Sadeghi Googheri Mohammad Sadegh, Housaindokht Mohammad Reza, Sabzyan Hassan
Biophysical Chemistry Laboratory, Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
Biophysical Chemistry Laboratory, Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran; Research and Technology Center of Biomolecules, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
J Mol Graph Model. 2015 Apr;57:9-19. doi: 10.1016/j.jmgm.2015.01.003. Epub 2015 Jan 14.
The deacylation step of acylated Candida Antarctica lipase B, which was acylated with methylcaprylate (MEC) and acetylcholine (ACh), has been studied by using density functional theory method. Free energies of the entire reaction were calculated for enzyme deacylation by water and hydrogen peroxide that represented hydrolysis and perhydrolysis reactions, respectively. The calculations displayed that a stepwise mechanism there was with the enzyme-product complex being a deep minimum on the free energy surfaces of both of two reactions. The tetrahedral intermediate formation was the rate-determining step of all reactions, which needed 8.1 to 10.5kcalmol(-1) for activation in different reactions. In the second stage of the reaction, fewer free energy barriers, between 4.7 and 5.9kcalmol(-1), were identified to enable the proton transfer from His224 to Ser105 and the breakdown of the tetrahedral intermediate. These calculated activation free energies approved theoretical possibility of both of two reactions for two substrates. Finally, an applied tool examined the interactions role in the stability and energy levels of different chemical species.
采用密度泛函理论方法研究了用辛酸甲酯（MEC）和乙酰胆碱（ACh）酰化的南极假丝酵母脂肪酶B的脱酰化步骤。分别计算了水和过氧化氢对酶脱酰化的整个反应自由能，它们分别代表水解反应和全水解反应。计算结果表明，存在一种逐步反应机制，酶-产物复合物在两个反应的自由能面上都是一个深陷的最小值。四面体中间体的形成是所有反应的速率决定步骤，在不同反应中其活化需要8.1至10.5千卡/摩尔（-1）。在反应的第二阶段，发现了较少的自由能垒，在4.7至5.9千卡/摩尔（-1）之间，这使得质子能够从His224转移到Ser105，并使四面体中间体分解。这些计算得到的活化自由能证实了两种底物的两种反应在理论上的可能性。最后，一个应用工具研究了不同化学物种在稳定性和能级方面的相互作用。
