Oxygen diffusion pathways in a cofactor-independent dioxygenase.
Oxygen diffusion pathways in a cofactor-independent dioxygenase.
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DOI：
10.1039/c5sc01638j
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发表时间：
2015-11-01
期刊：
影响因子：
8.4
通讯作者：
Roitberg AE
中科院分区：
文献类型：
--
作者：
Di Russo NV;Condurso HL;Li K;Bruner SD;Roitberg AE
实验和计算研究相结合，揭示了氧的主要扩散途径，提供了对辅因子不依赖的加氧酶如何控制立体特异性和防止氧化失活的洞察。分子氧在各种酶反应中起着重要的作用。通过最近的研究工作，结合计算和实验方法，出现了一种关于O2扩散的新观点，其中特定的通道将O2引导到活动位置。这项工作的重点是DpgC，一种辅因子非依赖的加氧酶。分子动力学模拟，结合诱变实验和氙离子结合数据，表明O2通过三条主要途径和四个不同的访问点到达该酶的活性部位。这些途径连接了一系列动态疏水口袋，将O2集中在酶底物的特定表面。广泛的分子动力学模拟提供了关于哪些途径更频繁使用的信息。这一数据与突变体的动力学测量结果是一致的，并且很难使用计算空穴位置的方法获得。综上所述，我们的结果表明，尽管DpgC在没有辅因子或金属的情况下激活O2的能力很少，但O2到达活性部位的方式与其他利用O2的蛋白质的方式相似：有多个通道可用，并且通路网络的结构可以提供区域和立体选择性。我们的结果表明，在氧气获取中存在共同的主题，这些主题在非常不同类型的蛋白质中是保守的。
A combination of experimental and computational studies reveals the main O2 diffusion pathways, providing insight into how cofactor-independent oxygenases control stereospecificity and prevent oxidative inactivation. Molecular oxygen plays an important role in a wide variety of enzymatic reactions. Through recent research efforts combining computational and experimental methods a new view of O2 diffusion is emerging, where specific channels guide O2 to the active site. The focus of this work is DpgC, a cofactor-independent oxygenase. Molecular dynamics simulations, together with mutagenesis experiments and xenon-binding data, reveal that O2 reaches the active site of this enzyme using three main pathways and four different access points. These pathways connect a series of dynamic hydrophobic pockets, concentrating O2 at a specific face of the enzyme substrate. Extensive molecular dynamics simulations provide information about which pathways are more frequently used. This data is consistent with the results of kinetic measurements on mutants and is difficult to obtain using computational cavity-location methods. Taken together, our results reveal that although DpgC is rare in its ability of activating O2 in the absence of cofactors or metals, the way O2 reaches the active site is similar to that reported for other O2-using proteins: multiple access channels are available, and the architecture of the pathway network can provide regio- and stereoselectivity. Our results point to the existence of common themes in O2 access that are conserved among very different types of proteins.