Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States.
Biochemistry. 2014 Jan 14;53(1):169-77. doi: 10.1021/bi4012644. Epub 2013 Dec 20.
Adenosylcobalamin (AdoCbl) serves as a source of reactive free radicals that are generated by homolytic scission of the coenzyme's cobalt-carbon bond. AdoCbl-dependent enzymes accelerate AdoCbl homolysis by ∼10(12)-fold, but the mechanism by which this is accomplished remains unclear. We have combined experimental and computational approaches to gain molecular-level insight into this process for glutamate mutase. Two residues, glutamate 330 and lysine 326, form hydrogen bonds with the adenosyl group of the coenzyme. A series of mutations that impair the enzyme's ability to catalyze coenzyme homolysis and tritium exchange with the substrate by 2-4 orders of magnitude were introduced at these positions. These mutations, together with the wild-type enzyme, were also characterized in silico by molecular dynamics simulations of the enzyme-AdoCbl-substrate complex with AdoCbl modeled in the associated (Co-C bond formed) or dissociated [adenosyl radical with cob(II)alamin] state. The simulations reveal that the number of hydrogen bonds between the adenosyl group and the protein side chains increases in the homolytically dissociated state, with respect to the associated state, for both the wild-type and mutant enzymes. The mutations also cause a progressive increase in the mean distance between the 5'-carbon of the adenosyl radical and the abstractable hydrogen of the substrate. Interestingly, the distance between the 5'-carbon and substrate hydrogen, determined computationally, was found to inversely correlate with the log k for tritium exchange (r = 0.93) determined experimentally. Taken together, these results point to a dual role for these residues: they both stabilize the homolytic state through electrostatic interactions between the protein and the dissociated coenzyme and correctly position the adenosyl radical to facilitate the abstraction of hydrogen from the substrate.
腺钴胺素 (AdoCbl) 作为反应性自由基的来源,这些自由基是通过辅酶的钴-碳键的均裂裂解产生的。AdoCbl 依赖性酶通过 ∼10(12)倍加速 AdoCbl 的均裂,但完成该过程的机制仍不清楚。我们结合实验和计算方法,获得了谷氨酸变位酶对此过程的分子水平的见解。两个残基,谷氨酸 330 和赖氨酸 326,与辅酶的腺苷基形成氢键。在这些位置引入了一系列突变,这些突变削弱了酶催化辅酶均裂和与底物进行氚交换的能力,降低了 2-4 个数量级。这些突变以及野生型酶,也通过分子动力学模拟进行了计算分析,模拟了酶-AdoCbl-底物复合物,其中 AdoCbl 以相关(形成 Co-C 键)或解离(腺苷基自由基与 cob(II)alamin)状态建模。模拟结果表明,与相关状态相比,在均裂解离状态下,腺苷基与蛋白质侧链之间的氢键数量增加,对于野生型和突变酶都是如此。这些突变还导致腺苷基自由基的 5'-碳与可提取底物氢之间的平均距离逐渐增加。有趣的是,通过计算确定的 5'-碳和底物氢之间的距离与实验确定的氚交换的 log k 值呈反比关系(r = 0.93)。综上所述,这些结果表明这些残基具有双重作用:它们通过蛋白质与解离的辅酶之间的静电相互作用稳定均裂状态,并且正确定位腺苷基自由基,以促进从底物中提取氢。