分子动力学模拟抗坏血酸对木瓜蛋白酶活性的影响

为探究抗坏血酸对木瓜蛋白酶活性的影响,以实验结果为基础,利用分子对接和分子模拟技术对二者的结合机制进行分析。结果表明：3种浓度(0.1、0.2、0.3 mmol/L)的抗坏血酸均能促进木瓜蛋白酶酶活性,平均激活率分别为10%、21%、28%,抗坏血酸浓度越高,激活作用越明显;分子模拟结果表明,木瓜蛋白酶与抗坏血酸结合后均方根误差呈略微上升的趋势,木瓜蛋白酶内部的氢键数量降低,结合前氢键数量平均值为146,而加入抗坏血酸后为143,总可及表面积增加2.38 nm²,且3个活性位点(Asp158、His159、Cys25)的均方根波动程度均增大,发挥主要催化作用的25号位半胱氨酸与2个辅助氨基酸的间距缩小。因此,木瓜蛋白酶的激活可能是由于抗坏血酸的加入引起了蛋白活性中心结构的变化,从而使木瓜蛋白酶更有利于发挥催化作用。

Molecular Dynamics Simulation of the Effect of Ascorbic Acid on the Protease Activity of Papain

In order to explore the effect of ascorbic acid on papain activity, the binding mechanism between them was investigated by molecular docking and molecular dynamics simulation. The findings demonstrated that ascorbic acid at all three concentrations tested (0.1, 0.2 and 0.3 mmol/L) could enhance papain activity with an average percentage of activation of 10%, 21%, and 28%, respectively, indicating that the higher the ascorbic acid concentration was, the more pronounced the activation effect was. The results of molecular dynamics simulation revealed that the root mean square deviation (RMSD) showed a slightly increasing trend after papain binding to ascorbic acid, and the average number of hydrogen bonds within the protease molecule decreased from 146 to 143. In addition, the total accessible surface area increased by 2.38 nm2, the root mean square fluctuations of the active sites Asp158, His159 and Cys25 increased, and the gap between Cys25, which plays the primary catalytic role, and the two auxiliary amino acids decreased. Accordingly, we concluded that ascorbic acid can change the structure of papain’s active center, thereby activing the protease.