å height) and the other long (~100 Å height)—reminiscent of the conformational transition of viral fusion proteins. Crystallographic and NMR spectroscopic characterization shows that both the short- and long-state sequences fold as designed. We sought to design bistable sequences for which both states are accessible, and obtained a single designed protein sequence that populates either the short state or the long state depending on the measurement conditions. The design of sequences which are poised to adopt two very different conformations sets the stage for creating large-scale conformational switches between structurally divergent forms.},
doi = {10.1073/pnas.1914808117},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 13,
volume = 117,
place = {United States},
year = {2020},
month = {3}
}

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Figures / Tables:

Fig. 1 Fig. 1: Design and in silico characterization of proteins with two distinct, well-defined ground states. (A) Design concept for protein backbones with a “short” and a “long” state. The backbone consists of a stable base, mobile flipping helices (red), tunable interface, and a flexible hinge (yellow). (B) Tunable interface betweenmore » the inner helices and flipping helices. Each of three positions can be a hydrogen bond (green, “A”) or hydrophobic (black, “X”) layer. (C) Fraction of top 10 scored Rosetta folding predictions that resemble the short, long, or other structure for each permutation of possible interface configurations. (D) Initial design scheme. Starting with the previously characterized protein 2L3HC3_13 (PDB ID 5J0H) (cyan), a monomer is extracted, cut to produce a flipping helix, and reconnected with a hinge to produce the backbone of the short or long state. (E) Final design scheme. Previously characterized proteins 2L3HC3_13 (cyan) and 2L3HC3_23 (blue) are fused via their inner helices, outer helices are trimmed, and the hinge length is chosen such that the flipping helices pack against each other in the long state.« less

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