Biochemistry (Moscow)最新文献_第8页

Towards Development of the 4C-Based Method Detecting Interactions of Plasmid DNA with Host Genome 开发基于 4C 的检测质粒 DNA 与宿主基因组相互作用的方法

IF 2.3 4区生物学

Biochemistry (Moscow) Pub Date : 2024-05-06 DOI: 10.1134/S0006297924040059

Alexandra P. Yan, Paul A. Salnikov, Maria M. Gridina, Polina S. Belokopytova, Veniamin S. Fishman

引用次数: 0

Acrylate Reductase of an Anaerobic Electron Transport Chain of the Marine Bacterium Shewanella woodyi 海洋细菌木希旺氏菌厌氧电子传递链的丙烯酸酯还原酶

IF 2.3 4区生物学

Biochemistry (Moscow) Pub Date : 2024-05-06 DOI: 10.1134/S0006297924040096

Yulia V. Bertsova, Marina V. Serebryakova, Vladimir A. Bogachev, Alexander A. Baykov, Alexander V. Bogachev

{"title":"Acrylate Reductase of an Anaerobic Electron Transport Chain of the Marine Bacterium Shewanella woodyi","authors":"Yulia V. Bertsova, Marina V. Serebryakova, Vladimir A. Bogachev, Alexander A. Baykov, Alexander V. Bogachev","doi":"10.1134/S0006297924040096","DOIUrl":"10.1134/S0006297924040096","url":null,"abstract":"Many microorganisms are capable of anaerobic respiration in the absence of oxygen, by using different organic compounds as terminal acceptors in electron transport chain. We identify here an anaerobic respiratory chain protein responsible for acrylate reduction in the marine bacterium Shewanella woodyi. When the periplasmic proteins of S. woodyi were separated by ion exchange chromatography, acrylate reductase activity copurified with an ArdA protein (Swoo_0275). Heterologous expression of S. woodyi ardA gene (swoo_0275) in Shewanella oneidensis MR-1 cells did not result in the appearance in them of periplasmic acrylate reductase activity, but such activity was detected when the ardA gene was co-expressed with an ardB gene (swoo_0276). Together, these genes encode flavocytochrome c ArdAB, which is thus responsible for acrylate reduction in S. woodyi cells. ArdAB was highly specific for acrylate as substrate and reduced only methacrylate (at a 22-fold lower rate) among a series of other tested 2-enoates. In line with these findings, acrylate and methacrylate induced ardA gene expression in S. woodyi under anaerobic conditions, which was accompanied by the appearance of periplasmic acrylate reductase activity. ArdAB-linked acrylate reduction supports dimethylsulfoniopropionate-dependent anaerobic respiration in S. woodyi and, possibly, other marine bacteria.","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140883812","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

Hippocampus under Pressure: Molecular Mechanisms of Development of Cognitive Impairments in SHR Rats 压力下的海马：SHR 大鼠认知障碍发展的分子机制

IF 2.3 4区生物学

Biochemistry (Moscow) Pub Date : 2024-05-06 DOI: 10.1134/S0006297924040102

Mikhail Yu. Stepanichev, Diana I. Mamedova, Natalia V. Gulyaeva

{"title":"Hippocampus under Pressure: Molecular Mechanisms of Development of Cognitive Impairments in SHR Rats","authors":"Mikhail Yu. Stepanichev, Diana I. Mamedova, Natalia V. Gulyaeva","doi":"10.1134/S0006297924040102","DOIUrl":"10.1134/S0006297924040102","url":null,"abstract":"Data from clinical trials and animal experiments demonstrate relationship between chronic hypertension and development of cognitive impairments. Here, we review structural and biochemical alterations in the hippocampus of SHR rats with genetic hypertension, which are used as a model of essential hypertension and vascular dementia. In addition to hypertension, dysfunction of the hypothalamic-pituitary-adrenal system observed in SHR rats already at an early age may be a key factor of changes in the hippocampus at the structural and molecular levels. Global changes at the body level, such as hypertension and neurohumoral dysfunction, are associated with the development of vascular pathology and impairment of the blood-brain barrier. Changes in multiple biochemical glucocorticoid-dependent processes in the hippocampus, including dysfunction of steroid hormones receptors, impairments of neurotransmitter systems, BDNF deficiency, oxidative stress, and neuroinflammation are accompanied by the structural alterations, such as cellular signs of neuroinflammation micro- and astrogliosis, impairments of neurogenesis in the subgranular neurogenic zone, and neurodegenerative processes at the level of synapses, axons, and dendrites up to the death of neurons. The consequence of this is dysfunction of hippocampus, a key structure of the limbic system necessary for cognitive functions. Taking into account the available results at various levels starting from the body and brain structure (hippocampus) levels to molecular one, we can confirm translational validity of SHR rats for modeling mechanisms of vascular dementia.","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140883903","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

Sample-Wise and Gene-Wise Comparisons Confirm a Greater Similarity of RNA and Protein Expression Data at the Level of Molecular Pathways and Suggest an Approach for the Data Quality Check in High-Throughput Expression Databases 样本和基因比较证实分子通路层面的 RNA 和蛋白质表达数据具有更高的相似性，并为高通量表达数据库的数据质量检查提供了一种方法

IF 2.3 4区生物学

Biochemistry (Moscow) Pub Date : 2024-05-06 DOI: 10.1134/S0006297924040126

Mikhail Raevskiy, Maxim Sorokin, Aleksandra Emelianova, Galina Zakharova, Elena Poddubskaya, Marianna Zolotovskaia, Anton Buzdin

{"title":"Sample-Wise and Gene-Wise Comparisons Confirm a Greater Similarity of RNA and Protein Expression Data at the Level of Molecular Pathways and Suggest an Approach for the Data Quality Check in High-Throughput Expression Databases","authors":"Mikhail Raevskiy, Maxim Sorokin, Aleksandra Emelianova, Galina Zakharova, Elena Poddubskaya, Marianna Zolotovskaia, Anton Buzdin","doi":"10.1134/S0006297924040126","DOIUrl":"10.1134/S0006297924040126","url":null,"abstract":"Identification of genes and molecular pathways with congruent profiles in the proteomic and transcriptomic datasets may result in the discovery of promising transcriptomic biomarkers that would be more relevant to phenotypic changes. In this study, we conducted comparative analysis of 943 paired RNA and proteomic profiles obtained for the same samples of seven human cancer types from The Cancer Genome Atlas (TCGA) and NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) [two major open human cancer proteomic and transcriptomic databases] that included 15,112 protein-coding genes and 1611 molecular pathways. Overall, our findings demonstrated statistically significant improvement of the congruence between RNA and proteomic profiles when performing analysis at the level of molecular pathways rather than at the level of individual gene products. Transition to the molecular pathway level of data analysis increased the correlation to 0.19-0.57 (Pearson) and 0.14-057 (Spearman), or 2-3-fold for some cancer types. Evaluating the gain of the correlation upon transition to the data analysis the pathway level can be used to refine the omics data by identifying outliers that can be excluded from the comparison of RNA and proteomic profiles. We suggest using sample- and gene-wise correlations for individual genes and molecular pathways as a measure of quality of RNA/protein paired molecular data. We also provide a database of human genes, molecular pathways, and samples related to the correlation between RNA and protein products to facilitate an exploration of new cancer transcriptomic biomarkers and molecular mechanisms at different levels of human gene expression.","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140884020","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

Functional Role of C-terminal Domains in the MSL2 Protein of Drosophila melanogaster 黑腹果蝇 MSL2 蛋白 C 端结构域的功能作用

IF 2.3 4区生物学

Biochemistry (Moscow) Pub Date : 2024-05-06 DOI: 10.1134/S0006297924040060

Evgeniya A. Tikhonova, Pavel G. Georgiev, Oksana G. Maksimenko

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Nonspecific Interactions in Transcription Regulation and Organization of Transcriptional Condensates 转录调控中的非特异性相互作用与转录凝聚体的组织

IF 2.3 4区生物学

Biochemistry (Moscow) Pub Date : 2024-05-06 DOI: 10.1134/S0006297924040084

Anna A. Valyaeva, Eugene V. Sheval

引用次数: 0

Cohesin Complex: Structure and Principles of Interaction with DNA 凝聚素复合物：结构及与 DNA 的相互作用原理

IF 2.3 4区生物学

Biochemistry (Moscow) Pub Date : 2024-05-06 DOI: 10.1134/S0006297924040011

Arkadiy K. Golov, Alexey A. Gavrilov

{"title":"Cohesin Complex: Structure and Principles of Interaction with DNA","authors":"Arkadiy K. Golov, Alexey A. Gavrilov","doi":"10.1134/S0006297924040011","DOIUrl":"10.1134/S0006297924040011","url":null,"abstract":"Accurate duplication and separation of long linear genomic DNA molecules is associated with a number of purely mechanical problems. SMC complexes are key components of the cellular machinery that ensures decatenation of sister chromosomes and compaction of genomic DNA during division. Cohesin, one of the essential eukaryotic SMC complexes, has a typical ring structure with intersubunit pore through which DNA molecules can be threaded. Capacity of cohesin for such topological entrapment of DNA is crucial for the phenomenon of post-replicative association of sister chromatids better known as cohesion. Recently, it became apparent that cohesin and other SMC complexes are, in fact, motor proteins with a very peculiar movement pattern leading to formation of DNA loops. This specific process has been called loop extrusion. Extrusion underlies multiple functions of cohesin beyond cohesion, but molecular mechanism of the process remains a mystery. In this review, we summarized the data on molecular architecture of cohesin, effect of ATP hydrolysis cycle on this architecture, and known modes of cohesin–DNA interactions. Many of the seemingly disparate facts presented here will probably be incorporated in a unified mechanistic model of loop extrusion in the not-so-distant future.","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140886464","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

Rational Design of Drugs Targeting G-Protein-Coupled Receptors: A Structural Biology Perspective 合理设计针对 G 蛋白偶联受体的药物：结构生物学视角

IF 2.3 4区生物学

Biochemistry (Moscow) Pub Date : 2024-05-06 DOI: 10.1134/S0006297924040138

Polina A. Khorn, Aleksandra P. Luginina, Vladimir A. Pospelov, Dmitrii E. Dashevsky, Andrey N. Khnykin, Olga V. Moiseeva, Nadezhda A. Safronova, Anatolii S. Belousov, Alexey V. Mishin, Valentin I. Borshchevsky

{"title":"Rational Design of Drugs Targeting G-Protein-Coupled Receptors: A Structural Biology Perspective","authors":"Polina A. Khorn, Aleksandra P. Luginina, Vladimir A. Pospelov, Dmitrii E. Dashevsky, Andrey N. Khnykin, Olga V. Moiseeva, Nadezhda A. Safronova, Anatolii S. Belousov, Alexey V. Mishin, Valentin I. Borshchevsky","doi":"10.1134/S0006297924040138","DOIUrl":"10.1134/S0006297924040138","url":null,"abstract":"G protein-coupled receptors (GPCRs) play a key role in the transduction of extracellular signals to cells and regulation of many biological processes, which makes these membrane proteins one of the most important targets for pharmacological agents. A significant increase in the number of resolved atomic structures of GPCRs has opened the possibility of developing pharmaceuticals targeting these receptors via structure-based drug design (SBDD). SBDD employs information on the structure of receptor–ligand complexes to search for selective ligands without the need for an extensive high-throughput experimental ligand screening and can significantly expand the chemical space for ligand search. In this review, we describe the process of deciphering GPCR structures using X-ray diffraction analysis and cryoelectron microscopy as an important stage in the rational design of drugs targeting this receptor class. Our main goal was to present modern developments and key features of experimental methods used in SBDD of GPCR-targeting agents to a wide range of specialists.","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140883970","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

Unique Role of Vimentin in the Intermediate Filament Proteins Family 波形蛋白在中间丝蛋白家族中的独特作用

IF 2.3 4区生物学

Biochemistry (Moscow) Pub Date : 2024-05-06 DOI: 10.1134/S0006297924040114

Irina B. Alieva, Anton S. Shakhov, Alexander A. Dayal, Aleksandra S. Churkina, Olga I. Parfenteva, Alexander A. Minin

{"title":"Unique Role of Vimentin in the Intermediate Filament Proteins Family","authors":"Irina B. Alieva, Anton S. Shakhov, Alexander A. Dayal, Aleksandra S. Churkina, Olga I. Parfenteva, Alexander A. Minin","doi":"10.1134/S0006297924040114","DOIUrl":"10.1134/S0006297924040114","url":null,"abstract":"Intermediate filaments (IFs), being traditionally the least studied component of the cytoskeleton, have begun to receive more attention in recent years. IFs are found in different cell types and are specific to them. Accumulated data have shifted the paradigm about the role of IFs as structures that merely provide mechanical strength to the cell. In addition to this role, IFs have been shown to participate in maintaining cell shape and strengthening cell adhesion. The data have also been obtained that point out to the role of IFs in a number of other biological processes, including organization of microtubules and microfilaments, regulation of nuclear structure and activity, cell cycle control, and regulation of signal transduction pathways. They are also actively involved in the regulation of several aspects of intracellular transport. Among the intermediate filament proteins, vimentin is of particular interest for researchers. Vimentin has been shown to be associated with a range of diseases, including cancer, cataracts, Crohn’s disease, rheumatoid arthritis, and HIV. In this review, we focus almost exclusively on vimentin and the currently known functions of vimentin intermediate filaments (VIFs). This is due to the structural features of vimentin, biological functions of its domains, and its involvement in the regulation of a wide range of basic cellular functions, and its role in the development of human diseases. Particular attention in the review will be paid to comparing the role of VIFs with the role of intermediate filaments consisting of other proteins in cell physiology.","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140884024","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

Modification of the Hi-C Technology for Molecular Genetic Analysis of Formalin-Fixed Paraffin-Embedded Sections of Tumor Tissues 改进 Hi-C 技术，对福尔马林固定的石蜡包埋肿瘤组织切片进行分子遗传分析

IF 2.3 4区生物学

Biochemistry (Moscow) Pub Date : 2024-05-06 DOI: 10.1134/S0006297924040047

Maria M. Gridina, Yana K. Stepanchuk, Miroslav A. Nurridinov, Timofey A. Lagunov, Nikita Yu. Torgunakov, Artem A. Shadsky, Anastasia I. Ryabova, Nikolay V. Vasiliev, Sergey V. Vtorushin, Tatyana S. Gerashchenko, Evgeny V. Denisov, Mikhail A. Travin, Maxim A. Korolev, Veniamin S. Fishman

{"title":"Modification of the Hi-C Technology for Molecular Genetic Analysis of Formalin-Fixed Paraffin-Embedded Sections of Tumor Tissues","authors":"Maria M. Gridina, Yana K. Stepanchuk, Miroslav A. Nurridinov, Timofey A. Lagunov, Nikita Yu. Torgunakov, Artem A. Shadsky, Anastasia I. Ryabova, Nikolay V. Vasiliev, Sergey V. Vtorushin, Tatyana S. Gerashchenko, Evgeny V. Denisov, Mikhail A. Travin, Maxim A. Korolev, Veniamin S. Fishman","doi":"10.1134/S0006297924040047","DOIUrl":"10.1134/S0006297924040047","url":null,"abstract":"Molecular genetic analysis of tumor tissues is the most important step towards understanding the mechanisms of cancer development; it is also necessary for the choice of targeted therapy. The Hi-C (high-throughput chromatin conformation capture) technology can be used to detect various types of genomic variants, including balanced chromosomal rearrangements, such as inversions and translocations. We propose a modification of the Hi-C method for the analysis of chromatin contacts in formalin-fixed paraffin-embedded (FFPE) sections of tumor tissues. The developed protocol allows to generate high-quality Hi-C data and detect all types of chromosomal rearrangements. We have analyzed various databases to compile a comprehensive list of translocations that hold clinical importance for the targeted therapy selection. The practical value of molecular genetic testing is its ability to influence the treatment strategies and to provide prognostic insights. Detecting specific chromosomal rearrangements can guide the choice of the targeted therapies, which is a critical aspect of personalized medicine in oncology.","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":null,"pages":null},"PeriodicalIF":2.3,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140886320","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