Topol Igor A, Nemukhin Alexander V, Salnikow Konstantin, Cachau Raul E, Abashkin Yuri G, Kasprzak Kazimierz S, Burt Stanley K
Advanced Biomedical Computing Center, SAIC Frederick, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA.
J Phys Chem A. 2006 Mar 30;110(12):4223-8. doi: 10.1021/jp055633k.
Enzymatic hydroxylation reactions carried out by 2-oxoglutarate (2OG) dependent iron-containing oxygenases were recently implicated in oxygen sensing. In addition to oxygen depletion, two metals, cobalt and nickel, are capable of inducing hypoxic stress in cells by inhibiting oxygenase activity. Two possible scenarios have been proposed for the explanation of the hypoxic effects of cobalt and nickel: oxidation of enzyme-bound iron following cobalt or nickel exposure, and substitution of iron by cobalt or nickel. Here, by using density functional theory calculations, we modeled the reaction route from the reaction components to the high-spin metal-oxide intermediate in the activation of oxygen molecule by 2OG-dependent enzymes for three metal ions Fe(II), Ni(II), and Co(II) in the active site. An initial molecular model was constructed based on the crystal structure of iron-containing asparaginyl hydroxylase (FIH-1). Nickel- and cobalt-containing enzymes were modeled by a consequent replacement of the iron in the active center. The energy profiles connecting stationary points on the potential surfaces were computed by using the intrinsic reaction coordinate (IRC) technique from the located transition states. The results of calculations show that the substitution of iron by nickel or cobalt modifies the reaction energy profile; however, qualitatively, the reaction mechanism remains essentially the same. Thus, we would postulate that if the iron ion in the active site were substitutable by nickel and/or cobalt ions enzyme activity would be considerably altered due to high activation barriers.
由2-氧代戊二酸（2OG）依赖性含铁加氧酶进行的酶促羟基化反应最近被认为与氧感应有关。除了氧耗竭外，两种金属钴和镍能够通过抑制加氧酶活性在细胞中诱导缺氧应激。已经提出了两种可能的情况来解释钴和镍的缺氧效应：钴或镍暴露后酶结合铁的氧化，以及钴或镍取代铁。在这里，通过使用密度泛函理论计算，我们模拟了在活性位点中三种金属离子Fe(II)、Ni(II)和Co(II)的2OG依赖性酶激活氧分子时从反应组分到高自旋金属氧化物中间体的反应途径。基于含铁天冬酰胺酰羟化酶（FIH-1）的晶体结构构建了初始分子模型。通过随后替换活性中心的铁来模拟含镍和含钴的酶。使用本征反应坐标（IRC）技术从定位的过渡态计算连接势能面上驻点的能量分布。计算结果表明，镍或钴取代铁会改变反应能量分布；然而，定性地说，反应机理基本保持不变。因此，我们推测，如果活性位点中的铁离子可被镍和/或钴离子取代，由于高活化能垒，酶活性将发生显著改变。
