Electronic and geometric structures of the blue copper site of azurin investigated by QM/MM hybrid calculations
Electronic and geometric structures of the blue copper site of azurin investigated by QM/MM hybrid calculations
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DOI：
10.1088/0953-8984/21/6/064235
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发表时间：
2009-02-11
影响因子：
2.7
通讯作者：
Tateno, Masaru
中科院分区：
文献类型：
--
作者：
Kang, Jiyoung;Ohta, Takehiro;Tateno, Masaru
采用量子力学和分子力学混合计算方法研究了完全溶剂化的天青蛋白中铜结合位点的电子结构和几何结构。两种类型的计算模型被应用到评估的影响，周围的环境活动的网站。在模型I中，采用自旋非限制的Hartree-Fock（UHF）/密度泛函理论（DFT）混合全电子B3 LYP方法，计算了QM区原子与周围蛋白质分子和溶剂水的部分点电荷之间的长距离静电相互作用.在模型II中，不允许QM哈密顿量被这些部分点电荷极化。模型I和II提供了铜配位结构的不同描述，特别是对于包括大偶极的配位键。事实上，Cu-O（Gly 45）和Cu-S（Cys 112）键对QM哈密顿量中的长距离静电相互作用的处理是敏感的。这表明，生物过程中发生的活性位点的蛋白质和溶剂的周围结构的调节，因此，参与的QM哈密顿量的长程静电相互作用的影响是至关重要的准确描述的金属酶的铜活性位点的电子结构。
The electronic and geometric structures of the copper-binding site in a fully solvated azurin were investigated using quantum mechanics (QM) and molecular mechanics (MM) hybrid calculations. Two types of computational models were applied to evaluate the effects of the environment surrounding the active site. In model I, long-distance electrostatic interactions between QM region atoms and partial point charges of the surrounding protein moieties and solvent water were calculated in a QM Hamiltonian, for which the spin-unrestricted Hartree-Fock (UHF)/density functional theory (DFT) hybrid all-electron calculation with the B3LYP functional was adopted. In model II, the QM Hamiltonian was not allowed to be polarized by those partial point charges. Models I and II provided different descriptions of the copper coordination structure, particularly for the coordinative bonds including a large dipole. In fact, the Cu-O(Gly45) and Cu-S(Cys112) bonds are sensitive to the treatment of long-distance electrostatic interactions in the QM Hamiltonian. This suggests that biological processes occurring in the active site are regulated by the surrounding structures of protein and solvent, and therefore the effects of long-range electrostatic interactions involved in the QM Hamiltonian are crucial for accurate descriptions of electronic structures of the copper active site of metalloenzymes.