Molecular Dynamics Simulations Guide Chimeragenesis and Engineered Control of Chemoselectivity in Diketopiperazine Dimerases
Molecular Dynamics Simulations Guide Chimeragenesis and Engineered Control of Chemoselectivity in Diketopiperazine Dimerases
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DOI：
10.1002/anie.202210254
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发表时间：
2023-02-17
影响因子：
16.6
通讯作者：
Sherman，David H.
中科院分区：
文献类型：
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作者：
Shende，Vikram V.;Harris，Natalia R.;Sherman，David H.
在色氨酸连接的二聚二酮哌嗪 (DKP) 的生物合成中，细胞色素 P450 选择性偶联 DKP 单体以生成各种复杂的异构框架。为了确定这些生物催化剂选择性的分子基础，我们获得了选择性 Csp2−N 键形成二聚酶 AspB 的高分辨率晶体结构。 AspB 结构与 C−C 和 C−N 键形成同系物 NzeB 的重叠显示没有显着的结构差异来解释它们不同的化学选择性。分子动力学 (MD) 模拟发现 NzeB 的一个区域相对于 AspB 具有更高的构象灵活性，并且该区域与单个活性位点突变的互换导致了一种催化排他性 CN 键形成的变体。 MD 模拟还表明，分子间 C−C 或 C−N 键的形成是机制变化的结果，并通过使用基质模拟物进行了实验支持。
In the biosynthesis of the tryptophan‐linked dimeric diketopiperazines (DKPs), cytochromes P450 selectively couple DKP monomers to generate a variety of intricate and isomeric frameworks. To determine the molecular basis for selectivity of these biocatalysts we obtained a high‐resolution crystal structure of selective Csp2−N bond forming dimerase, AspB. Overlay of the AspB structure onto C−C and C−N bond forming homolog NzeB revealed no significant structural variance to explain their divergent chemoselectivities. Molecular dynamics (MD) simulations identified a region of NzeB with increased conformational flexibility relative to AspB, and interchange of this region along with a single active site mutation led to a variant that catalyzes exclusive C−N bond formation. MD simulations also suggest that intermolecular C−C or C−N bond formation results from a change in mechanism, supported experimentally through use of a substrate mimic.