Biochemistry (Moscow)最新文献

{"title":"Genetic and Molecular Basis of Cone Opsin Phototransduction","authors":"Hanwen Cao,&nbsp;Nora Puig-Puig,&nbsp;Alejandro Cruz,&nbsp;Karl-Wilhelm Koch,&nbsp;Pere Garriga","doi":"10.1134/S0006297926601061","DOIUrl":"10.1134/S0006297926601061","url":null,"abstract":"<p>The vertebrate visual system contains a sophisticated physiological assembly of highly-specialized proteins that mediate light stimuli to be processed by the brain. Two types of cells, the rod and cone cells, are involved in detecting dim and bright light, respectively. The rod cell contains rhodopsin whose structure and function has been extensively studied and the molecular interactions involving rhodopsin and the other proteins of the phototransduction cascade have been dissected in great detail, although several mechanistic features remain to be determined. The cone phototransduction process has been less studied, particularly at the cone opsin structural level, and some conformational and mechanistic information has been inferred from analogy to the rod system. In spite of this, current efforts of investigation are focused on the study of the structure and function of cone opsins and other proteins of the cone phototransduction system. In this review we cover the current knowledge on the genetic and molecular aspects of cone opsins and the consequences of cone opsin mutations on the structure and function of these photoreceptor proteins causing vision disorders ranging from mild color vision abnormalities to severe cone-mediated retinal degeneration. A second part of the review is dedicated to the analysis of the molecular interactions involving calcium-binding proteins (such as recoverin and guanylate cyclase-activating proteins) in zebrafish which has emerged as a very useful model organism for the study of cone opsin phototransduction particularly in the deactivation steps of the visual phototransduction cascade.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":"91 8","pages":"1341 - 1358"},"PeriodicalIF":2.1,"publicationDate":"2026-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148838331","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}

{"title":"Erratum to: Diagnostics of Synucleinopathies by Protein Amplification Methods: Methodological and Bibliometric Analysis","authors":"Alexander A. Groshkov,&nbsp;Nataliya A. Kolotyeva,&nbsp;Pavel P. Tregub,&nbsp;Victoria I. Zhdankina,&nbsp;Yulia K. Komleva,&nbsp;Alla B. Salmina,&nbsp;Sergey N. Illarioshkin","doi":"10.1134/S0006297926080018","DOIUrl":"10.1134/S0006297926080018","url":null,"abstract":"","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":"91 8","pages":"1480 - 1480"},"PeriodicalIF":2.1,"publicationDate":"2026-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148838305","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}

{"title":"Photoreversible Reactions of Visual and Microbial Rhodopsins","authors":"Mikhail A. Ostrovsky,&nbsp;Olga A. Smitienko,&nbsp;Tatiana B. Feldman","doi":"10.1134/S0006297926601267","DOIUrl":"10.1134/S0006297926601267","url":null,"abstract":"<p>The review discusses experimental findings and theoretical studies of photoreversible transformations of retinal-containing proteins (rhodopsins). Understanding these processes is essential for elucidating the mechanisms of photochemical and conformational transformations of these proteins. Particular emphasis is placed on visual rhodopsins, as photoreversibility plays a crucial role in its physiological regeneration in the rhabdoms of invertebrates and the cone photoreceptors of the vertebrate retina. In recent years, interest in the mechanisms of photoreversible reactions in retinal-containing proteins has grown substantially, driven by their potential applications as active components in optoelectronic devices and biosensors.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":"91 8","pages":"1359 - 1375"},"PeriodicalIF":2.1,"publicationDate":"2026-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148838332","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}

{"title":"EF-Hand Calcium-Binding Motif: Novel Structural and Functional Insights","authors":"Konstantin A. Denessiouk,&nbsp;Evgeny A. Permyakov,&nbsp;Alexander I. Denesyuk,&nbsp;Sergey E. Permyakov","doi":"10.1134/S0006297926601115","DOIUrl":"10.1134/S0006297926601115","url":null,"abstract":"<p>The EF-hand motif is one of the most widespread calcium-binding protein motifs in nature, mediating calcium signaling across a variety of biological processes. While structural and functional properties of the individual proteins within the EF-hand superfamily are well studied, general principles governing organization and function of these proteins are only now being elucidated. This review examines some of these emerging patterns, including recently discovered structural elements of the EF-hand motif (EF-hand zone, one-residue and three-residue units, local “Clamp” units, and “black” and “gray” clusters). Additionally, we discuss the ability of certain EF-hand proteins to recognize a broad spectrum of protein targets, as well as their zinc-binding properties. New structural data on the EF-hand domain allow proposing a structural-functional classification for the proteins in this family. Furthermore, tendency of some EF-hand proteins toward promiscuity and zinc binding significantly expands their functional importance.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":"91 8","pages":"1376 - 1395"},"PeriodicalIF":2.1,"publicationDate":"2026-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148838094","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}

{"title":"Experimental Models of Acute Liver Failure in Mice: From Pathogenesis and Inflammatory Cascades to the Role of Intestine","authors":"Fedor A. Sysonov,&nbsp;Ekaterina A. Gorshkova,&nbsp;Konstantin E. Menshikov,&nbsp;Marina S. Drutskaya,&nbsp;Sergey A. Nedospasov,&nbsp;Ekaterina O. Gubernatorova","doi":"10.1134/S000629792660239X","DOIUrl":"10.1134/S000629792660239X","url":null,"abstract":"<p>Acute liver failure (ALF) is a severe pathological condition with high mortality, arising from diverse etiologies and involving multiple pathogenetic mechanisms. ALF is often accompanied by multi-organ failure due to infectious complications. Because of disease’s rapid progression, clinical studies of ALF remain limited, making the search for novel therapeutic strategies targeting specific molecular pathways and biochemical cascades a pressing task. Preclinical <i>in vivo</i> models are unique tools for reproducing individual aspects of ALF development. However, there is still no consensus on the gold-standard experimental animal model that fully captures ALF pathogenesis. This review systematically categorizes existing mouse models of ALF, outlining their advantages and with respect to the translational applicability of the data obtained. Among these models, we highlight the LPS/D‑GalN model as the most reliable in reproducing key stages of ALF development complicated by bacterial infection. Using this model as an example, we describe the known stages of pathogenesis, supported by the experiments with pharmacologically active substances and the use of various genetically modified mouse lines. Finally, special attention is given to the intestine as an organ that sustains significant damage during ALF progression in both clinical cases and most animal models.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":"91 8","pages":"1432 - 1448"},"PeriodicalIF":2.1,"publicationDate":"2026-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148838186","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}

{"title":"Age-Related Alterations in Retinal Monoamine Neuromodulation during AMD-Like Retinopathy Development in Rats","authors":"Darya V. Telegina,&nbsp;Alena O. Kutlimetova,&nbsp;Arseniy E. Izyurov,&nbsp;Alexander V. Kulikov,&nbsp;Nataliya G. Kolosova","doi":"10.1134/S0006297926600870","DOIUrl":"10.1134/S0006297926600870","url":null,"abstract":"<p>Aging is the major risk factor for age-related macular degeneration (AMD), a leading cause of vision loss in aging populations. Increasing evidence suggests that alterations of neurotransmitter systems contribute to the pathogenesis of AMD. Although biogenic amines in the retina were first detected over 50 years ago, their age-related dynamics and role in AMD development are still poorly understood. Here, we compare age-related changes in the concentrations of norepinephrine, serotonin, dopamine, and their main metabolites in the retinas of senescence-accelerated OXYS rats that develop an AMD-like retinopathy and Wistar rats. We also assessed activities of monoamine oxidases (MAOs) and tyrosine hydroxylase and compared changes in these activities with transcriptome data on genes associated with biogenic amine pathways. The results revealed that in OXYS rats, retinal aging and progression of AMD-like retinopathy are primarily associated with alterations in the dopaminergic system. Specifically, dopamine and its main metabolite DOPAC were present in the retinas at higher levels than serotonin and 5-hydroxyindoleacetic acid. Furthermore, the development of retinopathy in OXYS rats was accompanied by elevated dopamine and DOPAC levels, decreased MAO activity, and changes in the expression of genes associated with the dopaminergic synapse signaling.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":"91 8","pages":"1406 - 1416"},"PeriodicalIF":2.1,"publicationDate":"2026-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148838335","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}

{"title":"Differential S-Acylation of Viral and Cellular Proteins: Structural Determinants, Enzymes, and Putative Functional Implications","authors":"Larisa V. Kordyukova,&nbsp;Marina V. Serebryakova,&nbsp;Irina S. Panina,&nbsp;Michael Veit","doi":"10.1134/S0006297926601905","DOIUrl":"10.1134/S0006297926601905","url":null,"abstract":"<p>S-acylation is post-translational attachment of fatty acid residues, mostly palmitoyl-groups to cysteines. This lipid modification could influence protein oligomerization, localization, and topology within the membrane, and could play a regulatory role in cellular signaling. Improvements in the experimental techniques, specifically, MALDI-TOF MS, have elevated the study of S-acylation to a level of refined detail. It was possible to conclusively show that, beyond palmitate, other types of fatty acids, such as stearate and oleate could be attached to the specific binding sites. For example, fusion proteins of the enveloped viruses have been shown to attach stearates exclusively to the cysteine located at the C-terminal end of the transmembrane domain, while cysteines in the cytoplasmic domain have been modified with palmitates. In addition, emerging evidence suggests that the covalently linked fatty acids in the viral fusion proteins could recruit cholesterol into the viral membrane. We termed this preferential attachment of fatty acid residues of different types to the specific sites, depending on their localization, as “differential” S-acylation. Furthermore, MALDI-TOF MS detected attachment of unsaturated fatty acids (oleates) to the GNAI protein in response to stearate supplementation, shifting this regulatory protein out of the detergent-resistant membranes (lipid rafts) and, consequently, exerting antitumor effect. Solving the first 3D-structures of DHHC acyltransferases allowed proposing a mechanism of different fatty acids selection. However, it remains unclear whether preference for the acyl chain length is determined by the structure of the enzyme, protein substrate, or by the lipid composition of the membrane. In this review, we summarize the latest advances in the study of protein S-acylation with different types of fatty acids and substantiate significance of this post-translational modification from both fundamental and practical perspectives.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":"91 7","pages":"1157 - 1173"},"PeriodicalIF":2.1,"publicationDate":"2026-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148628485","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}

{"title":"Generation of Bacteriochlorophyll Triplets by the Mutant Reaction Center of Cereibacter sphaeroides G(M71)L/A(M260)W","authors":"Tatiana Yu. Fufina,&nbsp;Ivan I. Proskuryakov,&nbsp;Irina B. Klenina,&nbsp;Lyudmila G. Vasilyeva","doi":"10.1134/S0006297926601279","DOIUrl":"10.1134/S0006297926601279","url":null,"abstract":"<p>In the photosynthetic membrane of the purple non-sulfur bacterium <i>Cereibacter sphaeroides</i>, light energy is absorbed by the pigments of light-harvesting complexes and transferred to the photoreaction center (RC), where it is converted into the electrochemical energy of separated charges. Molecules of the bacteriochlorophyll (BChl) dimer P, monomeric BChl, bacteriopheophytin, and ubiquinone are involved in the process of photoinduced electron transfer in RCs. At all stages of the photochemical process, triplet states of pigments are produced with a certain probability, which in native RCs are quenched by the carotenoid molecules. In this study, probability of the bacteriochlorophyll triplet states formation in RCs was artificially increased using site-directed mutagenesis. The amino acid substitution Ala-M260 → Trp leads to the removal of ubiquinone molecule from the active electron transfer branch of the RC, while the Gly-M71 → Leu substitution closes the carotenoid binding site. As a result, electron transfer from the primary donor P to ubiquinone is blocked, leading to rapid recombination of the separated charges and formation of the P triplets. In this work, we investigated thermal stability, spectral and photochemical properties of the mutant RC, as well as EPR spectra, and lifetime of P triplets under various conditions. It was shown that in the double mutant RC, deactivation of the triplet state of P is slowed down, and its interaction with oxygen is observed, apparently generating population of the chemically active state of singlet-excited oxygen. The obtained RCs are of interest for biotechnological applications as potential photosensitizers.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":"91 7","pages":"1256 - 1264"},"PeriodicalIF":2.1,"publicationDate":"2026-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148628488","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}

{"title":"Substrate Specificity of T4 RNA Ligase 1 in Intramolecular Ligation of Single-Stranded DNA","authors":"Assol R. Sakhabutdinova,&nbsp;Ayzilya A. Shakirova,&nbsp;Ravil R. Garafutdinov","doi":"10.1134/S0006297925603983","DOIUrl":"10.1134/S0006297925603983","url":null,"abstract":"<p>Ligation of nucleic acids by DNA and RNA ligases is a routine method in molecular biology. Enzymatic ligation is increasingly used in the development of novel methods for detecting specific nucleotide sequences, as well as in non-biological DNA application. In this study, we investigated how the type of 5′- and 3′-terminal nucleotides affects the efficiency of single-stranded DNA cyclization. Model oligodeoxyribonucleotides (ODNs) 23, 39, and 45 nucleotides in length, representing all possible combinations of the donor and acceptor terminal nucleotides, were used as substrates. The substrate specificity of T4 RNA ligase 1 was assessed by analyzing the primary structure of amplicons generated through rolling circle amplification (RCA) of ligation products. For longer ODNs (39 and 45 nt), T4 RNA ligase 1 most efficiently cyclized substrates containing 5′-CC or 5′-TT donor dinucleotides and 3′-AA acceptor dinucleotide. Among the 23-nt ODNs, efficient cyclization was observed predominantly for a single substrate containing 5′-TT and 3′-AA terminal dinucleotides, likely reflecting a greater flexibility of AT-rich DNA. Substrates containing 5′-dGG and 3′-dGG dinucleotides showed the lowest propensity for cyclization. These findings provide guidance for selecting substrate sequences that maximize the yield of circular DNA products.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":"91 7","pages":"1174 - 1186"},"PeriodicalIF":2.1,"publicationDate":"2026-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1134/S0006297925603983.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148628722","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Regulation of Neutrophil Adhesion and Immune Response: Influence of ATP, Adenosine, and Iodoacetic Acid","authors":"Svetlana I. Galkina,&nbsp;Ekaterina A. Golenkina,&nbsp;Alexander L. Ksenofontov,&nbsp;Marina V. Serebryakova,&nbsp;Larisa V. Kordyukova,&nbsp;Natalia V. Fedorova,&nbsp;Vladimir I. Stadnichuk,&nbsp;Ludmila A. Baratova,&nbsp;Galina F. Sud’ina","doi":"10.1134/S0006297926601243","DOIUrl":"10.1134/S0006297926601243","url":null,"abstract":"<p>Neutrophils, key effector cells of the innate immune system, infiltrate infected tissues, adhere to them, and destroy pathogens by releasing the bactericidal content of intracellular granules and producing reactive oxygen species (ROS) and nitric oxide (NO). However, these aggressive antimicrobial products of neutrophil secretion can damage surrounding tissues and initiate inflammation. Adenosine, which is produced in excess by damaged tissues, is known to limit the neutrophil immune response and suppress inflammation, acting primarily through adenosine receptors. We compared the effects of ATP, adenosine, and iodoacetic acid (IAA), an inhibitor of glycolysis, on neutrophil adhesion to fibronectin and accompanying secretion of free amino acids, proteins, ROS, and NO. Our results indicate that the immunosuppressive effect of adenosine is unlikely to be due to the inhibition of oxidative stress or protein secretion. Neither ATP nor adenosine altered ROS and NO production during neutrophil adhesion, whereas IAA suppressed it. ATP did not affect the composition of secreted proteins, while adenosine stimulated the release of aggressive components of primary granules. We also investigated previously undescribed dynamics of secretion of the amino acid hydroxylysine by neutrophils during adhesion: ATP stimulated, while adenosine and IAA selectively and strongly inhibited hydroxylysine release. Hydroxylysine is a product of lysyl hydroxylase (LH), whose expression and activity positively correlate with cell invasiveness and metastatic potential of various types of tumor cells. Given the similarities between neutrophils and tumor cells in energy metabolism and invasive capacity, we hypothesize that adenosine and IAA may suppress immune responses by inhibiting neutrophil infiltration into tissues through selective blocking of LH activity/hydroxylysine release. Further studies are required to directly test this hypothesis.</p>","PeriodicalId":483,"journal":{"name":"Biochemistry (Moscow)","volume":"91 7","pages":"1241 - 1255"},"PeriodicalIF":2.1,"publicationDate":"2026-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148628481","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}