De novo design of protein homodimers containing tunable symmetric protein pockets.
De novo design of protein homodimers containing tunable symmetric protein pockets.
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DOI：
10.1073/pnas.2113400119
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发表时间：
2022-07-26
影响因子：
11.1
通讯作者：
中科院分区：
文献类型：
--
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能够结合任意小分子的蛋白质可以产生新的生物传感器或药物。虽然近年来在从零开始设计能够结合非对称分子的蛋白质方面取得了相当大的进展，但在促进对称分子的结合方面却做得很少。在这里，我们提出了一种方法来生成具有不同中心腔的C2对称蛋白文库，这些文库可以在未来被功能化以结合一系列C2对称小分子，用于配体可控细胞工程等应用。我们表明，31%的我们设计的蛋白质折叠到所需的四元态，当实验表征，并且是超稳定的。在生物学中，功能遵循形式，小分子的结合需要带有与配体形状相匹配的口袋的蛋白质。对于设计与对称配体的结合，具有匹配对称性的蛋白质寡聚物是有利的，因为每个蛋白质亚基都可以与配体产生相同的相互作用。在这里，我们描述了一种设计具有不同大小和形状口袋的超稳定C2对称蛋白质的一般方法。我们首先设计了一种重复蛋白，它具有连续的曲率，但螺旋上升较低，然后将它们对接到C2对称的同型二聚体中，以产生广泛的C2对称腔。我们利用这种方法设计了数千种C2对称同型二聚体，并对其中的101种进行了实验表征。其中31个经小角度x射线散射证实，2个经晶体学分析证实与计算设计模型非常吻合。这些支架为结合广泛的C2对称化合物提供了丰富的起点。
Proteins capable of binding arbitrary small molecules could enable the generation of new biosensors or medicines. While considerable progress has been made in recent years to design proteins from scratch capable of binding asymmetric molecules, little work has been done to facilitate the binding of symmetric molecules. Here, we present a method for generating libraries of C2 symmetric proteins with diverse central cavities that could be functionalized in the future to bind a range of C2 symmetric small molecules for applications such as ligand controllable cell engineering. We show that 31% of our designed proteins fold to the desired quaternary state, when experimentally characterized, and are hyperstable. Function follows form in biology, and the binding of small molecules requires proteins with pockets that match the shape of the ligand. For design of binding to symmetric ligands, protein homo-oligomers with matching symmetry are advantageous as each protein subunit can make identical interactions with the ligand. Here, we describe a general approach to designing hyperstable C2 symmetric proteins with pockets of diverse size and shape. We first designed repeat proteins that sample a continuum of curvatures but have low helical rise, then docked these into C2 symmetric homodimers to generate an extensive range of C2 symmetric cavities. We used this approach to design thousands of C2 symmetric homodimers, and characterized 101 of them experimentally. Of these, the geometry of 31 were confirmed by small angle X-ray scattering and 2 were shown by crystallographic analyses to be in close agreement with the computational design models. These scaffolds provide a rich set of starting points for binding a wide range of C2 symmetric compounds.
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DOI：
10.1007/978-1-62703-691-7_18
发表时间：
2014
期刊：
Methods in molecular biology (Clifton, N.J.)
影响因子：
--
作者：
Dyer, Kevin N;Hammel, Michal;Rambo, Robert P;Tsutakawa, Susan E;Rodic, Ivan;Classen, Scott;Tainer, John A;Hura, Greg L
通讯作者：
Hura, Greg L
影响因子：
14.8
作者：
Greenfield, Norma J.
通讯作者：
Greenfield, Norma J.
影响因子：
21.8
作者：
Fallas JA;Ueda G;Sheffler W;Nguyen V;McNamara DE;Sankaran B;Pereira JH;Parmeggiani F;Brunette TJ;Cascio D;Yeates TR;Zwart P;Baker D
通讯作者：
Baker D
影响因子：
14.8
作者：
Faiella, Marina;Andreozzi, Concetta;Lombardi, Angela
通讯作者：
Lombardi, Angela
影响因子：
7.7
作者：
Ueda, George;Antanasijevic, Aleksandar;Baker, David
通讯作者：
Baker, David