6CZH

Structure of a redesigned beta barrel, mFAP0, bound to DFHBI

6CZH の概要

• エントリーDOI: 10.2210/pdb6czh/pdb
• 分子名称: mFAP0, (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one (3 entities in total)
• 機能のキーワード: beta barrel, rossetta, computational, de novo, ligand binder, de novo protein
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 24979.58

構造登録者

Doyle, L.A.,Stoddard, B.L. (登録日: 2018-04-09, 公開日: 2018-09-19, 最終更新日: 2024-03-13)

主引用文献

Dou, J.,Vorobieva, A.A.,Sheffler, W.,Doyle, L.A.,Park, H.,Bick, M.J.,Mao, B.,Foight, G.W.,Lee, M.Y.,Gagnon, L.A.,Carter, L.,Sankaran, B.,Ovchinnikov, S.,Marcos, E.,Huang, P.S.,Vaughan, J.C.,Stoddard, B.L.,Baker, D.
De novo design of a fluorescence-activating beta-barrel.
Nature, 561:485-491, 2018

PubMed Abstract: 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.

PubMed: 30209393
DOI: 10.1038/s41586-018-0509-0

実験手法

X-RAY DIFFRACTION (1.8 Å)