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

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

doi:10.1073/pnas.1914808117

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

Journal Article · Wed Mar 18 00:00:00 EDT 2020 · Proceedings of the National Academy of Sciences of the United States of America

DOI:https://doi.org/10.1073/pnas.1914808117· OSTI ID:1625056

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Univ. of Washington, Seattle, WA (United States); Univ. of California, Berkeley, CA (United States)
Univ. of California, Santa Cruz, CA (United States)
Univ. of Washington, Seattle, WA (United States)
Stanford Univ., CA (United States)
Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

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.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); USDOE Office of Science (SC), Biological and Environmental Research (BER); National Institute of Health

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625056

Alternate ID(s):: OSTI ID: 1646850

Journal Information:: Proceedings of the National Academy of Sciences of the United States of America, Vol. 117, Issue 13; ISSN 0027-8424

Publisher:: National Academy of SciencesCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 30 works

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

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