Molekulyarnaya Biologiya最新文献_第6页

[A Bioinformatics Method for Identification of Human Proteases Active against Viral Envelope Glycoproteins: A Case Study on the SARS-CoV-2 Spike Protein]. [鉴定对病毒包膜糖蛋白有活性的人类蛋白酶的生物信息学方法：SARS-CoV-2尖峰蛋白案例研究]。

Molekulyarnaya Biologiya Pub Date : 2024-01-01 DOI: 10.31857/S0026898424010176, EDN: NRZZBT

E V Matveev, G V Ponomarev, M D Kazanov

{"title":"[A Bioinformatics Method for Identification of Human Proteases Active against Viral Envelope Glycoproteins: A Case Study on the SARS-CoV-2 Spike Protein].","authors":"E V Matveev, G V Ponomarev, M D Kazanov","doi":"10.31857/S0026898424010176, EDN: NRZZBT","DOIUrl":"10.31857/S0026898424010176, EDN: NRZZBT","url":null,"abstract":"Many viruses, including SARS-CoV-2, the coronavirus responsible for the COVID-19 pandemic, enter host cells through a process of cell-viral membrane fusion that is activated by proteolytic enzymes. Typically, these enzymes are host cell proteases. Identifying the proteases that activate the virus is not a simple task but is important for the development of new antiviral drugs. In this study, we developed a bioinformatics method for identifying proteases that can cleave viral envelope glycoproteins. The proposed approach involves the use of predictive models for the substrate specificity of human proteases and the application of a structural analysis method for predicting the vulnerability of protein regions to proteolysis based on their 3D structures. Specificity models were constructed for 169 human proteases using information on their known substrates. A previously developed method for structural analysis of potential proteolysis sites was applied in parallel with specificity models. Validation of the proposed approach was performed on the SARS-CoV-2 spike protein, whose proteolysis sites have been well studied.","PeriodicalId":39818,"journal":{"name":"Molekulyarnaya Biologiya","volume":"58 1","pages":"171-177"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141471408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

[Long Noncoding RNAs MEG3, TUG1, and hsa-miR-21-3p Are Potential Diagnostic Biomarkers for Coronary Artery Disease]. [长非编码 RNA MEG3、TUG1 和 hsa-miR-21-3p 是冠状动脉疾病的潜在诊断生物标记物】。］

Molekulyarnaya Biologiya Pub Date : 2024-01-01

M Abdelgawad, H Y Abdallah, A Fareed, A E Ahmed

{"title":"[Long Noncoding RNAs MEG3, TUG1, and hsa-miR-21-3p Are Potential Diagnostic Biomarkers for Coronary Artery Disease].","authors":"M Abdelgawad, H Y Abdallah, A Fareed, A E Ahmed","doi":"","DOIUrl":"","url":null,"abstract":"Peripheral blood biomarkers are of particular importance to diagnose certain diseases including coronary artery disease (CAD) due to their non-invasiveness. Investigating the expression of noncoding RNAs (ncRNAs) paves the way to early disease diagnosis, prognosis, and treatment. Consequently, in this research, we aimed to investigate a panel of ncRNAs as potential biomarkers in patients with coronary artery disease. Two different groups have been designed (control and CAD). All participants were subjected to interviews and clinical examinations. Peripheral blood samples were collected, and plasma was extracted. At the same time, target ncRNAs have been selected based on literature review and bioinformatic analysis, and later they underwent investigation using quantitative real-time PCR. The selected panel encompassed the long non-coding RNAs (lncRNAs) MEG3, TUG1, and SRA1, and one related microRNA (miRNA): hsa-miR-21-3p. We observed statistically significant upregulation in MEG3, TUG1, and hsa-miR21-3p in CAD patients compared to control participants (p-value < 0.01). Nevertheless, SRA1 exhibited downregulation with no statistical significance (p-value > 0.05). All ncRNAs under study displayed a significantly strong correlation with disease incidence, age, and smoking. Network construction revealed a strong relationship between MEG3 and TUG1. ROC analysis indicated high potentiality for hsa-miR-21-3p to be a promising biomarker for CAD. Moreover, MEG3 and TUG1 displayed distinguished diagnostic discrimination but less than hsa-miR-21-3p, all of them exhibited strong statistical significance differences between CAD and control groups. Conclusively, this research pinpointed that MEG3, TUG1, and hsa-miR-21-3p are potential biomarkers of CAD incidence and diagnosis.","PeriodicalId":39818,"journal":{"name":"Molekulyarnaya Biologiya","volume":"57 6","pages":"40-42"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138809905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

[Regulation of Retrotransposons in Drosophila melanogaster Somatic Tissues]. [黑腹果蝇体细胞组织中转座子的调控]。

Molekulyarnaya Biologiya Pub Date : 2024-01-01 DOI: 10.31857/S0026898424010094, EDN: ODXKBV

P A Milyaeva, I V Kukushkina, A R Lavrenov, I V Kuzmin, A I Kim, L N Nefedova

引用次数: 0

[Genome Stability of Bacillus velezensis after Two-Year Exposure in Open Space]. [露天暴露两年后 Velezensis 杆菌基因组的稳定性]。

Molekulyarnaya Biologiya Pub Date : 2024-01-01 DOI: 10.31857/S0026898424010047, EDN: OHOJPL

S V Fialkina, E A Deshevaya, A L Rakitin, O I Orlov

{"title":"[Genome Stability of Bacillus velezensis after Two-Year Exposure in Open Space].","authors":"S V Fialkina, E A Deshevaya, A L Rakitin, O I Orlov","doi":"10.31857/S0026898424010047, EDN: OHOJPL","DOIUrl":"https://doi.org/10.31857/S0026898424010047, EDN: OHOJPL","url":null,"abstract":"Spore-forming bacteria have a unique resistance to negative environmental conditions, including aggressive space factors, and are an excellent model for studying adaptation mechanisms and survival strategies at the molecular level. The study analyzed the genome of Bacillus velezensis, which remained viable after a 2-year exposure in outer space on the outer surface of the ISS as part of the Test space experiment. A comparative analysis of the draft genomes of the exhibit strain and the ground control did not reveal significant changes; the average nucleotide identity was 99.98%, which indicates the ability of microorganisms to maintain genome stability in space conditions, due to both increased stress resistance of bacterial spores and efficient operation of the system of repair of accumulated changes. The study of a single nucleotide polymorphism in the genome of B. velezensis revealed nine point substitutions, three of which are in intergenic regions, six in protein-coding genes, three of them are missense mutations, two nucleotide deletions leading to a shift in the reading frame, and one synonymous substitution. The profiles of the housekeeping genes were determined during MLST typing and it was found that the allelic profiles obtained for B. velezensis T15.2 and 924 strains do not correspond to any of the previously described sequence types. The presented results indicate the ability of B. velezensis bacteria to maintain the viability of spores and the integrity of the genome for a long time under extreme conditions of outer space, which is important for the problem of planetary protection, as well as the potential possibility of performing biotechnological processes based on B. velezensis during space exploration.","PeriodicalId":39818,"journal":{"name":"Molekulyarnaya Biologiya","volume":"58 1","pages":"43-53"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141471410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

[Latent Macrophage and Immature B Cell Lines Generated with Hygromycin-Resistant Murine Gammaherpesvirus 68 Genome Expresses Modest Levels of Viral miRNAs]. [使用耐百日咳霉素的小鼠伽马疱疹病毒 68 基因组生成的潜伏巨噬细胞和未成熟 B 细胞系表达适度水平的病毒 miRNA】。］

Molekulyarnaya Biologiya Pub Date : 2024-01-01 DOI: : 10.31857/S0026898424010148, EDN: NVDCRY

M Kara

{"title":"[Latent Macrophage and Immature B Cell Lines Generated with Hygromycin-Resistant Murine Gammaherpesvirus 68 Genome Expresses Modest Levels of Viral miRNAs].","authors":"M Kara","doi":": 10.31857/S0026898424010148, EDN: NVDCRY","DOIUrl":"https://doi.org/: 10.31857/S0026898424010148, EDN: NVDCRY","url":null,"abstract":"Murine gammaherpesvirus 68 (MHV68) establishes latency mainly in B cells and causes lymphomas reminiscent of human gammaherpesvirus diseases in laboratory mice. To study the molecular mechanism of virus infection and how the viral determinants control cell and eventually cause tumorigenesis, readily available latently infected cell lines are essential. For in vitro MHV68 latency studies, only two cell culture systems have been available. Gammaherpesviruses are known to infect developing B cells and macrophages, therefore we aimed to expand the MHV68 latently infected cell line repertoire. Here, several latently infected immature B cell and macrophage-like cell line clones were generated. Hygromycin-resistant recombinant MHV68 was isolated from a laboratory-made latent cell line, HE2.1, and propagated to develop stable cell lines that carry the viral genome under hygromycin selection. Subclones of these cells lines were analyzed for viral miRNA expression by TaqMan qPCR and assessed for expression of a lytic viral transcript M3. The cell lines maintain the viral genome as an episome shown by the digestion-circularization PCR assay. Latently infected cell lines generated here do not express viral miRNAs higher than the parental cell line. However, these cell lines may provide an alternative tool to study latency mechanisms and miRNA target identification studies.","PeriodicalId":39818,"journal":{"name":"Molekulyarnaya Biologiya","volume":"58 1","pages":"154-156"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141471411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

[Metabolic Heterogeneity of Tumors]. [肿瘤的代谢异质性]。

Molekulyarnaya Biologiya Pub Date : 2023-11-01 DOI: 10.31857/S0026898423060186, EDN: QIJIYQ

M V Shirmanova, S D Sinyushkina, A D Komarova

引用次数: 0

[The Redox-Catalytic Properties of Cobalamins]. [钴胺的氧化还原催化特性]。

Molekulyarnaya Biologiya Pub Date : 2023-11-01 DOI: 10.31857/S0026898423060174, EDN: QIFDSC

Yu V Shatalin, V S Shubina, M E Solovieva, V S Akatov

引用次数: 0

[Identification of Melittin-Like Proteins with a Molecular Weight of 67 κDa that Interact with Na^(+)/K^(+)-ATPase]. [与 Na^(+)/K^(+)-ATPase 相互作用的分子量为 67 κDa 的 Melittin 样蛋白的鉴定]。

Molekulyarnaya Biologiya Pub Date : 2023-11-01 DOI: 10.31857/S0026898423060216, EDN: QLKRWL

L A Varfolomeeva, E A Klimanova, S V Sidorenko, D A Fedorov, O D Lopina

{"title":"[Identification of Melittin-Like Proteins with a Molecular Weight of 67 κDa that Interact with Na^(+)/K^(+)-ATPase].","authors":"L A Varfolomeeva, E A Klimanova, S V Sidorenko, D A Fedorov, O D Lopina","doi":"10.31857/S0026898423060216, EDN: QLKRWL","DOIUrl":"https://doi.org/10.31857/S0026898423060216, EDN: QLKRWL","url":null,"abstract":"Melittin, a peptide from bee venom, was found to be able to interact with many proteins, including calmodulin target proteins and ion-transporting P-type ATPases. It is assumed that melittin mimics a protein module involved in protein-protein interactions within cells. Previously, a Na^(+)/K^(+)-ATPase containing the α1 isoform of the catalytic subunit was found to co-precipitate with a protein with a molecular weight of about 70 κDa that interacts with antibodies against melittin by cross immunoprecipitation. In the presence of a specific Na^(+)/K^(+)-ATPase inhibitor (ouabain), the amount of protein with a molecular weight of 70 κDa interacting with Na^(+)/K^(+)-ATPase increases. In order to identify melittin-like protein from murine kidney homogenate, a fraction of melittin-like proteins with a molecular weight of approximately 70 κDa was obtained using affinity chromatography with immobilized antibodies specific to melittin. By mass spectrometry analysis, the obtained protein fraction was found to contain three molecular chaperones of Hsp70 superfamily: mitochondrial mtHsp70 (mortalin), Hsp73, Grp78 (BiP) of endoplasmic reticulum. These data suggest that chaperones from the HSP-70 superfamily contain a melittin-like module.","PeriodicalId":39818,"journal":{"name":"Molekulyarnaya Biologiya","volume":"57 6","pages":"1077-1083"},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138809815","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

[Nitric Oxide(II) in the Biology of Chlorophyta]. [叶绿体生物学中的一氧化氮（II）]。

Molekulyarnaya Biologiya Pub Date : 2023-11-01 DOI: 10.31857/S002689842306006X, EDN: QZMDJN

E V Ermilova

{"title":"[Nitric Oxide(II) in the Biology of Chlorophyta].","authors":"E V Ermilova","doi":"10.31857/S002689842306006X, EDN: QZMDJN","DOIUrl":"https://doi.org/10.31857/S002689842306006X, EDN: QZMDJN","url":null,"abstract":"NO is a gaseous signaling redox-active molecule that functions in various eukaryotes. However, its synthesis, turnover, and effects in cells are specific in plants in several aspects. Compared with higher plants, the role of NO in Chlorophyta has not been investigated enough. However, some of the mechanisms for controlling the levels of this signaling molecule have been characterized in model green algae. In Chlamydomonas reinhardtii, NO synthesis is carried out by a dual system of nitrate reductase and NO-forming nitrite reductase. Other mechanisms that might produce NO from nitrite are associated with components of the mitochondrial electron-transport chain. In addition, NO formation in some green algae proceeds by an oxidative mechanism similar to that in mammals. The recent discovery of L-arginine-dependent NO synthesis in the colorless alga Polytomella parva suggests the existence of a protein complex with enzyme activities that are similar to animal nitric oxide synthase. This latter finding paves the way for further research into potential members of the NO synthases family in Chlorophyta. Beyond synthesis, the regulatory processes to maintain intracellular NO levels are also an integral part for its function in cells. Members of the truncated hemoglobins family with dioxygenase activity can convert NO to nitrate, as was shown for C. reinhardtii. In addition, the implication of NO reductases in NO scavenging has also been described. Even more intriguing, unlike in animals, the typical NO/cGMP signaling module appears not to be used by green algae. S-nitrosylated glutathione, which is considered the main reservoir for NO, provides NO signals to proteins. In Chlorophyta, protein S-nitrosation is one of the key mechanisms of action of the redox molecule. In this review, we discuss the current state-of-the-art and possible future directions related to the biology of NO in green algae.","PeriodicalId":39818,"journal":{"name":"Molekulyarnaya Biologiya","volume":"57 6","pages":"916-924"},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138809977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

[Cytochrome bd as Antioxidant Redox Enzyme]. [作为抗氧化氧化还原酶的细胞色素 bd]。

Molekulyarnaya Biologiya Pub Date : 2023-11-01 DOI: 10.31857/S0026898423060034, EDN: QOYAOW

V B Borisov, M R Nastasi, E Forte

{"title":"[Cytochrome bd as Antioxidant Redox Enzyme].","authors":"V B Borisov, M R Nastasi, E Forte","doi":"10.31857/S0026898423060034, EDN: QOYAOW","DOIUrl":"https://doi.org/10.31857/S0026898423060034, EDN: QOYAOW","url":null,"abstract":"One of the main functions of enzyme complexes that constitute electron transport (respiratory) chains of organisms is to maintain cellular redox homeostasis by oxidizing reducing equivalents, NADH and quinol. Cytochrome bd is a unique terminal oxidase of the chains of many bacteria including pathogenic species. This redox enzyme couples the oxidation of ubiquinol or menaquinol by molecular oxygen to the generation of proton motive force, a universal energy currency. The latter is used by the organism to produce ATP, another cellular energy currency, via oxidative phosphorylation. Escherichia coli contains two bd-type oxidases, bd-I and bd-II, encoded by the cydAB and appCB operons, respectively. Surprisingly, both bd enzymes make a further contribution to molecular mechanisms of maintaining the appropriate redox balance in the bacterial cell by means of elimination of reactive oxygen species, such as hydrogen peroxide. This review summarizes recent data on the redox-modulated H2O2-scavenging activities of cytochromes bd-I and bd-II from E. coli. The possibility of such antioxidant properties in cytochromes bd from other bacteria is also discussed.","PeriodicalId":39818,"journal":{"name":"Molekulyarnaya Biologiya","volume":"57 6","pages":"1084"},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138809739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0