A multiplexed bacterial two-hybrid for rapid characterization of protein-protein interactions and iterative protein design.
A multiplexed bacterial two-hybrid for rapid characterization of protein-protein interactions and iterative protein design.
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DOI：
10.1038/s41467-023-38697-x
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发表时间：
2023-08-02
影响因子：
16.6
通讯作者：
Kosuri S
中科院分区：
文献类型：
--
作者：
Boldridge WC;Ljubetič A;Kim H;Lubock N;Szilágyi D;Lee J;Brodnik A;Jerala R;Kosuri S
蛋白质-蛋白质相互作用（PPI）对于生物功能至关重要，其应用范围从药物设计到合成细胞电路。卷曲螺旋已被用作研究特异性的序列决定因素的模型。然而，由于正交性预测不准确以及大规模测试的困难，构建性能良好的正交盘绕线圈对组仍然具有挑战性。为了解决这个问题，我们开发了下一代细菌双杂交（NGB2H）方法，该方法允许使用下一代测序读数以定量和可扩展的方式快速探索编程蛋白质库的相互作用。我们设计、构建和测试大量正交合成卷曲线圈，分析了 8,000 多个 PPI，并使用该数据集训练更准确的卷曲线圈评分算法 (iCipa)。在描述了近 18,000 个新 PPI 的特征后，我们据我们所知确定了迄今为止最大的一组正交卷曲线圈，其中有 15 个目标相互作用。我们的方法为正交 PPI 的设计提供了强大的工具。蛋白质-蛋白质相互作用（PPI）对于生物功能至关重要，其应用范围从药物设计到合成细胞电路。在这里，作者开发了一种测定和计算方法来识别更多的正交卷曲线圈对，这对于生物过程和药物设计至关重要。
Protein-protein interactions (PPIs) are crucial for biological functions and have applications ranging from drug design to synthetic cell circuits. Coiled-coils have been used as a model to study the sequence determinants of specificity. However, building well-behaved sets of orthogonal pairs of coiled-coils remains challenging due to inaccurate predictions of orthogonality and difficulties in testing at scale. To address this, we develop the next-generation bacterial two-hybrid (NGB2H) method, which allows for the rapid exploration of interactions of programmed protein libraries in a quantitative and scalable way using next-generation sequencing readout. We design, build, and test large sets of orthogonal synthetic coiled-coils, assayed over 8,000 PPIs, and used the dataset to train a more accurate coiled-coil scoring algorithm (iCipa). After characterizing nearly 18,000 new PPIs, we identify to the best of our knowledge the largest set of orthogonal coiled-coils to date, with fifteen on-target interactions. Our approach provides a powerful tool for the design of orthogonal PPIs. Protein-protein interactions (PPIs) are crucial for biological functions and have applications ranging from drug design to synthetic cell circuits. Here the authors develop an assay and computational methods to identify more orthogonal coiled-coil pairs, critical for biological processes and drug design.
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影响因子：
16.6
作者：
Aupič J;Strmšek Ž;Lapenta F;Pahovnik D;Pisanski T;Drobnak I;Ljubetič A;Jerala R
通讯作者：
Jerala R
DOI：
10.31449/inf.v43i1.2693
发表时间：
2019-03-01
期刊：
INFORMATICA-AN INTERNATIONAL JOURNAL OF COMPUTING AND INFORMATICS
影响因子：
--
作者：
Brodnik, Andrej;Palangetic, Marko;Jovicic, Vladan
通讯作者：
Jovicic, Vladan
影响因子：
56.9
作者：
Chen, Zibo;Kibler, Ryan D.;Baker, David
通讯作者：
Baker, David
影响因子：
15
作者：
Drobnak, Igor;Gradisar, Helena;Jerala, Roman
通讯作者：
Jerala, Roman
影响因子：
14.9
作者：
Sidore, Angus M.;Plesa, Calin;Kosuri, Sriram
通讯作者：
Kosuri, Sriram