通过体外定点突变的计算机设计和分子建模优化II型大肠杆菌L-天冬酰胺酶活性。
Molecular Modeling and Optimization of Type II E.coli l-Asparginase Activity by in silico Design and in vitro Site-directed Mutagenesis.
发表日期:2023 Aug 27
作者:
Mahdieh Mahboobi, Ali-Hatef Salmanian, Hamid Sedighian, Bijan Bambai
来源:
The protein journal
摘要:
L-天门冬氨酸酶(也称为L-ASNase)是一种至关重要的治疗酶,广泛用于急性淋巴细胞白血病(ALL)的化疗药物治疗中。此外,除了临床行业,该酶还被用于食品工业,作为食品加工试剂,以降低丙烯酰胺的含量。改善L-ASNase酶的活性和动力学参数可能会导致更高的效率,从而实现实际成果。为了实现这个目标,我们选择了位置88上的甘氨酸残基作为潜在突变,具有有利的结果。在本研究中,首先通过多种无机模拟分析,如分子动力学和分子对接,寻找合适的甘氨酸88位点突变。然后,采用合理的设计作为改进酶的分子性质的最佳策略。
我们的无机模拟发现显示,G88Q、G88L、G88K和G88A这四种突变可能能够增加L-ASNase的天门冬氨酸酶活性。每个酶的催化效率(kcat/Km)是与野生型形式比较突变体的催化活性的最重要特征。实验室实验证明,G88Q突变体的kcat/Km比大肠杆菌K12 ASNase II(野生型)高出36.32%,这表明L-ASNase的活性在较低浓度的L-ASN下得到了改善。突变体的L-ASNase活性的动力学特征鉴定证实了相对于野生型酶,在L-ASN为底物时具有较高的周转速率(kcat)。
无机模拟分析和实验室实验证明,与其他突变(G88L、G88K和G88A)相比,G88Q突变可能会改善L-ASNase的动力学特性。© 2023. 作者单独获得Springer Science+Business Media, LLC, part of Springer Nature的独家许可。
L-asparaginase (also known as L-ASNase) is a crucial therapeutic enzyme that is widely used in treatment of ALL (acute lymphoblastic leukemia) as a chemotherapeutic drug. Besides, this enzyme is used in the food industry as a food processing reagent to reduce the content of acrylamide in addition to the clinical industry. The improvement of activity and kinetic parameters of the L-ASNase enzyme may lead to higher efficiency resulting in practical achievement. In order to achieve this goal, we chosen glycine residue in position 88 as a potential mutation with advantageous outcomes.In this study, firstly to find the appropriate mutation on glycine 88, various in silico analyses, such as MD simulation and molecular docking, were carried out. Then, the rational design was adopted as the best strategy for molecular modifications of the enzyme to improve its enzymatic properties.Our in silico findings show that the four mutations G88Q, G88L, G88K, and G88A may be able to increase L-ASNase's asparaginase activity. The catalytic efficiency of each enzyme (kcat/Km) is the most important feature for comparing the catalytic activity of the mutants with the wild type form. The laboratory experiments showed that the kcat/Km for the G88Q mutant is 36.32% higher than the Escherichia coli K12 ASNase II (wild type), which suggests that L-ASNase activity is improved at lower concentration of L-ASN. Kinetic characterization of the mutants L-ASNase activity confirmed the high turnover rate (kcat) with ASN as substrate relative to the wild type enzyme.In silico analyses and laboratory experiments demonstrated that the G88Q mutation rather than other mutation (G88L, G88K, and G88A) could improve the kinetics of L-ASNase.© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.