Motif-directed redesign of enzyme specificity.
Motif-directed redesign of enzyme specificity.
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DOI：
10.1002/pro.2417
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发表时间：
2014-03
期刊：
影响因子：
8
通讯作者：
Havranek, James J.
中科院分区：
文献类型：
--
作者：
Borgo, Benjamin;Havranek, James J.
计算蛋白质设计依赖于几个近似，包括使用固定的骨架和旋转异构体，将蛋白质设计简化为一个计算上容易处理的问题。然而，允许主干和非旋转体的灵活性可以带来更准确的设计和更大的构象多样性。对这个额外的构象空间进行详尽的采样是具有挑战性的，而且往往是不可能的。在这里，我们报告了一种计算方法，它利用预先选择的天然相互作用库来指导骨架灵活性，以适应这些功能接触的放置。使用这些被称为基序的本地相互作用模块，提高了实现相互作用的可能性，前提是可以识别适当的主干扰动。此外，它允许定向搜索构象空间，减少了寻找低能量构象所需的采样。我们在Rosetta中实现了基于Motif的设计算法，并通过重新设计蛋氨酸氨基肽酶的底物特异性来测试该方法的有效性。总而言之，天然酶已经进化成催化具有非凡特异性的广泛的化学反应。计算酶设计试图通过改变这些现有酶的目标底物来产生新的化学活性。我们已经实施了一种新的方法来重新设计酶的特异性，并在模型系统上展示了它的有效性。
Computational protein design relies on several approximations, including the use of fixed backbones and rotamers, to reduce protein design to a computationally tractable problem. However, allowing backbone and off-rotamer flexibility leads to more accurate designs and greater conformational diversity. Exhaustive sampling of this additional conformational space is challenging, and often impossible. Here, we report a computational method that utilizes a preselected library of native interactions to direct backbone flexibility to accommodate placement of these functional contacts. Using these native interaction modules, termed motifs, improves the likelihood that the interaction can be realized, provided that suitable backbone perturbations can be identified. Furthermore, it allows a directed search of the conformational space, reducing the sampling needed to find low energy conformations. We implemented the motif-based design algorithm in Rosetta, and tested the efficacy of this method by redesigning the substrate specificity of methionine aminopeptidase. In summary, native enzymes have evolved to catalyze a wide range of chemical reactions with extraordinary specificity. Computational enzyme design seeks to generate novel chemical activities by altering the target substrates of these existing enzymes. We have implemented a novel approach to redesign the specificity of an enzyme and demonstrated its effectiveness on a model system.
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影响因子：
56.9
作者：
Dahiyat, BI;Mayo, SL
通讯作者：
Mayo, SL
影响因子：
8
作者：
Liao, YD;Jeng, JC;Chang, ST
通讯作者：
Chang, ST
影响因子：
2.9
作者：
Lowther, WT;Orville, AM;Matthews, BW
通讯作者：
Matthews, BW
DOI：
10.1073/pnas.97.19.10383
发表时间：
2000-09-12
影响因子：
11.1
作者：
Kuhlman, B;Baker, D
通讯作者：
Baker, D
影响因子：
7
作者：
Frottin, Frederic;Martinez, Aude;Meinnel, Thierry
通讯作者：
Meinnel, Thierry