Computational Biology and Bioinformatics Group, Biological Sciences Division , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States.
Molecular Modeling & Design at leadXpro Villigen , Canton of Aargau , Switzerland.
J Phys Chem B. 2019 Mar 14;123(10):2210-2216. doi: 10.1021/acs.jpcb.8b10820. Epub 2019 Mar 5.
Vitamin B-dependent enzymes catalyze several difficult radical reactions. There are fundamental open questions that need to be addressed to fully understand the formation of highly reactive radical species, its dynamics, and interaction with the substrate and enzyme. In this work, ab initio molecular dynamics was performed within a QM/MM framework on a reduced AdoCbl cofactor, which was taken as a post proton-coupled electron transfer initial step for the activation of the AdoCbl-dependent methylmalonyl CoA mutase enzyme. The calculated free-energy profile reveals two possible pathways, stepwise (I) and concerted (II) for the reductive Co-C cleavage and subsequent H-abstraction. The computed activation barrier from metadynamics for both the pathways is comparable (78.5 and 76.2 kJ/mol, respectively); however, the concerted pathway may be preferred kinetically because it avoids the formation of a high-energy radical intermediate with possibly a larger recrossing rate. Our results are consistent with the previous conductor hypothesis, indicating the explicit role of cob(II)alamin in stabilizing the radical intermediate involved in the H-atom transfer.
依赖维生素 B 的酶催化了几个困难的自由基反应。为了全面了解高反应性自由基物种的形成、动力学及其与底物和酶的相互作用，仍存在一些需要解决的基本开放性问题。在这项工作中，在QM/MM 框架内进行了简化的 AdoCbl 辅因子的从头算分子动力学模拟，该辅因子被视为质子偶联电子转移后激活 AdoCbl 依赖的甲基丙二酰辅酶 A 变位酶的初始步骤。计算出的自由能曲线揭示了两种可能的途径，逐步（I）和协同（II）的还原 Co-C 断裂和随后的 H 提取。从元动力学计算出的两条途径的活化势垒相当（分别为 78.5 和 76.2 kJ/mol）；然而，协同途径可能在动力学上更有利，因为它避免了形成可能具有更大重连率的高能自由基中间体。我们的结果与之前的导体假说一致，表明 cob(II)alamin 在稳定涉及 H 原子转移的自由基中间体方面发挥了明确的作用。
