小擎子 (2023-01-31 23:12):
#paper doi:10.1038/s41467-022-35237-x Nat Commun., 2022, Sourcing thermotolerant poly(ethylene terephthalate) hydrolase scaffolds from natural diversity。将HMM方法与机器学习相结合,以鉴定PET水解酶,根据序列预测酶的最佳活性温度。从公开数据库获得序列和环境最佳生长温度(OGT),只保留OGT大于50℃的序列,对于没有OGT信息的序列,使用计算氨基酸特征的支持向量机方法训练机器学习模型(ThermoProt)来区分来自嗜热菌大于50℃的8000种蛋白和来自非嗜热菌的小于50℃的8000种蛋白。ThremProt表现出86.6%的准确率。选择了74种假定的耐热PET水解酶进行实验筛选。实验筛选出了23种热稳定酶,均未被报道,并且超过先前报道的36种酶的PET水解酶活性。
IF:14.700Q1 Nature communications, 2022-12-21. DOI: 10.1038/s41467-022-35237-x PMID: 36543766
Sourcing thermotolerant poly(ethylene terephthalate) hydrolase scaffolds from natural diversity
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Abstract:
Enzymatic deconstruction of poly(ethylene terephthalate) (PET) is under intense investigation, given the ability of hydrolase enzymes to depolymerize PET to its constituent monomers near the polymer glass transition temperature. To date, reported PET hydrolases have been sourced from a relatively narrow sequence space. Here, we identify additional PET-active biocatalysts from natural diversity by using bioinformatics and machine learning to mine 74 putative thermotolerant PET hydrolases. We successfully express, purify, and assay 51 enzymes from seven distinct phylogenetic groups; observing PET hydrolysis activity on amorphous PET film from 37 enzymes in reactions spanning pH from 4.5-9.0 and temperatures from 30-70 °C. We conduct PET hydrolysis time-course reactions with the best-performing enzymes, where we observe differences in substrate selectivity as function of PET morphology. We employed X-ray crystallography and AlphaFold to examine the enzyme architectures of all 74 candidates, revealing protein folds and accessory domains not previously associated with PET deconstruction. Overall, this study expands the number and diversity of thermotolerant scaffolds for enzymatic PET deconstruction.
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