Pub Date : 2024-05-06DOI: 10.1134/s0006297924040023
Arkadiy K. Golov, Alexey A. Gavrilov
Abstract
The most prominent representatives of multisubunit SMC complexes, cohesin and condensin, are best known as structural components of mitotic chromosomes. It turned out that these complexes, as well as their bacterial homologues, are molecular motors, the ATP-dependent movement of these complexes along DNA threads leads to the formation of DNA loops. In recent years, we have witnessed an avalanche-like accumulation of data on the process of SMC dependent DNA looping, also known as loop extrusion. This review briefly summarizes the current understanding of the place and role of cohesin-dependent extrusion in cell physiology and presents a number of models describing the potential molecular mechanism of extrusion in a most compelling way. We conclude the review with a discussion of how the capacity of cohesin to extrude DNA loops may be mechanistically linked to its involvement in sister chromatid cohesion.
摘要 多亚基 SMC 复合物的最主要代表--凝聚素和冷凝素--作为有丝分裂染色体的结构成分最为人熟知。事实证明,这些复合体以及它们的细菌同源物都是分子马达,这些复合体沿 DNA 线的 ATP 依赖性运动导致了 DNA 环的形成。近年来,关于依赖于 SMC 的 DNA 环(又称环挤出)过程的数据如雪崩般不断积累。这篇综述简要总结了目前对依赖于凝聚素的挤压在细胞生理学中的地位和作用的理解,并提出了一些模型,以最引人注目的方式描述了挤压的潜在分子机制。最后,我们将讨论凝聚素挤出 DNA 环的能力如何与其参与姐妹染色单体内聚的机理相关联。
{"title":"Cohesin-Dependent Loop Extrusion: Molecular Mechanics and Role in Cell Physiology","authors":"Arkadiy K. Golov, Alexey A. Gavrilov","doi":"10.1134/s0006297924040023","DOIUrl":"https://doi.org/10.1134/s0006297924040023","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>The most prominent representatives of multisubunit SMC complexes, cohesin and condensin, are best known as structural components of mitotic chromosomes. It turned out that these complexes, as well as their bacterial homologues, are molecular motors, the ATP-dependent movement of these complexes along DNA threads leads to the formation of DNA loops. In recent years, we have witnessed an avalanche-like accumulation of data on the process of SMC dependent DNA looping, also known as loop extrusion. This review briefly summarizes the current understanding of the place and role of cohesin-dependent extrusion in cell physiology and presents a number of models describing the potential molecular mechanism of extrusion in a most compelling way. We conclude the review with a discussion of how the capacity of cohesin to extrude DNA loops may be mechanistically linked to its involvement in sister chromatid cohesion.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140886517","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}
Pub Date : 2024-04-08DOI: 10.1134/s0006297924030027
Roman Y. Sidorov, Alexander G. Tkachenko
Abstract
The synthesis of (p)ppGpp alarmones plays a vital role in the regulation of metabolism suppression, growth rate control, virulence, bacterial persistence, and biofilm formation. The (p)ppGpp alarmones are synthesized by proteins of the RelA/SpoT homolog (RSH) superfamily, including long bifunctional RSH proteins and small alarmone synthetases. Here, we investigated enzyme kinetics and dose-dependent enzyme inhibition to elucidate the mechanism of 4-(4,7-dimethyl-1,2,3,4-tetrahydronaphthalen-1-yl)pentanoic acid (DMNP) action on the (p)ppGpp synthetases RelMsm and RelZ from Mycolicibacterium smegmatis and RelMtb from Mycobacterium tuberculosis. DMNP was found to inhibit the activity of RelMtb. According to the enzyme kinetics analysis, DMNP acts as a noncompetitive inhibitor of RelMsm and RelZ. Based on the results of molecular docking, the DMNP-binding site is located in the proximity of the synthetase domain active site. This study might help in the development of alarmone synthetase inhibitors, which includes relacin and its derivatives, as well as DMNP – a synthetic analog of the marine coral metabolite erogorgiaene. Unlike conventional antibiotics, alarmone synthetase inhibitors target metabolic pathways linked to the bacterial stringent response. Although these pathways are not essential for bacteria, they regulate the development of adaptation mechanisms. Combining conventional antibiotics that target actively growing cells with compounds that impede bacterial adaptation may address challenges associated with antimicrobial resistance and bacterial persistence.
{"title":"The Mechanism of Inhibition of Mycobacterial (p)ppGpp Synthetases by a Synthetic Analog of Erogorgiaene","authors":"Roman Y. Sidorov, Alexander G. Tkachenko","doi":"10.1134/s0006297924030027","DOIUrl":"https://doi.org/10.1134/s0006297924030027","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>The synthesis of (p)ppGpp alarmones plays a vital role in the regulation of metabolism suppression, growth rate control, virulence, bacterial persistence, and biofilm formation. The (p)ppGpp alarmones are synthesized by proteins of the RelA/SpoT homolog (RSH) superfamily, including long bifunctional RSH proteins and small alarmone synthetases. Here, we investigated enzyme kinetics and dose-dependent enzyme inhibition to elucidate the mechanism of 4-(4,7-dimethyl-1,2,3,4-tetrahydronaphthalen-1-yl)pentanoic acid (DMNP) action on the (p)ppGpp synthetases Rel<sub>Msm</sub> and RelZ from <i>Mycolicibacterium smegmatis</i> and Rel<sub>Mtb</sub> from <i>Mycobacterium tuberculosis</i>. DMNP was found to inhibit the activity of Rel<sub>Mtb</sub>. According to the enzyme kinetics analysis, DMNP acts as a noncompetitive inhibitor of Rel<sub>Msm</sub> and RelZ. Based on the results of molecular docking, the DMNP-binding site is located in the proximity of the synthetase domain active site. This study might help in the development of alarmone synthetase inhibitors, which includes relacin and its derivatives, as well as DMNP – a synthetic analog of the marine coral metabolite erogorgiaene. Unlike conventional antibiotics, alarmone synthetase inhibitors target metabolic pathways linked to the bacterial stringent response. Although these pathways are not essential for bacteria, they regulate the development of adaptation mechanisms. Combining conventional antibiotics that target actively growing cells with compounds that impede bacterial adaptation may address challenges associated with antimicrobial resistance and bacterial persistence.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140580072","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}
Pub Date : 2024-04-08DOI: 10.1134/s0006297924030052
Sergei V. Shekhovtsov, Yana L. Vorontsova, Irina A. Slepneva, Dmitry N. Smirnov, Ekaterina E. Khrameeva, Alexey Shatunov, Tatiana V. Poluboyarova, Nina A. Bulakhova, Ekaterina N. Meshcheryakova, Daniil I. Berman, Viktor V. Glupov
Abstract
The Siberian frog Rana amurensis has a uniquely high tolerance to hypoxia among amphibians, as it is able to withstand several months underwater with almost no oxygen (0.2 mg/liter) vs. several days for other studied species. Since it was hypothesized that hypoxia actives the antioxidant defense system in hypoxia-tolerant animals, one would expect similar response in R.amurensis. Here, we studied the effect of hypoxia in the Siberian frog based on the transcriptomic data, activities of antioxidant enzyme, and content of low-molecular-weight antioxidants. Exposure to hypoxia upregulated expression of three relevant transcripts (catalase in the brain and two aldo-keto reductases in the liver). The activities of peroxidase in the blood and catalase in the liver were significantly increased, while the activity of glutathione S-transferase in the liver was reduced. The content of low-molecular-weight antioxidants (thiols and ascorbate) in the heart and liver was unaffected. In general, only a few components of the antioxidant defense system were affected by hypoxia, while most remained unchanged. Comparison to other hypoxia-tolerant species suggests species-specific adaptations to hypoxia-related ROS stress.
{"title":"The Impact of Long-Term Hypoxia on the Antioxidant Defense System in the Siberian Frog Rana amurensis","authors":"Sergei V. Shekhovtsov, Yana L. Vorontsova, Irina A. Slepneva, Dmitry N. Smirnov, Ekaterina E. Khrameeva, Alexey Shatunov, Tatiana V. Poluboyarova, Nina A. Bulakhova, Ekaterina N. Meshcheryakova, Daniil I. Berman, Viktor V. Glupov","doi":"10.1134/s0006297924030052","DOIUrl":"https://doi.org/10.1134/s0006297924030052","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>The Siberian frog <i>Rana amurensis</i> has a uniquely high tolerance to hypoxia among amphibians, as it is able to withstand several months underwater with almost no oxygen (0.2 mg/liter) vs. several days for other studied species. Since it was hypothesized that hypoxia actives the antioxidant defense system in hypoxia-tolerant animals, one would expect similar response in <i>R.</i> <i>amurensis</i>. Here, we studied the effect of hypoxia in the Siberian frog based on the transcriptomic data, activities of antioxidant enzyme, and content of low-molecular-weight antioxidants. Exposure to hypoxia upregulated expression of three relevant transcripts (catalase in the brain and two aldo-keto reductases in the liver). The activities of peroxidase in the blood and catalase in the liver were significantly increased, while the activity of glutathione S-transferase in the liver was reduced. The content of low-molecular-weight antioxidants (thiols and ascorbate) in the heart and liver was unaffected. In general, only a few components of the antioxidant defense system were affected by hypoxia, while most remained unchanged. Comparison to other hypoxia-tolerant species suggests species-specific adaptations to hypoxia-related ROS stress.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140586836","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}
Pub Date : 2024-04-08DOI: 10.1134/s0006297924030039
Kurnegala Manikanta, Manoj Paul, Vaddaragudisalu D. Sandesha, Shanmuga S. Mahalingam, Thimmasandra Narayan Ramesh, Krishnegowda Harishkumar, Shashank S. Koundinya, Shivanna Naveen, Kempaiah Kemparaju, Kesturu S. Girish
Abstract
Platelets are known for their indispensable role in hemostasis and thrombosis. However, alteration in platelet function due to oxidative stress is known to mediate various health complications, including cardiovascular diseases and other health complications. To date, several synthetic molecules have displayed antiplatelet activity; however, their uses are associated with bleeding and other adverse effects. The commercially available curcumin is generally a mixture of three curcuminoids: curcumin, demethoxycurcumin, and bisdemethoxycurcumin. Although crude curcumin is known to inhibit platelet aggregation, the effect of purified curcumin on platelet apoptosis, activation, and aggregation remains unclear. Therefore, in this study, curcumin was purified from a crude curcumin mixture and the effects of this preparation on the oxidative stress-induced platelet apoptosis and activation was evaluated. 2,2′-Azobis(2-methylpropionamidine) dihydrochloride (AAPH) compound was used as an inducer of oxidative stress. Purified curcumin restored AAPH-induced platelet apoptotic markers like reactive oxygen species, intracellular calcium level, mitochondrial membrane potential, cardiolipin peroxidation, cytochrome c release from mitochondria to the cytosol, and phosphatidyl serine externalization. Further, it inhibited the agonist-induced platelet activation and aggregation, demonstrating its antiplatelet activity. Western blot analysis confirms protective effect of the purified curcumin against oxidative stress-induced platelet apoptosis and activation via downregulation of MAPKs protein activation, including ASK1, JNK, and p-38. Together, these results suggest that the purified curcumin could be a potential therapeutic bioactive molecule to treat the oxidative stress-induced platelet activation, apoptosis, and associated complications.
{"title":"Oxidative Stress-Induced Platelet Apoptosis/Activation: Alleviation by Purified Curcumin via ASK1-JNK/p-38 Pathway","authors":"Kurnegala Manikanta, Manoj Paul, Vaddaragudisalu D. Sandesha, Shanmuga S. Mahalingam, Thimmasandra Narayan Ramesh, Krishnegowda Harishkumar, Shashank S. Koundinya, Shivanna Naveen, Kempaiah Kemparaju, Kesturu S. Girish","doi":"10.1134/s0006297924030039","DOIUrl":"https://doi.org/10.1134/s0006297924030039","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>Platelets are known for their indispensable role in hemostasis and thrombosis. However, alteration in platelet function due to oxidative stress is known to mediate various health complications, including cardiovascular diseases and other health complications. To date, several synthetic molecules have displayed antiplatelet activity; however, their uses are associated with bleeding and other adverse effects. The commercially available curcumin is generally a mixture of three curcuminoids: curcumin, demethoxycurcumin, and bisdemethoxycurcumin. Although crude curcumin is known to inhibit platelet aggregation, the effect of purified curcumin on platelet apoptosis, activation, and aggregation remains unclear. Therefore, in this study, curcumin was purified from a crude curcumin mixture and the effects of this preparation on the oxidative stress-induced platelet apoptosis and activation was evaluated. 2,2′-Azobis(2-methylpropionamidine) dihydrochloride (AAPH) compound was used as an inducer of oxidative stress. Purified curcumin restored AAPH-induced platelet apoptotic markers like reactive oxygen species, intracellular calcium level, mitochondrial membrane potential, cardiolipin peroxidation, cytochrome <i>c</i> release from mitochondria to the cytosol, and phosphatidyl serine externalization. Further, it inhibited the agonist-induced platelet activation and aggregation, demonstrating its antiplatelet activity. Western blot analysis confirms protective effect of the purified curcumin against oxidative stress-induced platelet apoptosis and activation via downregulation of MAPKs protein activation, including ASK1, JNK, and p-38. Together, these results suggest that the purified curcumin could be a potential therapeutic bioactive molecule to treat the oxidative stress-induced platelet activation, apoptosis, and associated complications.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140586757","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}
Pub Date : 2024-04-08DOI: 10.1134/s0006297924030015
Aleksandr V. Zhuravlev, Oleg V. Vetrovoy, Ekaterina S. Zalomaeva, Ekaterina S. Egozova, Ekaterina A. Nikitina, Elena V. Savvateeva-Popova
Abstract
Courtship suppression is a behavioral adaptation of the fruit fly. When majority of the females in a fly population are fertilized and non-receptive for mating, a male, after a series of failed attempts, decreases its courtship activity towards all females, saving its energy and reproductive resources. The time of courtship decrease depends on both duration of unsuccessful courtship and genetically determined features of the male nervous system. Thereby, courtship suppression paradigm can be used for studying molecular mechanisms of learning and memory. p-Cofilin, a component of the actin remodeling signaling cascade and product of LIM-kinase 1 (LIMK1), regulates Drosophila melanogaster forgetting in olfactory learning paradigm. Previously, we have shown that limk1 suppression in the specific types of nervous cells differently affects fly courtship memory. Here, we used Gal4 > UAS system to induce limk1 overexpression in the same types of neurons. limk1 activation in the mushroom body, glia, and fruitless neurons decreased learning index compared to the control strain or the strain with limk1 knockdown. In cholinergic and dopaminergic/serotoninergic neurons, both overexpression and knockdown of limk1 impaired Drosophila short-term memory. Thus, proper balance of the limk1 activity is crucial for normal cognitive activity of the fruit fly.
{"title":"Overexpression of the limk1 Gene in Drosophila melanogaster Can Lead to Suppression of Courtship Memory in Males","authors":"Aleksandr V. Zhuravlev, Oleg V. Vetrovoy, Ekaterina S. Zalomaeva, Ekaterina S. Egozova, Ekaterina A. Nikitina, Elena V. Savvateeva-Popova","doi":"10.1134/s0006297924030015","DOIUrl":"https://doi.org/10.1134/s0006297924030015","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>Courtship suppression is a behavioral adaptation of the fruit fly. When majority of the females in a fly population are fertilized and non-receptive for mating, a male, after a series of failed attempts, decreases its courtship activity towards all females, saving its energy and reproductive resources. The time of courtship decrease depends on both duration of unsuccessful courtship and genetically determined features of the male nervous system. Thereby, courtship suppression paradigm can be used for studying molecular mechanisms of learning and memory. p-Cofilin, a component of the actin remodeling signaling cascade and product of LIM-kinase 1 (LIMK1), regulates <i>Drosophila melanogaster</i> forgetting in olfactory learning paradigm. Previously, we have shown that <i>limk1</i> suppression in the specific types of nervous cells differently affects fly courtship memory. Here, we used Gal4 > UAS system to induce <i>limk1</i> overexpression in the same types of neurons. <i>limk1</i> activation in the mushroom body, glia, and <i>fruitless</i> neurons decreased learning index compared to the control strain or the strain with <i>limk1</i> knockdown. In cholinergic and dopaminergic/serotoninergic neurons, both overexpression and knockdown of <i>limk1</i> impaired <i>Drosophila</i> short-term memory. Thus, proper balance of the <i>limk1 </i>activity is crucial for normal cognitive activity of the fruit fly.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140586831","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}
Pub Date : 2024-04-08DOI: 10.1134/s0006297924030118
Nina P. Trubitsina, Anton B. Matiiv, Tatyana M. Rogoza, Anna A. Zudilova, Mariya D. Bezgina, Galina A. Zhouravleva, Stanislav A. Bondarev
Abstract
Less than ten years ago, evidence began to accumulate about association between the changes in the composition of gut microbiota and development of human synucleinopathies, in particular sporadic form of Parkinson’s disease. We collected data from more than one hundred and thirty experimental studies that reported similar results and summarized the frequencies of detection of different groups of bacteria in these studies. It is important to note that it is extremely rare that a unidirectional change in the population of one or another group of microorganisms (only an elevation or only a reduction) was detected in the patients with Parkinson’s disease. However, we were able to identify several groups of bacteria that were overrepresented in the patients with Parkinson’s disease in the analyzed studies. There are various hypotheses about the molecular mechanisms that explain such relationships. Usually, α-synuclein aggregation is associated with the development of inflammatory processes that occur in response to the changes in the microbiome. However, experimental evidence is accumulating on the influence of bacterial proteins, including amyloids (curli), as well as various metabolites, on the α-synuclein aggregation. In the review, we provided up-to-date information about such examples.
{"title":"Role of the Gut Microbiome and Bacterial Amyloids in the Development of Synucleinopathies","authors":"Nina P. Trubitsina, Anton B. Matiiv, Tatyana M. Rogoza, Anna A. Zudilova, Mariya D. Bezgina, Galina A. Zhouravleva, Stanislav A. Bondarev","doi":"10.1134/s0006297924030118","DOIUrl":"https://doi.org/10.1134/s0006297924030118","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>Less than ten years ago, evidence began to accumulate about association between the changes in the composition of gut microbiota and development of human synucleinopathies, in particular sporadic form of Parkinson’s disease. We collected data from more than one hundred and thirty experimental studies that reported similar results and summarized the frequencies of detection of different groups of bacteria in these studies. It is important to note that it is extremely rare that a unidirectional change in the population of one or another group of microorganisms (only an elevation or only a reduction) was detected in the patients with Parkinson’s disease. However, we were able to identify several groups of bacteria that were overrepresented in the patients with Parkinson’s disease in the analyzed studies. There are various hypotheses about the molecular mechanisms that explain such relationships. Usually, α-synuclein aggregation is associated with the development of inflammatory processes that occur in response to the changes in the microbiome. However, experimental evidence is accumulating on the influence of bacterial proteins, including amyloids (curli), as well as various metabolites, on the α-synuclein aggregation. In the review, we provided up-to-date information about such examples.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140586833","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}
Pub Date : 2024-04-08DOI: 10.1134/s0006297924030167
Ekaterina Minskaia, Alima Galieva, Alexander D. Egorov, Roman Ivanov, Alexander Karabelsky
In this article the funding section was misprinted unintentionally. The funding statement should be corrected as follows:
A.D.E. was supported by the Russian Science Foundation and Kuban Science Foundation (project no. 22-14-20046). E.M., A.G., A.K., and R.A.I. were supported by the internal projects GTH-RND-2011 and GTH-RND-2112.
{"title":"Erratum to: Viral Vectors in Gene Replacement Therapy","authors":"Ekaterina Minskaia, Alima Galieva, Alexander D. Egorov, Roman Ivanov, Alexander Karabelsky","doi":"10.1134/s0006297924030167","DOIUrl":"https://doi.org/10.1134/s0006297924030167","url":null,"abstract":"<p>In this article the funding section was misprinted unintentionally. The funding statement should be corrected as follows:</p> <p>A.D.E. was supported by the Russian Science Foundation and Kuban Science Foundation (project no. 22-14-20046). E.M., A.G., A.K., and R.A.I. were supported by the internal projects GTH-RND-2011 and GTH-RND-2112.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140580167","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}
Pub Date : 2024-04-08DOI: 10.1134/s0006297924030076
Tatiana F. Kikhai, Yulia Yu. Agapkina, Tatiana A. Prikazchikova, Maria V. Vdovina, Sofia P. Shekhtman, Sofia V. Fomicheva, Sergey P. Korolev, Marina B. Gottikh
Abstract
Structural organization of HIV-1 integrase is based on a tetramer formed by two protein dimers. Within this tetramer, the catalytic domain of one subunit of the first dimer interacts with the N-terminal domain of the second dimer subunit. It is the tetrameric structure that allows both ends of the viral DNA to be correctly positioned relative to the cellular DNA and to realize catalytic functions of integrase, namely 3′-processing and strand transfer. However, during the HIV-1 replicative cycle, integrase is responsible not only for the integration stage, it is also involved in reverse transcription and is necessary at the stage of capsid formation of the newly formed virions. It has been suggested that HIV-1 integrase is a structurally dynamic protein and its biological functions depend on its structure. Accordingly, studying interactions between the domains of integrase that provide its tetrameric structure is important for understanding its multiple functions. In this work, we investigated the role of three amino acids of the catalytic domain, I182, R187, and K188, located in the contact region of two integrase dimers in the tetramer structure, in reverse transcription and integration. It has been shown that the R187 residue is extremely important for formation of the correct integrase structure, which is necessary at all stages of its functional activity. The I182 residue is necessary for successful integration and is not important for reverse transcription, while the K188 residue, on the contrary, is involved in formation of the integrase structure, which is important for the effective reverse transcription.
摘要 HIV-1 整合酶的结构组织以两个二聚体蛋白形成的四聚体为基础。在这个四聚体中,第一个二聚体的一个亚基的催化结构域与第二个二聚体亚基的 N 端结构域相互作用。正是这种四聚体结构使病毒 DNA 的两端相对于细胞 DNA 正确定位,并实现整合酶的催化功能,即 3′处理和链转移。然而,在 HIV-1 复制周期中,整合酶不仅负责整合阶段,还参与反转录,并且在新形成的病毒的囊膜形成阶段也是必要的。有人认为,HIV-1 整合酶是一种结构动态蛋白,其生物功能取决于其结构。因此,研究提供四聚体结构的整合酶结构域之间的相互作用对于理解其多种功能非常重要。在这项工作中,我们研究了位于四聚体结构中两个整合酶二聚体接触区的催化结构域的三个氨基酸 I182、R187 和 K188 在反向转录和整合中的作用。研究表明,R187 残基对形成正确的整合酶结构极为重要,这在其功能活动的各个阶段都是必要的。I182 残基是成功整合所必需的,对反转录并不重要,而相反,K188 残基参与整合酶结构的形成,对有效的反转录非常重要。
{"title":"Role of I182, R187, and K188 Amino Acid Residues in the Catalytic Domain of HIV-1 Integrase in the Processes of Reverse Transcription and Integration","authors":"Tatiana F. Kikhai, Yulia Yu. Agapkina, Tatiana A. Prikazchikova, Maria V. Vdovina, Sofia P. Shekhtman, Sofia V. Fomicheva, Sergey P. Korolev, Marina B. Gottikh","doi":"10.1134/s0006297924030076","DOIUrl":"https://doi.org/10.1134/s0006297924030076","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>Structural organization of HIV-1 integrase is based on a tetramer formed by two protein dimers. Within this tetramer, the catalytic domain of one subunit of the first dimer interacts with the N-terminal domain of the second dimer subunit. It is the tetrameric structure that allows both ends of the viral DNA to be correctly positioned relative to the cellular DNA and to realize catalytic functions of integrase, namely 3′-processing and strand transfer. However, during the HIV-1 replicative cycle, integrase is responsible not only for the integration stage, it is also involved in reverse transcription and is necessary at the stage of capsid formation of the newly formed virions. It has been suggested that HIV-1 integrase is a structurally dynamic protein and its biological functions depend on its structure. Accordingly, studying interactions between the domains of integrase that provide its tetrameric structure is important for understanding its multiple functions. In this work, we investigated the role of three amino acids of the catalytic domain, I182, R187, and K188, located in the contact region of two integrase dimers in the tetramer structure, in reverse transcription and integration. It has been shown that the R187 residue is extremely important for formation of the correct integrase structure, which is necessary at all stages of its functional activity. The I182 residue is necessary for successful integration and is not important for reverse transcription, while the K188 residue, on the contrary, is involved in formation of the integrase structure, which is important for the effective reverse transcription.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140586763","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}
Pub Date : 2024-04-08DOI: 10.1134/s0006297924030106
Daria A. Belinskaia, Natalia N. Shestakova
Abstract
Some tricyclic antidepressants (TCAs), including amitriptyline (ATL), clomipramine (CLO), and desipramine (DES), are known to be effective for management of neuropathic pain. It was previously determined that ATL, CLO, and DES are capable of voltage-dependent blocking of NMDA receptors of glutamate (NMDAR), which play a key role in pathogenesis of neuropathic pain. Despite the similar structure of ATL, CLO, and DES, efficacy of their interaction with NMDAR varies significantly. In the study presented here, we applied molecular modeling methods to investigate the mechanism of binding of ATL, CLO, and DES to NMDAR and to identify structural features of the drugs that determine their inhibitory activity against NMDAR. Molecular docking of the studied TCAs into the NMDAR channel was performed. Conformational behavior of the obtained complexes in the lipid bilayer was simulated by the method of molecular dynamics (MD). A single binding site (upper) for the tertiary amines ATL and CLO and two binding sites (upper and lower) for the secondary amine DES were identified inside the NMDAR channel. The upper and lower binding sites are located along the channel axis at different distances from the extracellular side of the plasma membrane. MD simulation revealed that the position of DES in the lower site is stabilized only in the presence of sodium cation inside the NMDAR channel. DES binds more strongly to NMDAR compared to ATL and CLO due to simultaneous interaction of two hydrogen atoms of its cationic group with the asparagine residues of the ion pore of the receptor. This feature may be responsible for the stronger side effects of DES. It has been hypothesized that ATL binds to NMDAR less efficiently compared to DES and CLO due to its lower conformational mobility. The identified features of the structure- and cation-dependent mechanism of interaction between TCAs and NMDAR will help in the further development of effective and safe analgesic therapy.
摘要一些三环类抗抑郁药(TCAs),包括阿米替林(ATL)、氯米帕明(CLO)和去甲丙咪嗪(DES),已知可有效治疗神经病理性疼痛。先前已确定 ATL、CLO 和 DES 能够电压依赖性阻断谷氨酸 NMDA 受体(NMDAR),而 NMDAR 在神经病理性疼痛的发病机制中起着关键作用。尽管 ATL、CLO 和 DES 的结构相似,但它们与 NMDAR 相互作用的功效却大不相同。在本文介绍的研究中,我们应用分子建模方法研究了 ATL、CLO 和 DES 与 NMDAR 的结合机制,并确定了决定其 NMDAR 抑制活性的药物结构特征。研究人员对所研究的 TCA 与 NMDAR 通道进行了分子对接。利用分子动力学(MD)方法模拟了所获复合物在脂质双分子层中的构象行为。在 NMDAR 通道内确定了叔胺 ATL 和 CLO 的单个结合位点(上部)以及仲胺 DES 的两个结合位点(上部和下部)。上部和下部结合位点沿通道轴线分布,与细胞质膜外侧的距离不同。MD 模拟显示,只有在 NMDAR 通道内存在钠离子时,DES 在下部位点的位置才会稳定。与 ATL 和 CLO 相比,DES 与 NMDAR 的结合力更强,这是因为其阳离子基团的两个氢原子同时与受体离子孔的天冬酰胺残基相互作用。这一特点可能是 DES 产生较强副作用的原因。据推测,与 DES 和 CLO 相比,ATL 与 NMDAR 的结合效率较低,因为其构象流动性较低。所发现的 TCA 与 NMDAR 之间结构和阳离子依赖性相互作用机制的特征将有助于进一步开发有效、安全的镇痛疗法。
{"title":"Structure- and Cation-Dependent Mechanism of Interaction of Tricyclic Antidepressants with NMDA Receptor According to Molecular Modeling Data","authors":"Daria A. Belinskaia, Natalia N. Shestakova","doi":"10.1134/s0006297924030106","DOIUrl":"https://doi.org/10.1134/s0006297924030106","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>Some tricyclic antidepressants (TCAs), including amitriptyline (ATL), clomipramine (CLO), and desipramine (DES), are known to be effective for management of neuropathic pain. It was previously determined that ATL, CLO, and DES are capable of voltage-dependent blocking of NMDA receptors of glutamate (NMDAR), which play a key role in pathogenesis of neuropathic pain. Despite the similar structure of ATL, CLO, and DES, efficacy of their interaction with NMDAR varies significantly. In the study presented here, we applied molecular modeling methods to investigate the mechanism of binding of ATL, CLO, and DES to NMDAR and to identify structural features of the drugs that determine their inhibitory activity against NMDAR. Molecular docking of the studied TCAs into the NMDAR channel was performed. Conformational behavior of the obtained complexes in the lipid bilayer was simulated by the method of molecular dynamics (MD). A single binding site (upper) for the tertiary amines ATL and CLO and two binding sites (upper and lower) for the secondary amine DES were identified inside the NMDAR channel. The upper and lower binding sites are located along the channel axis at different distances from the extracellular side of the plasma membrane. MD simulation revealed that the position of DES in the lower site is stabilized only in the presence of sodium cation inside the NMDAR channel. DES binds more strongly to NMDAR compared to ATL and CLO due to simultaneous interaction of two hydrogen atoms of its cationic group with the asparagine residues of the ion pore of the receptor. This feature may be responsible for the stronger side effects of DES. It has been hypothesized that ATL binds to NMDAR less efficiently compared to DES and CLO due to its lower conformational mobility. The identified features of the structure- and cation-dependent mechanism of interaction between TCAs and NMDAR will help in the further development of effective and safe analgesic therapy.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140586751","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}
Pub Date : 2024-04-08DOI: 10.1134/s0006297924030155
Olga O. Sokol, Nikolai A. Nikitin, Ekaterina A. Evtushenko, Olga V. Karpova, Irina N. Matveeva, Svetlana A. Gryn, Vera M. Popova, Igor V. Ivanov, Yuri N. Fedorov, Irina Y. Litenkova
Abstract
Rabies is a zoonotic disease with high lethality. Most human deaths are associated with the bites received from dogs and cats. Vaccination is the most effective method of preventing rabies disease in both animals and humans. In this study, the ability of an adjuvant based on recombinant Salmonella typhimurium flagellin to increase protective activity of the inactivated rabies vaccine in mice was evaluated. A series of inactivated dry culture vaccine for dogs and cats “Rabikan” (strain Shchelkovo-51) with addition of an adjuvant at various dilutions were used. The control preparation was a similar series of inactivated dry culture vaccine without an adjuvant. Protective activity of the vaccine preparations was evaluated by the NIH potency test, which is the most widely used and internationally recommended method for testing effectiveness of the inactivated rabies vaccines. The value of specific activity of the tested rabies vaccine when co-administered with the adjuvant was significantly higher (48.69 IU/ml) than that of the vaccine without the adjuvant (3.75 IU/ml). Thus, recombinant flagellin could be considered as an effective adjuvant in the composition of future vaccine preparations against rabies virus.
{"title":"Protective Activity of Inactivated Rabies Vaccine Using Flagellin-Based Adjuvant","authors":"Olga O. Sokol, Nikolai A. Nikitin, Ekaterina A. Evtushenko, Olga V. Karpova, Irina N. Matveeva, Svetlana A. Gryn, Vera M. Popova, Igor V. Ivanov, Yuri N. Fedorov, Irina Y. Litenkova","doi":"10.1134/s0006297924030155","DOIUrl":"https://doi.org/10.1134/s0006297924030155","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Abstract</h3><p>Rabies is a zoonotic disease with high lethality. Most human deaths are associated with the bites received from dogs and cats. Vaccination is the most effective method of preventing rabies disease in both animals and humans. In this study, the ability of an adjuvant based on recombinant <i>Salmonella typhimurium</i> flagellin to increase protective activity of the inactivated rabies vaccine in mice was evaluated. A series of inactivated dry culture vaccine for dogs and cats “Rabikan” (strain Shchelkovo-51) with addition of an adjuvant at various dilutions were used. The control preparation was a similar series of inactivated dry culture vaccine without an adjuvant. Protective activity of the vaccine preparations was evaluated by the NIH potency test, which is the most widely used and internationally recommended method for testing effectiveness of the inactivated rabies vaccines. The value of specific activity of the tested rabies vaccine when co-administered with the adjuvant was significantly higher (48.69 IU/ml) than that of the vaccine without the adjuvant (3.75 IU/ml). Thus, recombinant flagellin could be considered as an effective adjuvant in the composition of future vaccine preparations against rabies virus.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":null,"pages":null},"PeriodicalIF":2.8,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140586838","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}