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Screening of small molecule inhibitors targeting DNA polymerase η
Jiajia CAO,Shumai YE,Ye ZHAO
Journal of Zhejiang University (Agriculture and Life Sciences)    2024, 50 (1): 35-41.   DOI: 10.3785/j.issn.1008-9209.2023.02.221
Abstract   HTML PDF (2598KB) ( 124 )  

The repair of DNA damage and maintenance of genomic stability are essential for the normal growth and adverse defense of plants and animals. In view of the genomic instability caused by the misincorporation of DNA polymerase, this study took DNA polymerase η as the research object and screened its possible small molecule inhibitors by computational simulated molecular docking and detected their enzyme kinetic parameters. The results showed that deoxyadenosine triphosphate (dATP) had an inhibitory effect on the activity of DNA polymerase η, resulting in a relative extension efficiency of 36% to 42%. Simulated molecular docking and in vitro experimental results showed that cyclic GMP-AMP (cGAMP) had a lower binding energy (with an affinity of -35.1 kJ/mol) than dATP (with an affinity of -26.7 kJ/mol) to DNA polymerase η. Enzyme kinetic experiments also showed that cGAMP had a stronger inhibitory ability than dATP and achieved the maximum effect at the concentration of 0.5 mmol/L (with a relative extension efficiency of 13%). Therefore, a potential small molecule inhibitor targeting DNA polymerase η was screened out in this study. At the same time, in view of the tolerance to antitumor drug (DNA damage agent) caused by high expression of this protein, these results provide a basis for the development of new drugs.

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Bioinformatics and expression analysis of heat shock protein genes in Trametes gibbosa
Xuxin YANG,Lianrong FENG,Yujie CHI,Shuying HAN
Journal of Zhejiang University (Agriculture and Life Sciences)    2023, 49 (6): 776-786.   DOI: 10.3785/j.issn.1008-9209.2022.10.261
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To investigate the function and structure of the heat shock protein (HSP) family in Trametes gibbosa,a cDNA library was constructed by collecting mycelial samples at different time under the sawdust treatment.All the HSP genes in this strain were screened by analyzing their transcriptome data; subsequently, bioinformatics analysis was performed for all the HSPs. Gene cloning and sequence structure analysis were performed for the HSP100 family, and the expression levels of the HSP100 genes were verified under the sawdust treatment by real-time fluorescent quantitative polymerase chain reaction (qRT-PCR). The results were as follows: A total of 32 HSP genes were screened and divided into five subclasses in T. gibbosa. Among the 32 HSPs, there were two HSP100, two HSP90, seven HSP70, one HSP60 and twenty small HSPs (sHSPs). In growth regulation, they had important functions, such as protein posttranslational modification, protein folding, and chaperonin. In T. gibbosa, HSPs were hydrophobic proteins with distinct physicochemical properties for different subclasses. The HSP100 family consist of an N-terminus, nucleotide-binding domain 1 (NBD1), NBD2, and the linker between the two NBDs. The NBDs had highly conserved Walker A and Walker B motifs and arginine finger residues. The qRT-PCR amplification results showed that there was obvious upregulation expression of HSP100 gene in T. gibbosa under the sawdust treatment. In summary, the classification of the HSP family in T. gibbosa is diverse and complex. Under stress conditions, the HSP100 family plays an important role in protein depolymerization, and its sequence and structure are relatively conserved. The above results can provide a theoretical basis for the study of T. gibbosa under stress.

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