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PDBsum entry 6d0t
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De novo protein
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PDB id
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6d0t
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References listed in PDB file
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Key reference
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Title
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De novo design of a fluorescence-Activating β-Barrel.
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Authors
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J.Dou,
A.A.Vorobieva,
W.Sheffler,
L.A.Doyle,
H.Park,
M.J.Bick,
B.Mao,
G.W.Foight,
M.Y.Lee,
L.A.Gagnon,
L.Carter,
B.Sankaran,
S.Ovchinnikov,
E.Marcos,
P.S.Huang,
J.C.Vaughan,
B.L.Stoddard,
D.Baker.
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Ref.
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Nature, 2018,
561,
485-491.
[DOI no: ]
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PubMed id
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Abstract
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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. 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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