De novo design of a fluorescence-activating β-barrel

Dou, Jiayi; Vorobieva, Anastassia A.; Sheffler, William; Doyle, Lindsey A.; Park, Hahnbeom; Bick, Matthew J.; Mao, Binchen; Foight, Glenna W.; Lee, Min Yen; Gagnon, Lauren A.; Carter, Lauren; Sankaran, Banumathi; Ovchinnikov, Sergey; Marcos, Enrique; Huang, Po-Ssu; Vaughan, Joshua C.; Stoddard, Barry L.; Baker, David

doi:10.1038/s41586-018-0509-0

Title: De novo design of a fluorescence-activating β-barrel

Journal Article · Wed Sep 12 00:00:00 EDT 2018 · Nature (London)

DOI:https://doi.org/10.1038/s41586-018-0509-0· OSTI ID:1601813

Dou, Jiayi ^[1]; Vorobieva, Anastassia A. ^[1]; Sheffler, William ^[1]; Doyle, Lindsey A. ^[2]; Park, Hahnbeom ^[1]; Bick, Matthew J. ^[1]; Mao, Binchen ^[3]; Foight, Glenna W. ^[3]; Lee, Min Yen ^[3]; Gagnon, Lauren A. ^[3]; Carter, Lauren ^[1]; Sankaran, Banumathi ^[4]; Ovchinnikov, Sergey ^[1]; Marcos, Enrique ^[1]; Huang, Po-Ssu ^[1]; Vaughan, Joshua C. ^[3]; Stoddard, Barry L. ^[2]; Baker, David ^[5]

Univ. of Washington, Seattle, WA (United States). Inst. for Protein Design
Fred Hutchinson Cancer Research Center, Seattle, WA (United States)
Univ. of Washington, Seattle, WA (United States)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Univ. of Washington, Seattle, WA (United States). Inst. for Protein Design, and Howard Hughes Medical Inst.

The regular arrangements of β-strands around a central axis in β-barrels and of α-helices in coiled coils contrast with the irregular tertiary structures of most globular proteins, and have fascinated structural biologists since they were first discovered. Simple parametric models have been used to design a wide range of α-helical coiled-coil structures, but to date there has been no success with β-barrels. Here we show that accurate de novo design of β-barrels requires considerable symmetry-breaking to achieve continuous hydrogen-bond connectivity and eliminate backbone strain. We then build ensembles of β-barrel backbone models with cavity shapes that match the fluorogenic compound DFHBI, and use a hierarchical grid-based search method to simultaneously optimize the rigid-body placement of DFHBI in these cavities and the identities of the surrounding amino acids to achieve high shape and chemical complementarity. The designs have high structural accuracy and bind and fluorescently activate DFHBI in vitro and in Escherichia coli, yeast and mammalian cells. Finally, this de novo design of small-molecule binding activity, using backbones custom-built to bind the ligand, should enable the design of increasingly sophisticated ligand-binding proteins, sensors and catalysts that are not limited by the backbone geometries available in known protein structures.

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

Sponsoring Organization:: USDOE Office of Science (SC); Fulbright Commission for Belgium and Luxembourg; National Institutes of Health (NIH)

Grant/Contract Number:: AC02-05CH11231; R01 GM115545

OSTI ID:: 1601813

Journal Information:: Nature (London), Vol. 561, Issue 7724; ISSN 0028-0836

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 177 works

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