Predicting Productive Binding Modes for Substrates and Carbocation Intermediates in Terpene Synthases-Bornyl Diphosphate Synthase as a Representative Case.
Predicting Productive Binding Modes for Substrates and Carbocation Intermediates in Terpene Synthases-Bornyl Diphosphate Synthase as a Representative Case.
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DOI：
10.1021/acscatal.8b00342
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发表时间：
2018-04-06
期刊：
影响因子：
12.9
通讯作者：
Tantillo DJ
中科院分区：
文献类型：
--
作者：
O'Brien TE;Bertolani SJ;Zhang Y;Siegel JB;Tantillo DJ
萜烯合酶包含一系列酶，可通过碳阳离子中间体的生成和保护，将无环低聚异戊二烯基二磷酸转化为具有复杂多环碳主链的萜烯天然产物。为了适应这种化学反应，萜烯合酶活性位点通常排列有烷基和芳香族侧链，即非极性侧链。预测整个萜烯合酶反应途径的正确的、机械相关的结合模式仍然是一个尚未解决的挑战。在这里，我们描述了一种识别此类模式的方法：TerDockin，一系列协议，用于预测底物碳骨架和衍生碳阳离子相对于萜烯合酶活性位点中结合的二磷酸基团的方向。使用冰片基二磷酸合酶的配方，我们预测了与所有当前实验观察结果一致的结合模式，包括同位素标记实验的结果和已知的立体选择性。此外，预测的结合模式概括了一项开创性研究的关键发现，该研究涉及该途径部分计算要求更高的 QM/MM 分子动力学方法。这项工作说明了 TerDockin 方法作为更复杂的计算起点的价值，并为该酶家族的合理工程奠定了基础。
Terpene synthases comprise a family of enzymes that convert acyclic oligo-isoprenyl diphosphates to terpene natural products with complex, polycyclic carbon backbones via the generation and protection of carbocation intermediates. To accommodate this chemistry, terpene synthase active sites generally are lined with alkyl and aromatic, i.e., nonpolar, sidechains. Predicting the correct, mechanistically relevant binding modes for entire terpene synthase reaction pathways remains an unsolved challenge. Here we describe a method for identifying such modes: TerDockin, a series of protocols to predict the orientation of carbon skeletons of substrates and derived carbocations relative to the bound diphosphate group in terpene synthase active sites. Using this recipe for bornyl diphosphate synthase, we have predicted binding modes that are consistent with all current experimental observations, including the results of isotope labeling experiments and known stereoselectivity. In addition, the predicted binding modes recapitulate key findings of a seminal study involving more computationally demanding QM/MM molecular dynamics methods on part of this pathway. This work illustrates the value of the TerDockin approach as a starting point for more involved calculations and sets the stage for the rational engineering of this family of enzymes.
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DOI：
10.1111/tpj.12702
发表时间：
2014-12
期刊：
The Plant journal : for cell and molecular biology
影响因子：
--
作者：
Byers KJ;Vela JP;Peng F;Riffell JA;Bradshaw HD Jr
通讯作者：
Bradshaw HD Jr
影响因子：
--
作者：
GONZALEZ, C;SCHLEGEL, HB
通讯作者：
SCHLEGEL, HB
影响因子：
3.2
作者：
Hong, Young J.;Tantillo, Dean J.
通讯作者：
Tantillo, Dean J.
影响因子：
15
作者：
Hong, Young J.;Tantillo, Dean J.
通讯作者：
Tantillo, Dean J.
影响因子：
4.4
作者：
BECKE, AD
通讯作者：
BECKE, AD