Polyakov Igor V, Kniga Artem E, Grigorenko Bella L, Nemukhin Alexander V
Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russian Federation.
Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, 119334, Russian Federation.
ACS Chem Neurosci. 2020 Aug 5;11(15):2296-2302. doi: 10.1021/acschemneuro.0c00250. Epub 2020 Jul 21.
We report the results of computational modeling of a three-dimensional all-atom structure of the membrane-associated protein encoded by the gene, aspartate -acetyltransferase, which is essential for brain synthesis of -acetyl-l-aspartate (NAA). The lack of experimentally derived three-dimensional structures of NAT8L poses one of the obstacles in studies of the mechanism of NAA formation and understanding the precise role of NAA in neurological disorders. We apply a computational protocol employing the contact map prediction, folding, homology modeling, and refinement to obtain a structure of NAT8L with the aspartate and acetyl coenzyme A cofactors in the protein molecule. To verify the computational protocol, we check its predictive power by reproducing the crystal structure of a related -acetyltransferase domain, specifically, that from the bacterial -acetylglutamate synthase. We show that the constructed NAT8L model correlates with structural features of the protein revealed in rare experimental studies. The obtained structure of the enzyme active site with the trapped reactants suggests a mechanism of the acetyl transfer upon NAA formation.
我们报告了由该基因编码的膜相关蛋白天冬氨酸 - 乙酰转移酶三维全原子结构的计算建模结果，该酶对脑内N - 乙酰 - L - 天冬氨酸（NAA）的合成至关重要。缺乏NAT8L的实验性三维结构是研究NAA形成机制以及理解NAA在神经疾病中确切作用的障碍之一。我们应用一种计算方案，该方案采用接触图预测、折叠、同源建模和优化，以获得蛋白质分子中含有天冬氨酸和乙酰辅酶A辅因子的NAT8L结构。为了验证该计算方案，我们通过重现相关N - 乙酰转移酶结构域（具体来说，来自细菌N - 乙酰谷氨酸合酶的结构域）的晶体结构来检验其预测能力。我们表明构建的NAT8L模型与罕见实验研究中揭示的蛋白质结构特征相关。所获得的带有捕获反应物的酶活性位点结构提示了NAA形成过程中乙酰转移的机制。
