Effects of local protein environment on the binding of diatomic molecules to heme in myoglobins. DFT and dispersion-corrected DFT studies.
Effects of local protein environment on the binding of diatomic molecules to heme in myoglobins. DFT and dispersion-corrected DFT studies.
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局部蛋白质环境对肌红蛋白中双原子分子与血红素结合的影响。
DOI：
10.1007/s00894-013-1864-2
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发表时间：
2013
影响因子：
2.2
通讯作者：
Watts,JohnD
中科院分区：
文献类型：
--
作者：
Liao,Meng-Sheng;Huang,Ming-Ju;Watts,JohnD
本文用密度泛函理论（DFT）和色散校正密度泛函理论（DFT）方法研究了一个野生型肌红蛋白（Mb）和两个突变体（H64 L和V68 N）的血红素-AB结合能（AB = CO，O2），其中H64 L和V68 N代表两种不同的、相反的情况。在计算中测试了几种色散校正方法。通过在计算系统中包括五个最近的周围残基来解释局部蛋白质环境的影响。与文献中的其他研究相比，本研究更详细地检查了组氨酸-64在远端囊袋中的特定作用。虽然目前的计算结果并没有改变以前的结论，远端组氨酸-64残基的氢键起着重要作用的O2/CO歧视Mb，更多的细节之间的相互作用的蛋白质环境和绑定配体已被揭示在这项研究中通过比较AB的结合能的卟啉和各种肌红蛋白。从一个系统到另一个系统的实验结合能的变化很好地再现的计算。在几何优化过程中，由于没有对留数的约束，色散修正是必要的，因为它可以显著地改善计算的结构和能量结果。
The heme-AB binding energies (AB = CO, O2) in a wild-type myoglobin (Mb) and two mutants (H64L, V68N) of Mb have been investigated in detail with both DFT and dispersion-corrected DFT methods, where H64L and V68N represent two different, opposite situations. Several dispersion correction approaches were tested in the calculations. The effects of the local protein environment were accounted for by including the five nearest surrounding residues in the calculated systems. The specific role of histidine-64 in the distal pocket was examined in more detail in this study than in other studies in the literature. Although the present calculated results do not change the previous conclusion that the hydrogen bonding by the distal histidine-64 residue plays a major role in the O2/CO discrimination by Mb, more details about the interaction between the protein environment and the bound ligand have been revealed in this study by comparing the binding energies of AB to a porphyrin and the various myoglobins. The changes in the experimental binding energies from one system to another are well reproduced by the calculations. Without constraints on the residues in geometry optimization, the dispersion correction is necessary, since it improves the calculated structures and energetic results significantly.