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IF 2.3 4区化学 Q3 CHEMISTRY, PHYSICAL Catalysis Letters Pub Date : 2025-03-17 DOI:10.1007/s10562-025-04974-1

Orkun Pinar

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引用次数: 0

摘要

由于长期积累，石油基塑料造成的环境问题日益严重。它们的持久性危害海洋和陆地生物，破坏食物链，并传播微塑料。工业化、现代生活方式和一次性产品导致塑料用量增加，也是造成这一问题的原因之一。减少塑料负面影响的有效策略包括减少废物、回收利用和开发可生物降解的生物聚合物。从这个意义上说，聚羟基烷酸（PHA）合成酶（PhaC）是生产具有成本效益的生物聚合物/生物塑料的重要酶。因此，本研究调查了四个不同的菌属（Azotobacter、Bacillus、Cupriavidus 和 Halomonas），它们都是著名的 PHA/Polyhydroxybutyrate (PHB) 生产者，之所以选择它们是因为它们在 PHA/PHB 生物合成方面具有公认的工业能力和代谢多功能性。由于基于 PHA 合成酶三维（3D）结构的信息不足，本报告首次通过对 AlphaFold 预测结构进行硅学比较分析来评估这些指定属的 PHA 合成酶。此外，挫折分析表明，Azotobacter、Cupriavidus 和 Halomonas PHA 合成酶的结构具有相似性，而芽孢杆菌则表现出独特的特征。识别潜在底物结合区域的高挫折残基有助于深入了解它们的功能动态和工程潜力。此外，还进行了分子对接分析，以评估 AlphaFold 预测的酶结构与其底物之间的相互作用，量化酶-底物复合物的结合能。这项工作的发现将有助于利用 AlphaFold 的先进功能同时了解预测的三维结构，从而对 PHA/PHB 生产商的 PHA 合成酶进行工程化研究。这种理解将有助于为未来创造更高效、更可持续的生物塑料。

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Comparative In Silico Structural Analysis of PHA Synthases from industrially Prominent PHA Producers

Environmental issues from petroleum-based plastics have intensified due to long-term accumulation. Their persistence harms marine and terrestrial life, disrupting food chains, and spreading microplastics. Increased plastic usage driven by industrialization, modern lifestyles, and disposable products contributes to this problem. An effective strategy to mitigate plastic’s negative impact includes waste reduction, recycling, and the development of biodegradable biopolymers. In this sense, polyhydroxyalkanoate (PHA) synthase (PhaC) is a vital enzyme for cost-effective biopolymer/bioplastic production. Thus, this study investigated four different genera (Azotobacter, Bacillus, Cupriavidus, and Halomonas) that are well-known PHA/Polyhydroxybutyrate (PHB) producers, selected due to their proven industrial capability and metabolic versatility in PHA/PHB biosynthesis. Since there has been inadequate information based on the three-dimensional (3D) structures of PHA synthase(s), this is the first report to assess the PHA synthase(s) of these indicated genera by conducting in silico comparative analyses on AlphaFold predicted structures. Furthermore, frustration analysis revealed structural similarities among Azotobacter, Cupriavidus, and Halomonas PHA synthases, while Bacillus exhibited a distinct profile. Identifying highly frustrated residues in potential substrate-binding regions offers insights into their functional dynamics and engineering potential. Molecular docking analysis was also performed to assess interactions between AlphaFold-predicted enzyme structures and their substrates, quantifying the binding energy of enzyme-substrate complexes. The findings of this work will contribute to the engineering of PHA synthase(s) of PHA/PHB producers with the simultaneous understanding of predicted 3D structures using the advanced capabilities of AlphaFold. This understanding will support the creation of more efficient and sustainable bioplastics for the future.

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来源期刊

Catalysis Letters 化学-物理化学

CiteScore

5.70

自引率

3.60%

发文量

327

审稿时长

1 months

期刊介绍： Catalysis Letters aim is the rapid publication of outstanding and high-impact original research articles in catalysis. The scope of the journal covers a broad range of topics in all fields of both applied and theoretical catalysis, including heterogeneous, homogeneous and biocatalysis. The high-quality original research articles published in Catalysis Letters are subject to rigorous peer review. Accepted papers are published online first and subsequently in print issues. All contributions must include a graphical abstract. Manuscripts should be written in English and the responsibility lies with the authors to ensure that they are grammatically and linguistically correct. Authors for whom English is not the working language are encouraged to consider using a professional language-editing service before submitting their manuscripts.