De novo design of a fluorescence-activating β-barrel.
De novo design of a fluorescence-activating β-barrel.
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DOI：
10.1038/s41586-018-0509-0
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发表时间：
2018-09
期刊：
影响因子：
64.8
通讯作者：
Baker D
中科院分区：
文献类型：
--
作者：
Dou J;Vorobieva AA;Sheffler W;Doyle LA;Park H;Bick MJ;Mao B;Foight GW;Lee MY;Gagnon LA;Carter L;Sankaran B;Ovchinnikov S;Marcos E;Huang PS;Vaughan JC;Stoddard BL;Baker D
β-链在β-桶中围绕中心轴的规则排列和α-螺旋在线圈中的规则排列与大多数球状蛋白质的不规则三级结构形成鲜明对比，并且自它们首次被发现以来就吸引了结构生物学家。简单的参数化模型已被用于设计各种α-螺旋盘状线圈结构，但迄今为止还没有成功的β-桶。本文表明，精确的β-桶从头设计需要相当大的对称性破坏，以实现连续的氢键连接并消除骨干应变。然后，我们构建了具有与荧光化合物DFHBI匹配的空腔形状的β-桶骨架模型集合，并使用基于分层网格的搜索方法同时优化DFHBI在这些空腔中的刚体位置以及周围氨基酸的身份，以实现高形状和化学互补性。该设计具有较高的结构精度，并在体外和大肠杆菌、酵母和哺乳动物细胞中结合和荧光激活DFHBI。这种小分子结合活性的从头设计，使用定制的骨架来结合配体，应该能够设计出越来越复杂的配体结合蛋白、传感器和催化剂，而不受已知蛋白质结构中可用的骨架几何形状的限制。
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 inEscherichia 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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影响因子：
64.8
作者：
MINOR, DL;KIM, PS
通讯作者：
KIM, PS
DOI：
10.1073/pnas.1014796108
发表时间：
2011-01-25
影响因子：
11.1
作者：
Hauser, Charlotte A. E.;Deng, Rensheng;Hauser, Ulrich A.
通讯作者：
Hauser, Ulrich A.
影响因子：
7.7
作者：
Bick MJ;Greisen PJ;Morey KJ;Antunes MS;La D;Sankaran B;Reymond L;Johnsson K;Medford JI;Baker D
通讯作者：
Baker D
DOI：
10.1093/bioinformatics/btr577
发表时间：
2011-12-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Fowler DM;Araya CL;Gerard W;Fields S
通讯作者：
Fields S
影响因子：
3
作者：
Gront, Dominik;Kmiecik, Sebastian;Kolinski, Andrzej
通讯作者：
Kolinski, Andrzej