Molecular Modeling Insights into Metal-Organic Frameworks (MOFs) as a Potential Matrix for Immobilization of Lipase: An In Silico Study.
Molecular Modeling Insights into Metal-Organic Frameworks (MOFs) as a Potential Matrix for Immobilization of Lipase: An In Silico Study.
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近年来，大量的注意力已经指向MOFs作为用于固定化酶的潜在基质。根据文献，基于金属有机框架（MOF）的结构在脂肪酶和MOF的有机组分之间提供疏水相互作用。为了确定提高生物催化剂的鲁棒性和稳定性的最佳方法，必须深入了解酶和配体之间的分子相互作用。在这方面，计算方法被证明是一个宝贵的资产。通过对文献的回顾，发现了许多关于脂肪酶与各种配体之间相互作用的报道。然而，缺乏可用的研究检查脂肪酶和MOF之间的相互作用。因此，必须了解皱褶假丝酵母脂肪酶（CRL）和沸石咪唑骨架（ZIF-8）之间的相互作用，以研究其工业实用性。本文提出了一个全面的调查利用分子建模方法，特别是分子对接和分子动力学（MD）模拟，研究CRL和ZIF-8之间的相互作用的目的。CRL是一种高度通用的酶，在许多行业中具有广泛的用途，这归因于其选择性和催化效率，其实施的不切实际性阻碍了其选择性和催化效率，导致天然催化活性的损失和不可重复使用性。酶的固定化是使其能够重复使用的必要步骤，并且它提供了在合成环境中调节生物催化剂的功能功效的方法。MOFs代表了一类新型的多孔材料，具有独特的最高级功能，使MOFs成为开发酶-MOFs复合材料的最佳基质。在这项研究中，我们采用分子模拟的方法，例如，分子对接和MD模拟，探索CRL和一个特定的MOF，ZIF-8之间的相互作用。本研究涉及CRL的二级结构分析和同源性建模，然后将ZIF-8与CRL对接。分子对接分析的结果表明，ZIF-8位于CRL的活性位点口袋内，在那里它与瓦尔-81、Phe-87、Ser-91、Asp-231、Thr-132、Lue-297、Phe-296、Phe-344、Thr-347和Ser-450形成氢键。MD模拟分析显示，CRL和ZIF-8对接复合物在整个模拟期间表现出稳定性，并且在整个模拟过程中保持初始对接复合物中存在的所有相互作用。这项研究的结果可以促进对CRL和ZIF-8之间相互作用的分子机制的理解，以及开发用于各种工业目的的固定化CRL。
In recent years, a significant amount of attention has been directed toward MOFs as a potential matrix for the immobilization of enzymes. As per the literature, structures based on metal-organic frameworks (MOFs) offer hydrophobic interaction between lipases and the organic component of the MOF. To ascertain the optimal approach for enhancing the robustness and stability of biocatalysts, it is imperative to gain insights into the molecular interactions between enzymes and ligands. In this regard, the computational methodology proves to be an invaluable asset. A review of the literature reveals numerous reports discussing the interaction between lipase and various ligands. However, there is a lack of available research examining the interaction between lipase and MOF. Hence, it is imperative to comprehend the interplay between Candida rugosa lipase (CRL) and the Zeolitic imidazolate framework (ZIF-8) in order to investigate its industrial practicality. This article presents a comprehensive investigation of the utilization of molecular modeling methodologies, specifically molecular docking and molecular dynamics (MD) simulation, for the purpose of studying the interaction between CRL and ZIF-8. CRL is a highly versatile enzyme that finds extensive utility in numerous industries, which is attributed to its selectivity and catalytic efficiency, which have been impeded by the impracticality of its implementation, leading to a loss of native catalytic activity and non-reusability. Enzyme immobilization is a necessary step for enabling its reuse, and it provides methods for regulating the biocatalyst’s functional efficacy in a synthetic setting. MOFs represent a novel category of porous materials possessing distinct superlative features that make MOFs an optimal host matrix for developing enzyme-MOF composites. In this study, we employed molecular modeling approaches, for instance, molecular docking and MD simulation, to explore the interactions between CRL and a specific MOF, ZIF-8. The present study involved conducting secondary structural analysis and homology modeling of CRL, followed by docking ZIF-8 with CRL. The results of the molecular docking analysis indicate that ZIF-8 was situated within the active site pocket of CRL, where it formed hydrogen bonds with Val-81, Phe-87, Ser-91, Asp-231, Thr-132, Lue-297, Phe-296, Phe-344, Thr-347, and Ser-450. The MD simulation analysis revealed that the CRL and ZIF-8 docked complex exhibited stability over the entire simulation period, and all interactions presented in the initial docked complex were maintained throughout the simulation. The findings derived from this investigation could promote comprehension of the molecular mechanisms underlying the interaction between CRL and ZIF-8 as well as the development of immobilized CRL for diverse industrial purposes.
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