de Oliveira Maycon Vinicius Damasceno, Calandrini Gabriel, da Costa Clauber Henrique Souza, da Silva de Souza Carlos Gabriel, Alves Cláudio Nahum, Silva José Rogério A, Lima Anderson H, Lameira Jerônimo
Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará, 66075-110, Brazil.
Núcleo de Ecologia Aquática e Pesca (NEAP), Universidade Federal do Pará, Belém, Pará, 66075-110, Brazil.
Sci Rep. 2025 Jan 22;15(1):2887. doi: 10.1038/s41598-024-84718-0.
Plastic poses a significant environmental impact due to its chemical resilience, leading to prolonged and degradation times and resulting in widespread adverse effects on global flora and fauna. Cutinases are essential enzymes in the biodegradation process of synthetic polymers like polyethylene terephthalate (PET), which recognized organisms can break down. Here, we used molecular dynamics and binding free energy calculations to explore the interaction of nine synthetic polymers, including PET, with Cutinase from Fusarium oxysporum (FoCut). According to our findings, the polymers poly(ethylene terephthalate) (PET), poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBH), poly(butylene succinate) (PBS), poly(butylene adipate-co-terephthalate) (PBAT) and poly(ε-caprolactone) (PCL) can bind to the Cutinase enzyme from F. oxysporum, indicating potential biodegradation activity for these polymers. PET exhibited the highest binding affinity (- 34.26 kcal/mol). Besides PET, the polymers PHBH, PBS, PBAT, and PCL also demonstrated significant affinities for the FoCut enzyme, with binding values of - 18.44, - 29.71, - 22.78, and - 22.26 kcal/mol, respectively. Additionally, analysis of the phylogenetic tree of cutinases produced by different organisms demonstrated that even though the organisms belong to different kingdoms, the cutinase from F. oxysporum (FoCut) showed biological similarity in its activity in degrading polymers with the cutinase enzyme from the bacterium Kineococcus radiotolerans and the fungus Moniliophthora roreri. Furthermore, the phylogenetic analysis demonstrated that the PETase enzyme has a very high similarity with the bacterial cutinase enzyme than with the fungal cutinase, therefore demonstrating that the PETase enzyme from Ideonella sakaiensis can easily be a modified bacterial cutinase enzyme that created a unique feature in biodegrading only the pet polymer through an evolutionary process due to its environment and its biochemical need for carbon. Our data demonstrate that bacterial cutinase enzymes have the same common ancestor as the PETase enzyme. Therefore, cutinases and PETase are interconnected through their biological similarity in biodegrading polymers. We demonstrated that important conserved regions, such as the Ser-Asp-His catalytic triad, exist in the enzyme's catalytic site and that all Cut enzymes from different organisms have the same region to couple with the polymer structures.
由于其化学稳定性，塑料对环境造成了重大影响，导致其降解时间延长，并对全球动植物产生广泛的不利影响。角质酶是聚对苯二甲酸乙二酯（PET）等合成聚合物生物降解过程中的关键酶，某些生物能够分解这种聚合物。在此，我们使用分子动力学和结合自由能计算来探究包括PET在内的九种合成聚合物与尖孢镰刀菌角质酶（FoCut）的相互作用。根据我们的研究结果，聚对苯二甲酸乙二酯（PET）、聚（3-羟基丁酸-co-3-羟基己酸）（PHBH）、聚丁二酸丁二醇酯（PBS）、聚己二酸/对苯二甲酸丁二酯（PBAT）和聚己内酯（PCL）等聚合物能够与尖孢镰刀菌的角质酶结合，表明这些聚合物具有潜在的生物降解活性。PET表现出最高的结合亲和力（-34.26千卡/摩尔）。除PET外，PHBH、PBS、PBAT和PCL等聚合物对FoCut酶也表现出显著的亲和力，结合值分别为-18.44、-29.71、-22.78和-22.26千卡/摩尔。此外，对不同生物产生的角质酶的系统发育树分析表明，尽管这些生物属于不同的界，但尖孢镰刀菌的角质酶（FoCut）在降解聚合物的活性方面与耐辐射动球菌的角质酶和可可毛色二孢菌的角质酶具有生物学相似性。此外，系统发育分析表明，PET水解酶与细菌角质酶的相似性高于与真菌角质酶的相似性，因此表明来自日本 Ideonella sakaiensis的PET水解酶很容易是一种经过修饰的细菌角质酶酶，由于其环境和对碳的生化需求，通过进化过程在仅生物降解pet聚合物方面创造了独特的特征。我们的数据表明，细菌角质酶与PET水解酶具有相同的共同祖先。因此，角质酶和PET水解酶通过它们在生物降解聚合物方面的生物学相似性相互联系。我们证明，在酶的催化位点存在重要的保守区域，如丝氨酸-天冬氨酸-组氨酸催化三联体，并且来自不同生物的所有Cut酶都有相同的区域与聚合物结构结合。
