Biochemistry (Moscow), Supplement Series A: Membrane and Cell Biology最新文献

{"title":"Testing SAXS Applicability for Detection of Illumination-Driven Structural Changes in the Purple Membranes from H. salinarum","authors":"A. Yu. Shishkin,&nbsp;D. D. Kuklina,&nbsp;E. A. Dronova,&nbsp;Yu. L. Ryzhykau","doi":"10.1134/S199074782470051X","DOIUrl":"10.1134/S199074782470051X","url":null,"abstract":"<p>Rhodopsins are photosensitive transmembrane proteins found in bacteria, archaea, and eukaryotes. Upon photon absorption, they undergo conformational changes critical for their physiological functions, such as ion transport and signal transduction. Microbial rhodopsins are key tools in optogenetics, with applications in biomedical research and clinical treatments. To advance optogenetic techniques, it is crucial to understand the molecular mechanisms of the rhodopsin photocycle. The key approach for studying these mechanisms, cryotrapping, has a setback associated with possible deterioration in resolution due to the unexpectedly large light-induced structural changes. To estimate the scale of these changes, small-angle X-ray scattering (SAXS) can be used. In this study, we applied SAXS to the investigation of light-induced structural changes in purple membranes (PMs) as their two-dimensional crystal organization makes them a suitable model object for studying light-induced changes in 3D rhodopsin crystals. SAXS data from illuminated and non-illuminated PM samples revealed detectable changes, including variations in membrane thickness and planar unit cell dimensions. Particularly, we observed a statistically significant increase in the radius of gyration for flat particles (<i>R</i>ₜ) of ~0.2 Å for the PMs with mutant <i>Hs</i>BR_E204Q, while no significant change was detected for wild-type <i>Hs</i>BR. However, wild-type <i>Hs</i>BR data showed a statistically significant shift in the (1, 1) Bragg peak position (Δ <i>q</i> ~ –10^–4 Å^–1; ~3% of the peak width) upon illumination. For <i>Hs</i>BR_E204Q data, the shift was two times greater; however, in this case due to the lower sample concentration ε_Δq was ~50%, making it difficult to compare the wild-type and mutant cases. Future experiments should aim for better signal-to-noise ratios using synchrotron radiation, higher sample concentrations, and longer exposure times.</p>","PeriodicalId":484,"journal":{"name":"Biochemistry (Moscow), Supplement Series A: Membrane and Cell Biology","volume":"19 1","pages":"99 - 105"},"PeriodicalIF":1.1,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143865409","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}

{"title":"Capabilities of SEC-SAXS Method in Research of Polydisperse Systems: The Case of Apoferritin","authors":"I. O. Bezruchko,&nbsp;D. D. Kuklina,&nbsp;E. A. Dronova,&nbsp;A. S. Kazantsev,&nbsp;A. A. Khokhlov,&nbsp;A. V. Vlasov,&nbsp;A. I. Kuklin,&nbsp;Yu. L. Ryzhykau","doi":"10.1134/S1990747824700405","DOIUrl":"10.1134/S1990747824700405","url":null,"abstract":"<p>Here we explore capabilities of size exclusion chromatography small-angle X-ray scattering method in case of horse spleen apoferritin solution as an example of a system with high oligomerization heterogeneity. For interpretation of the experimental data, we considered models of polydisperse solution containing monomers, dimers, and trimers of apoferritin globules. Dimers were defined only by intercenter distance <i>L</i>, while trimers were characterized by both <i>L</i> and apical corner value φ. We showed that a reasonable description of the major part of the chromatogram could be reached using the model containing monomers, dimers and one type of trimers with φ about 110°–120°. In the case of two types of trimers in the model, optimal φ values were 110°–140° and 90°–110°; however, the approximation results were considered as ambiguous. Validation of the preferred model (<i>L</i> = 12.5 nm, φ = 120°) showed insufficient description of the experimental data for the left part of the chromatogram (elution volume &lt;12.2 mL) indicating the presence of aggregates in these fractions. Application of the method provided the opportunity to calculate concentrations for oligomers consisting of less than four apoferritin globules, and select averaging range for different fractions properly.</p>","PeriodicalId":484,"journal":{"name":"Biochemistry (Moscow), Supplement Series A: Membrane and Cell Biology","volume":"19 1","pages":"20 - 26"},"PeriodicalIF":1.1,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143865452","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}

{"title":"Long Time-Scale Classical MD Simulation of Hymenobacter psoromatis Rhodopsin with Carotenoid: An Initial Step for Photochemical Investigation","authors":"A. Kh. Taldaev,&nbsp;D. A. Fedotov,&nbsp;I. S. Okhrimenko","doi":"10.1134/S1990747824700545","DOIUrl":"10.1134/S1990747824700545","url":null,"abstract":"<p>Nowadays, only a few structures of rhodopsins bound with carotenoid were obtained and functionally characterized. Nevertheless, rhodopsins-carotenoids complexes are promising molecular systems for understanding the light-harvesting process in bacteria since such complexes show ability to absorb a significant part of solar energy coming to the Earth surface. The understanding of energy absorption and transfer mechanisms in the carotenoid-retinal complex of rhodopsin would provide significant progress in different areas of modern bioscience such as ecology, protein engineering, optogenetics, etc. Here we present a long (1 µs) molecular dynamical investigation of the structure of microbial rhodopsin from an Antarctic bacterium <i>Hymenobacter</i> <i>psoromatis</i> (strain PAMC26554) (HbR1) and zeaxanthin. The structure of rhodopsin was predicted with a new multi-modal foundation for molecular structure prediction Chai-1 and used for classical MD validation in a 10 × 10 × 12 nm box in a hydrated explicit lipid bilayer. Our simulations show tight binding of the carotenoid and rhodopsin with the average distance equal to 0.25 nm between the closest atoms of carotenoid and retinal.</p>","PeriodicalId":484,"journal":{"name":"Biochemistry (Moscow), Supplement Series A: Membrane and Cell Biology","volume":"19 1","pages":"115 - 121"},"PeriodicalIF":1.1,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143865410","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}

{"title":"Comparative Analysis of High-Resolution Structures of Membrane Proteins","authors":"S. A. Zhuravlev,&nbsp;A. S. Kazantsev,&nbsp;S. D. Ivashchenko,&nbsp;D. D. Kuklina,&nbsp;Y. L. Ryzhykau","doi":"10.1134/S1990747824700594","DOIUrl":"10.1134/S1990747824700594","url":null,"abstract":"<p>This paper presents a statistical analysis and comparison of all existing as of November 20, 2024 membrane protein structures that are represented in the most widely used databases mpstruc, Orientations of Proteins in Membranes (OPM), SCOP and PDBTM, with the total number of structures now reaching 13956. We evaluated the resolution dependencies of structure-derived membrane proteins on their size-related physical characteristics, such as molecular weight, radius and size of the hydrophilic part. Based on the obtained dependencies, we compared the resolving methods of X-ray diffraction and electron microscopy structures, and also compared the methods of protein crystallization <i>in surfo</i> and <i>in meso</i>. The change over time in the number of membrane protein structures obtained by different methods was also examined to analyze trends in structural biology. In 2024, cryo-electron microscopy has emerged as the dominant method, contributing to nearly half of the solved structures, now representing 49.6% of the total. The obtained results demonstrate that the resolution of structures obtained by X-ray diffraction on protein crystals, on average, tends to worsen with increasing protein size, while in electron microscopy, which has recently gained enormous popularity, there is no such trend, but the average resolution is worse. It was also shown that the character of the dependence of resolution on protein size is the same (within error) for the two most common methods of membrane proteins crystallization: in lipid cubic phases (<i>in meso</i>) and in detergent micelles (<i>in surfo</i>). Thus, statistically, neither of these two methods can be considered a priori preferable for achieving better resolution.</p>","PeriodicalId":484,"journal":{"name":"Biochemistry (Moscow), Supplement Series A: Membrane and Cell Biology","volume":"19 1","pages":"145 - 149"},"PeriodicalIF":1.1,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143865381","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}

{"title":"Influence of Expression Temperature on the Adenosine Phosphate Bound State of Recombinant BsDesK","authors":"D. D. Kuklina,&nbsp;T. N. Murugova,&nbsp;M. I. Rulev,&nbsp;Yu. L. Ryzhykau","doi":"10.1134/S1990747824700478","DOIUrl":"10.1134/S1990747824700478","url":null,"abstract":"<p>In this study, we investigated thermosensitive histidine kinase DesK from <i>Bacillus subtilis</i> with the aim of obtaining a monodisperse protein preparation suitable for further structural studies. A homogeneous sample, both in terms of oligomeric state and ligand binding, is favorable for electron microscopy or X-ray diffraction applications. The binding of ATP is required for autophosphorylation activity of DesK, thus we aimed at developing heterologous expression techniques that would yield ATP-bound protein. We focused on two critical factors that may influence ATP binding: the nutrient composition of the growth medium and the expression temperature. Protein characterization was performed using size-exclusion chromatography, with absorbance monitored at both 280 and 260 nm to assess protein homogeneity and nucleotide binding. Our results indicate that while nutrient composition had a negligible effect on the relative amount of ATP-bound protein, expression temperature played a significant role. Specifically, lowering the expression temperature from 37°C to 20°C at the time of induction markedly increased the proportion of ATP-bound DesK oligomers.</p>","PeriodicalId":484,"journal":{"name":"Biochemistry (Moscow), Supplement Series A: Membrane and Cell Biology","volume":"19 1","pages":"66 - 72"},"PeriodicalIF":1.1,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143865557","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}

{"title":"The International Scientific Conference “Biomembranes 2024”","authors":"I. S. Okhrimenko,&nbsp;A. V. Mishin,&nbsp;I. Y. Gushchin","doi":"10.1134/S1990747824700375","DOIUrl":"10.1134/S1990747824700375","url":null,"abstract":"","PeriodicalId":484,"journal":{"name":"Biochemistry (Moscow), Supplement Series A: Membrane and Cell Biology","volume":"19 1","pages":"1 - 2"},"PeriodicalIF":1.1,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143865560","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}

{"title":"Trials of lux-Biosensors in Expeditions to the Northern Seas: Barents, Kara, and Laptev","authors":"G. V. Volkov,&nbsp;U. S. Novoyatlova,&nbsp;A. A. Utkina,&nbsp;V. I. Krolenko,&nbsp;O. P. Konovalova,&nbsp;S. V. Bazhenov,&nbsp;M. Yu. Kolobov,&nbsp;I. V. Manukhov","doi":"10.1134/S1990747824700582","DOIUrl":"10.1134/S1990747824700582","url":null,"abstract":"<p>Bacterial biosensors based on the <i>Escherichia coli</i> and <i>Bacillus subtilis</i> whole cells are used to study toxicological characteristics of biologically active compounds and toxicants, and are applicable for ecological studies. This work describes the trials of <i>lux</i>-biosensors in the marine research expedition in the northern seas: Barents, Kara, and Laptev. The presence of toxicants in samples of bottom sediments and tissues of marine invertebrates was estimated by the activation of stress promoters in biosensor cells. It was shown that the collected samples generally did not show toxicological characteristics in terms of the ability to activate oxidative stress and SOS response. However, several samples were able to activate transcription of the DNA glycosylase promoter in biosensor bacterial cells. This effect was shown for some samples of bottom sediments and arthropod tissues from <i>Mesidothea sabini</i> var. <i>sabini.</i>, Pycnogonida and some Amphipoda.</p>","PeriodicalId":484,"journal":{"name":"Biochemistry (Moscow), Supplement Series A: Membrane and Cell Biology","volume":"19 1","pages":"139 - 144"},"PeriodicalIF":1.1,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143865382","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}

{"title":"The Role of Cristae Regulatory Proteins in Mitochondrial Dysfunction in an Experimentally Induced Hyperthyroidism Model","authors":"N. I. Venediktova,&nbsp;I. N. Solomadin,&nbsp;V. P. Medvedeva","doi":"10.1134/S1990747824700570","DOIUrl":"10.1134/S1990747824700570","url":null,"abstract":"<p>In this work we investigated the rearrangements in the cristae structure and possible connection of these changes with the level of MICOS proteins in rat liver mitochondria in experimentally induced hyperthyroidism. A model of hyperthyroidism (HT) was induced by chronic administration of thyroxine. A change in the structure of liver mitochondria of hyperthyroid rats (HR) was found to consist of swollen organelles with a slightly altered number of cristae. A part of mitochondria (13%) in HR had vacuolized matrix with simultaneously reduced number of cristae. An increase in the protein levels of MIC 60, MIC 25, and MIC 19 was shown in the HT condition, while the quantity of MIC 10 was unchanged. In turn, the levels of SAMM 50 and OPA1 were reduced in HR. The data obtained indicate that excess thyroid hormones cause partial changes in the structure of liver mitochondria and reduce the content of SAMM50 and OPA1 proteins, which can be considered as possible targets for investigating therapeutic strategies for metabolic disorders associated with mitochondrial dysfunction.</p>","PeriodicalId":484,"journal":{"name":"Biochemistry (Moscow), Supplement Series A: Membrane and Cell Biology","volume":"19 1","pages":"133 - 138"},"PeriodicalIF":1.1,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143865385","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}

{"title":"Effects of 24-Hydroxycholesterol on the ATP-Induced Trigeminal Nerve Electrical Activity and the Mast Cells Degranulation","authors":"K. R. Gilizhdinova,&nbsp;D. A. Nurmieva,&nbsp;A. S. Ananev,&nbsp;A. M. Petrov,&nbsp;G. F. Sitdikova","doi":"10.1134/S1990747824700454","DOIUrl":"10.1134/S1990747824700454","url":null,"abstract":"<p>The trigeminovascular system plays a pivotal role in the generation of nociceptive activity, which underlies pain in migraine and includes trigeminal nerve afferents, dura mater vessels, and mast cells. Adenosine triphosphate (ATP) is one of the main mediators of the interaction between vessels, nerve endings, and mast cells. ATP activates P2X3 receptors of trigeminal nerve afferents and P2X7 receptors of mast cells. 24-Hydroxycholesterol is the primary brain cholesterol metabolite synthesized by neurons and is capable of freely entering the bloodstream by crossing the blood–brain barrier. The purpose of this study was to examine the impact of 24-hydroxycholesterol on the electrical activity of trigeminal nerve afferents triggered by ATP application and on the mast cells degranulation in rat brain meninges. The electrical activity of the trigeminal nerve was recorded using an extracellular electrode in a rat hemiskull preparation, mast cells were stained with toluidine blue. 24-Hydroxycholesterol had no direct effect on the frequency of action potentials of trigeminal nerve but suppressed the response triggered by ATP application. Furthermore, incubation of meninges in 24-hydroxycholesterol resulted in a reduction in mast cell degranulation in response to ATP. Therefore, 24-hydroxycholesterol prevented the activation of trigeminal afferents either directly by reducing the activity of ionotropic ATP receptors or indirectly by stabilizing mast cells.</p>","PeriodicalId":484,"journal":{"name":"Biochemistry (Moscow), Supplement Series A: Membrane and Cell Biology","volume":"19 1","pages":"52 - 59"},"PeriodicalIF":1.1,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143865455","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}

{"title":"Effects of Carbamylated Darbepoetin on Mitochondrial Contacts in Primary Neuronal Cultures","authors":"O. M. Shirokova,&nbsp;R. A. Sokolov,&nbsp;V. I. Pershin,&nbsp;M. S. Guseva,&nbsp;I. V. Mukhina","doi":"10.1134/S1990747824700521","DOIUrl":"10.1134/S1990747824700521","url":null,"abstract":"<p>Erythropoietin (EPO) is a hormone that plays a dual role: it regulates erythropoiesis and works as a neuroprotector, the synthesis of which is activated by brain cells in response to hypoxia. Several clinical trials showed that administration of EPO against anemia caused the improvement of cognitive brain functions, however the mechanisms of this action have not yet been characterized. Recently, the usage of Carbamylated darbepoetin (CdEpo), which is neuroprotective but lacks hematopoietic activity and has a more prolonged half-life, has become an attractive tool. The influence of administration of 100 ng/mL CdEpo on the activity and ultrastructural organization of mature hippocampal cultures in normoxic conditions was assessed. It was found that the application of CdEpo in normoxic conditions causes a negative neurotropic influence on neuronal activity that was measured via calcium imaging. Calcium imaging data revealed that CdEpo caused a decrease in the frequency of calcium oscillations; however, the duration of calcium events slightly increased. The decrease in neuronal activity upon administration of CdEpo coincided with compartment-dependent ultrastructural changes. In axons, there was an increase in total mitochondrial area with a decrease in mitochondrial and endoplasmic reticulum contact surface, and in neuronal soma, there was an increase in the surface of intermitochondrial contacts.</p>","PeriodicalId":484,"journal":{"name":"Biochemistry (Moscow), Supplement Series A: Membrane and Cell Biology","volume":"19 1","pages":"89 - 98"},"PeriodicalIF":1.1,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143865559","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}