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首页> 外文期刊>Dalton transactions: An international journal of inorganic chemistry >DFT calculations of comparative energetics and ENDOR/Mossbauerproperties for two protonation states of the iron dimer cluster ofribonucleotide reductase intermediate X
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DFT calculations of comparative energetics and ENDOR/Mossbauerproperties for two protonation states of the iron dimer cluster ofribonucleotide reductase intermediate X

机译：核糖核苷酸还原酶中间体X的铁二聚体簇的两个质子化状态的比较能量学和ENDOR / Mossbauer性质的DFT计算

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Two models (I and II) for the active site structure of class-I ribonucleotide reductase (RNR)intermediate X in subunit R2 have been studied in this paper, using broken-symmetry densityfunctional theory (DFT) incorporated with the conductor like screening (COSMO) solvation modeland with the finite-difference Poisson-Boltzmann self-consistent reaction field (PB-SCRF) calculations.Only one of the bridging groups between the two iron centers is different between model-I andmodel-II. Model-I contains two woxo bridges, while model-II has one bridging oxo and one bridginghydroxo. These are large active site models including up to the fourth coordination shell H-bondingresidues. MOssbauer and ENDOR hyperfine property calculations show that model-I is more likely torepresent the active site structure of RNR-X. However, energetically our pK, calculations at first highlyfavored the bridging oxo and hydroxo (in model-II) structure of the diiron center rather than having thedi-oxo bridge (in model-I). Since the Arg236 and the nearby Lys42, which are very close to the diironcenter, are on the protein surface of RNR-R2, it is highly feasible that one or two anion groups insolution would interact with the positively charged side chains of Arg236 and Lys42. The aniongroup(s) can be a reductant, phosphate, sulfate, nitrate, and other negatively charged groups existing inbiological environments or in the buffer of the experiment. Since sulfate ions certainly exist in the bufferof the ENDOR experiment, we have examined the effect of the sulfate (5042-, surrounded by explicitwater molecules) H-bonding to the side chain of Arg236. We find that when sulfate interacts withArg236, the carboxylate group of Asp237 tends to be protonated, and once Asp237 is protonated, theFe(m)Fe(tv) center in X favors the di-oxo bridge (model-I). This would explain that the ENDORobserved RNR-X active site structure is likely to be represented by model-I rather than model-II.
机译：本文利用破坏对称对称密度泛函理论（DFT）并结合了类似导体的筛选（COSMO），研究了R2亚基中I类核糖核苷酸还原酶（RNR）中间体X的活性位点结构的两种模型（I和II）溶剂化模型和有限差分Poisson-Boltzmann自洽反应场（PB-SCRF）计算。模型I和模型II中只有两个铁心之间的桥接基团不同。模型I包含两个woxo桥，模型II具有一个桥接氧代和一个桥接羟基。这些是大型活动站点模型，包括多达第四个配位壳H键合残基。 MOssbauer和ENDOR超细性质的计算表明，模型I更可能代表RNR-X的活性位点结构。但是，从精力上讲，我们的pK计算首先高度支持了diiron中心的桥接氧代和羟基（在II型中）结构，而不是使用di-oxo桥（在I型中）。由于非常靠近二铁中心的Arg236和附近的Lys42位于RNR-R2的蛋白质表面上，因此一个或两个阴离子基团的溶解与Arg236和Lys42的带正电荷的侧链相互作用是非常可行的。阴离子基团可以是存在于生物环境中或在实验缓冲液中的还原剂，磷酸根，硫酸根，硝酸根和其他带负电荷的基团。由于ENDOR实验的缓冲液中肯定存在硫酸根离子，因此我们检查了硫酸根（5042-，被显性水分子包围）H键键至Arg236侧链的作用。我们发现，当硫酸盐与Arg236相互作用时，Asp237的羧酸酯基趋于被质子化，并且一旦Asp237被质子化，X中的Fe（m）Fe（tv）中心就倾向于二氧代桥（I型）。这可以解释ENDOR观察到的RNR-X活性位点结构可能由模型I而不是模型II表示。

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