FEBS Open Bio最新文献_第7页

Revealing protein structures: crystallization of protein-ligand complexes - co-crystallization and crystal soaking. 揭示蛋白质结构：蛋白质配体复合物的结晶--共晶和晶体浸泡。

IF 2.8 4区生物学

FEBS Open Bio Pub Date : 2024-10-20 DOI: 10.1002/2211-5463.13913

Barbora Kaščáková, Anna Koutská, Michaela Burdová, Petra Havlíčková, Ivana Kutá Smatanová

引用次数: 0

Viral entry mechanisms: the role of molecular simulation in unlocking a key step in viral infections. 病毒进入机制：分子模拟在揭示病毒感染关键步骤中的作用。

IF 2.8 4区生物学

FEBS Open Bio Pub Date : 2024-10-14 DOI: 10.1002/2211-5463.13908

Mariana Valério, Carolina C Buga, Manuel N Melo, Cláudio M Soares, Diana Lousa

{"title":"Viral entry mechanisms: the role of molecular simulation in unlocking a key step in viral infections.","authors":"Mariana Valério, Carolina C Buga, Manuel N Melo, Cláudio M Soares, Diana Lousa","doi":"10.1002/2211-5463.13908","DOIUrl":"https://doi.org/10.1002/2211-5463.13908","url":null,"abstract":"Viral infections are a major global health concern, affecting millions of people each year. Viral entry is one of the crucial stages in the infection process, but its details remain elusive. Enveloped viruses are enclosed by a lipid membrane that protects their genetic material and these viruses are linked to various human illnesses, including influenza, and COVID-19. Due to the advancements made in the field of molecular simulation, significant progress has been made in unraveling the dynamic processes involved in viral entry of enveloped viruses. Simulation studies have provided deep insight into the function of the proteins responsible for attaching to the host receptors and promoting membrane fusion (fusion proteins), deciphering interactions between these proteins and receptors, and shedding light on the functional significance of key regions, such as the fusion peptide. These studies have already significantly contributed to our understanding of this critical aspect of viral infection and assisted the development of effective strategies to combat viral diseases and improve global health. This review focuses on the vital role of fusion proteins in facilitating the entry process of enveloped viruses and highlights the contributions of molecular simulation studies to uncover the molecular details underlying their mechanisms of action.","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":" ","pages":""},"PeriodicalIF":2.8,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142461387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Hippocampal tau-induced GRIN3A deficiency in Alzheimer's disease 阿尔茨海默病中海马tau诱导的GRIN3A缺乏症

IF 2.8 4区生物学

FEBS Open Bio Pub Date : 2024-10-13 DOI: 10.1002/2211-5463.13904

Sang-Eun Lee, Soomin Park, Rian Kang, Taehoon Lee, Won Jong Yu, Sunghoe Chang, Jong-Chan Park

{"title":"Hippocampal tau-induced GRIN3A deficiency in Alzheimer's disease","authors":"Sang-Eun Lee, Soomin Park, Rian Kang, Taehoon Lee, Won Jong Yu, Sunghoe Chang, Jong-Chan Park","doi":"10.1002/2211-5463.13904","DOIUrl":"10.1002/2211-5463.13904","url":null,"abstract":"Alzheimer's disease (AD) is characterized by significant alterations in hippocampal function and structure, but the molecular mechanisms underlying the hippocampal region remain elusive. We integrated multiple transcriptome datasets including human or rat hippocampus (GSE173955, GSE129051, GSE84422) to identify candidate genes. Subsequent analyses including gene ontology analysis and protein–protein interaction mapping were performed to identify key genes and pathways. We found that glutamate ionotropic receptor NMDA-type subunit 3A (GRIN3A) and glutamate metabotropic receptor 8 (GRM8), which are related to the glutamatergic system, were the top two annotated genes and directly related to MAPT, which encodes a tau protein. Since there is no direct evidence of interaction between tauopathy and these genes in AD, further transcriptomic data (GSE125957, GSE56772) from tau transgenic mice and experimental validations through primary rat hippocampal neurons and induced pluripotent stem cell (iPSC)-derived brain organoids were performed. Interestingly, we identified that decreased NR3A (encoded by GRIN3A) and mGluR8 (encoded by GRM8) are correlated with tauopathy and loss of postsynaptic function in AD. Taken together, our results identified a novel tauopathy biomarker GRIN3A in AD. Furthermore, our findings suggest that an integrated approach combining public databases and diverse experimental validations can contribute to the advancement of precision medicine therapies.","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"14 12","pages":"2059-2071"},"PeriodicalIF":2.8,"publicationDate":"2024-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/2211-5463.13904","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142461384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A novel plasmid-based experimental system in Saccharomyces cerevisiae that enables the introduction of 10 different plasmids into cells 基于质粒的新型酿酒酵母实验系统，可将 10 种不同质粒引入细胞。

IF 2.8 4区生物学

FEBS Open Bio Pub Date : 2024-10-10 DOI: 10.1002/2211-5463.13893

Geyao Dong, Tsuyoshi Nakai, Tetsuo Matsuzaki

引用次数: 0

Characterization of two bacterial tyrosinases from the halophilic bacterium Hahella sp. CCB MM4 relevant for phenolic compounds oxidation in wetlands 嗜卤细菌 Hahella sp. CCB MM4 中与湿地酚类化合物氧化有关的两种细菌酪氨酸酶的特征。

IF 2.8 4区生物学

FEBS Open Bio Pub Date : 2024-10-09 DOI: 10.1002/2211-5463.13906

Gustavo de Almeida Santos, Andrea N. B. Englund, Eirin L. Dalleywater, Åsmund Kjendseth Røhr

{"title":"Characterization of two bacterial tyrosinases from the halophilic bacterium Hahella sp. CCB MM4 relevant for phenolic compounds oxidation in wetlands","authors":"Gustavo de Almeida Santos, Andrea N. B. Englund, Eirin L. Dalleywater, Åsmund Kjendseth Røhr","doi":"10.1002/2211-5463.13906","DOIUrl":"10.1002/2211-5463.13906","url":null,"abstract":"Tyrosinases (TYRs) are type-3 copper proteins that are widely distributed in nature. They can hydroxylate and oxidize phenolic molecules and are mostly known for producing melanins that confer protection against photo induced damage. TYRs are also thought to play an important role in the ‘latch mechanism’, where high concentrations of phenolic compounds inhibit oxidative decomposition of organic biomass and subsequent CO2 release, especially relevant in wetland environments. In the present study, we describe two TYRs, HcTyr1 and HcTyr2, from halophilic bacterium Hahella sp. CCB MM4 previously isolated at Matang mangrove forest in Perak, Malaysia. The structure of HcTyr1 was determined by X-ray crystallography at a resolution of 1.9 Å and represents an uncharacterized group of prokaryotic TYRs as demonstrated by a sequence similarity network analysis. The genes encoding the enzymes were cloned, expressed, purified and thoroughly characterized by biochemical methods. HcTyr1 was able to self-cleave its lid-domain (LID) in a protease independent manner, whereas the LID of HcTyr2 was essential for activity and stability. Both enzymes showed variable activity in the presence of different metals, surfactants and NaCl, and were able to oxidize lignin constituents. The high salinity tolerance of HcTyr1 indicates that the enzyme can be an efficient catalyst in the habitat of the host.","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"14 12","pages":"2038-2058"},"PeriodicalIF":2.8,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/2211-5463.13906","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389213","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

TGF-β effects on adipogenesis of 3T3-L1 cells differ in 2D and 3D cell culture conditions TGF-β 对 3T3-L1 细胞脂肪生成的影响在二维和三维细胞培养条件下有所不同。

IF 2.8 4区生物学

FEBS Open Bio Pub Date : 2024-10-08 DOI: 10.1002/2211-5463.13890

Araya Umetsu, Megumi Watanabe, Tatsuya Sato, Megumi Higashide, Nami Nishikiori, Masato Furuhashi, Hiroshi Ohguro

{"title":"TGF-β effects on adipogenesis of 3T3-L1 cells differ in 2D and 3D cell culture conditions","authors":"Araya Umetsu, Megumi Watanabe, Tatsuya Sato, Megumi Higashide, Nami Nishikiori, Masato Furuhashi, Hiroshi Ohguro","doi":"10.1002/2211-5463.13890","DOIUrl":"10.1002/2211-5463.13890","url":null,"abstract":"The TGF-β superfamily plays a pivotal role in the regulation of adipogenesis, but little is known about the potential differential role of the three isoforms of TGF-β, TGF-β-1~3. To further elucidate their role, two-dimensionally (2D) and three-dimensionally (3D) cultured 3T3-L1 mouse preadipocytes were subjected to the following analyses: (a) qPCR analysis of adipogenesis-related factors and major extracellular matrix protein (2D and /or 3D), (b) lipid staining by Oil Red O (2D) or BODIPY (3D), (c) Seahorse cellular metabolic measurement (2D), and (d) size and stiffness measurements of 3D 3T3-L1 spheroids. In the 2D cultured 3T3-L1 cells, mRNA expression levels of adipogenesis-related genes and Oil Red O lipid staining intensity were significantly increased by adipogenesis and they were substantially decreased following treatment with 0.1 nm TGF-β isoforms, with TGF-β2 having the greater effects. Consistent with these results, treatment with TGF-β2 resulted in suppression of mitochondrial and glycolytic functions in 2D cultured 3T3-L1 cells. However, the inhibitory effect of TGF-β on adipogenesis decreased under 3D spheroid culture conditions and TGF-β isoforms did not affect adipogenesis-induced (a) enlargement and downsizing of 3T3-L1 spheroids, (b) increase in BODIPY lipid staining intensity, and (c) up-regulation of the mRNA expression of adipogenesis-related genes. The findings presented herein suggest that the three TGF-β isoforms have different suppressive effects on adipogenesis-related cellular properties of 2D cultured 3T3-L1 cells and that their effects decrease under 3D spheroid culture conditions.","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"14 12","pages":"2026-2037"},"PeriodicalIF":2.8,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/2211-5463.13890","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cylindracin, a Cys-rich protein expressed in the fruiting body of Cyclocybe cylindracea, inhibits growth of filamentous fungi but not yeasts or bacteria 圆柱孢子菌子实体中表达的一种富含 Cys 的蛋白质 Cylindracin 能抑制丝状真菌的生长，但不能抑制酵母或细菌。

IF 2.8 4区生物学

FEBS Open Bio Pub Date : 2024-10-08 DOI: 10.1002/2211-5463.13910

Yamato Kuratani, Chika Abematsu, Keisuke Ekino, Takuji Oka, Masashi Shin, Makoto Iwata, Hiroto Ohta, Shoji Ando

{"title":"Cylindracin, a Cys-rich protein expressed in the fruiting body of Cyclocybe cylindracea, inhibits growth of filamentous fungi but not yeasts or bacteria","authors":"Yamato Kuratani, Chika Abematsu, Keisuke Ekino, Takuji Oka, Masashi Shin, Makoto Iwata, Hiroto Ohta, Shoji Ando","doi":"10.1002/2211-5463.13910","DOIUrl":"10.1002/2211-5463.13910","url":null,"abstract":"Mushrooms are the fruiting bodies of fungi and are important reproductive structures that produce and disseminate spores. The Pri3 gene was originally reported to be specifically expressed in the primordia (a precursor to the mature fruiting body) of the edible mushroom Cyclocybe aegerita. Here, we cloned a Pri3-related cDNA from Cyclocybe cylindracea, another species in the same genus, and showed that the gene is specifically expressed at the pileus surface of the immature fruiting body but not in the primordia. Immunohistochemistry showed that the translated protein is secreted into a polysaccharide layer of the pileus surface. The recombinant C-terminal Cys-rich domain of the protein showed antifungal activity against three filamentous fungi and inhibited hyphal growth and conidiogenesis. These results suggest that the PRI3-related protein of C. cylindracea, named cylindracin, plays an important role in the defense against pathogens.","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"14 11","pages":"1805-1824"},"PeriodicalIF":2.8,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/2211-5463.13910","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142389214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Domain swapping: a mathematical model for quantitative assessment of structural effects 域交换：定量评估结构效应的数学模型。

IF 2.8 4区生物学

FEBS Open Bio Pub Date : 2024-10-06 DOI: 10.1002/2211-5463.13911

Irena Roterman, Katarzyna Stapor, Dawid Dułak, Leszek Konieczny

引用次数: 0

Mitochondria: the beating heart of the eukaryotic cell 线粒体：真核细胞跳动的心脏。

IF 2.8 4区生物学

FEBS Open Bio Pub Date : 2024-10-04 DOI: 10.1002/2211-5463.13884

Johannes M. Herrmann

引用次数: 0

PRMT1-mediated arginine methylation promotes YAP activation and hepatocellular carcinoma proliferation PRMT1 介导的精氨酸甲基化促进 YAP 活化和肝细胞癌增殖。

IF 2.8 4区生物学

FEBS Open Bio Pub Date : 2024-10-04 DOI: 10.1002/2211-5463.13909

Jian Yu, Beibei Yu, Zushun Peng, Jianfeng Zhang, Juhui Sun, Bo Yang, Liushiyang Xu, De Luo

{"title":"PRMT1-mediated arginine methylation promotes YAP activation and hepatocellular carcinoma proliferation","authors":"Jian Yu, Beibei Yu, Zushun Peng, Jianfeng Zhang, Juhui Sun, Bo Yang, Liushiyang Xu, De Luo","doi":"10.1002/2211-5463.13909","DOIUrl":"10.1002/2211-5463.13909","url":null,"abstract":"The activity of Hippo signaling is commonly dysregulated in various human malignancies, including hepatocellular carcinoma (HCC). YAP, the key effector of Hippo pathway, is regulated through several posttranslational modifications. However, the mechanism by which YAP is regulated by arginine methylation remains unknown. In this study, immunoprecipitation and mass spectrometry were used to identify the arginine methylation site of YAP in HCC cells. The transcriptional activity of YAP and TEAD were further characterized by real-time qPCR and immunofluorescence assay, and a subcutaneous and orthotopic tumor mouse model was used to assess the effect of PRMT1-knockdown on HCC tumor growth. The result of mass spectrometry analysis identified that YAP was methylated at arginine 124. Moreover, we found that arginine methyltransferase PRMT1 interacted with YAP to mediate its arginine methylation, thus inhibited YAP phosphorylation and promoted YAP activity in the nucleus. PRMT1 was up-regulated in HCC tissues and positively associated with the expressions of YAP target genes. Silencing PRMT1 in HCC cells inhibited cell proliferation and tumor growth, while PRMT1-overexpression promoted HCC growth through YAP methylation. Our study reveals that PRMT1-mediated arginine methylation at R124 is mutually exclusive with YAP S127 phosphorylation, thereby facilitating YAP activity in the nucleus and promoting tumorigenesis in HCC.","PeriodicalId":12187,"journal":{"name":"FEBS Open Bio","volume":"14 12","pages":"2104-2112"},"PeriodicalIF":2.8,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/2211-5463.13909","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142375359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0