Biochimie最新文献

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Phototropin localization and interactions regulate photophysiological processes in Chlamydomonas reinhardtii. 趋光素定位和相互作用调节莱茵衣藻的光生理过程。
IF 3
Biochimie Pub Date : 2025-08-16 DOI: 10.1016/j.biochi.2025.08.014
Sunita Sharma, Kumari Sushmita, Rajani Singh, Sibaji K Sanyal, Suneel Kateriya
{"title":"Phototropin localization and interactions regulate photophysiological processes in Chlamydomonas reinhardtii.","authors":"Sunita Sharma, Kumari Sushmita, Rajani Singh, Sibaji K Sanyal, Suneel Kateriya","doi":"10.1016/j.biochi.2025.08.014","DOIUrl":"10.1016/j.biochi.2025.08.014","url":null,"abstract":"<p><p>Phototropin, a blue-light sensing serine/threonine kinase, plays a pivotal role in regulating diverse photophysiological processes in both plants and algae. In Chlamydomonas reinhardtii, phototropin (CrPhot) localizes to the eyespot and flagella, coordinating key cellular functions such as phototaxis, photosynthesis, gametogenesis, and chlorophyll biosynthesis. Although prior studies have identified phototropin interactions with signaling proteins such as channelrhodopsins and light-harvesting complex proteins, its broader interaction network and regulatory mechanisms remain poorly understood. In this study, we identified novel protein partners of phototropin and their roles in modulating its regulatory functions in C. reinhardtii. Employing a range of intraflagellar transport (IFT) mutants of C. reinhardtii, we demonstrated that phototropin localization to the flagella and eyespot is IFT-mediated. Our results reveal novel interactions between phototropin and other photoreceptors, including-channelrhodopsins (ChR1 and ChR2), chlamyopsin 6, LOV-histidine kinases (LOV-HK1, LOV-HK2) and the signaling protein- 14-3-3. CRISPR-Cas9 generated knockouts of phototropin led to reduced expression of ChR1 and 14-3-3, accompanied by impaired photomotility of the mutants. Additionally, gene expression of LOV-HK1 and LOV-HK2 were found to be elevated under UV-light in C. reinhardtii and these had altered expression in phototropin knockout line. These findings provide novel insights into phototropin interactome and elucidate molecular mechanisms underlying its localization and signaling functions in C. reinhardtii. This work advances our understanding of phototropin-mediated signal transduction and lays the groundwork for future exploration of its broader physiological roles in cellular responses.</p>","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144877237","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Using protein blocks to build custom fragment libraries from protein structures. 使用蛋白质块从蛋白质结构构建自定义片段库。
IF 3
Biochimie Pub Date : 2025-08-13 DOI: 10.1016/j.biochi.2025.08.011
Surbhi Dhingra, Stéphane Téletchéa, Ramanathan Sowdhamini, Yves-Henri Sanejouand, Alexandre G de Brevern, Frédéric Cadet, Bernard Offmann
{"title":"Using protein blocks to build custom fragment libraries from protein structures.","authors":"Surbhi Dhingra, Stéphane Téletchéa, Ramanathan Sowdhamini, Yves-Henri Sanejouand, Alexandre G de Brevern, Frédéric Cadet, Bernard Offmann","doi":"10.1016/j.biochi.2025.08.011","DOIUrl":"10.1016/j.biochi.2025.08.011","url":null,"abstract":"<p><p>The remarkable structural diversity of modern proteins reflects millions of years of evolution, during which sequence space has expanded while many structural features remain conserved. This conservation is evident not only among homologous proteins but also in the recurrence of supersecondary motifs across unrelated proteins, underscoring the abundance and robustness of these structural units. Here, we present a novel pipeline for generating customized protein fragment libraries using protein blocks (PBs)-a structural alphabet that encodes local backbone conformations. Our method efficiently extracts structurally similar fragments from a curated, non-redundant protein structure database by converting three-dimensional structures into one-dimensional PB sequences. By integrating predicted PB sequences with the PB-ALIGN and PB-kPRED tools, our approach identifies relevant fragments independently of sequence homology. Fragment quality is further assessed using a new scoring function that combines secondary structure similarity and PB alignment metrics. The resulting libraries contain fragments of at least seven PBs (11 amino acid residues), covering over 70 % of the local backbone structure. Our results demonstrate that PBs enable efficient mining of high-quality structural fragments from diverse protein spaces, including proteins with disordered regions. The pipeline is accessible as an online tool (PB-Frag, http://pbpred-us2b.univ-nantes.fr/pbfrag).</p>","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-08-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144859983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Inhibition of proteolytic activity of Bothrops alternatus venom by two small molecules and docking analysis against a snake venom metalloproteinase. 两个小分子抑制蛇毒蛋白水解活性及其与蛇毒金属蛋白酶的对接分析。
IF 3
Biochimie Pub Date : 2025-08-12 DOI: 10.1016/j.biochi.2025.08.009
Silvina M Echeverría, Giuliana C Blanco, María Del Carmen Gauna Pereira, Silvana L Maruñak, José M Ferreras, Claudia C Gay
{"title":"Inhibition of proteolytic activity of Bothrops alternatus venom by two small molecules and docking analysis against a snake venom metalloproteinase.","authors":"Silvina M Echeverría, Giuliana C Blanco, María Del Carmen Gauna Pereira, Silvana L Maruñak, José M Ferreras, Claudia C Gay","doi":"10.1016/j.biochi.2025.08.009","DOIUrl":"10.1016/j.biochi.2025.08.009","url":null,"abstract":"<p><p>The only effective treatment against snakebites is the administration of antivenom. Snake venom metalloproteinases (SVMPs) play a key role in the pathogenesis of envenomation. In this work, the ability of two molecules to inhibit the proteolytic activity of Bothrops alternatus venom and its PIII SVMP (baltergin) was studied: a dye (alizarin red S: Az) and a vitamin (l-ascorbic acid: AA). Neutralization of hemorrhage and docking analysis were also carried out. The inhibition of the proteolytic activity, showed the IC<sub>50</sub> for Az (3.6 mM) was 52 times lower than for AA (188.2 mM). Az was not only able to inhibit casein degradation but also a milk protein compatible with beta-lactoglobulin, meanwhile AA was only capable of inhibit the degradation of casein. Both molecules were able to completely inhibit the action of baltergin on casein degradation. It was also observed that the antioxidant activity of Az increased, while the activity of AA decreased after exposition to visible radiation. As a result, Az induced an increase in its proteolytic inhibitory potential, although no significant changes were observed with AA. A partial neutralization of hemorrhage was observed, representing 46 % of inhibition, only for Az at a venom:molecule ratio (m:m) of 1:4. It was demonstrated that Az interacts with PIII SVMPs through more bonds than with AA, which makes it fit better in the vicinity of the catalytic site. Natural (or synthetic) dyes open up a new range of possibilities for exploring alternatives for the complementary treatment of snakebites.</p>","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144857186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Evaluate the impact of PM2.5 in different macrophage types under the influence of seasonal changes and anthropogenic activities. 评估PM2.5在季节变化和人为活动影响下对不同巨噬细胞类型的影响。
IF 3
Biochimie Pub Date : 2025-08-11 DOI: 10.1016/j.biochi.2025.08.010
Yung-Jui Chen, Meng-Hsin Li, Fang-Yi Gu, Yu-Cheng Chen, Hong-Lin Chan, Hsiu-Chuan Chou
{"title":"Evaluate the impact of PM<sub>2.5</sub> in different macrophage types under the influence of seasonal changes and anthropogenic activities.","authors":"Yung-Jui Chen, Meng-Hsin Li, Fang-Yi Gu, Yu-Cheng Chen, Hong-Lin Chan, Hsiu-Chuan Chou","doi":"10.1016/j.biochi.2025.08.010","DOIUrl":"10.1016/j.biochi.2025.08.010","url":null,"abstract":"<p><p>Particulate matter (PM) in air pollution has become a major environmental concern due to its potential health impacts, which vary seasonally and with human activities. While PM is often monitored for concentration, its chemical composition is equally important, especially regarding its effects on the immune system, which remain poorly understood. This study investigates the biological effects of PM2.5 on macrophages collected in different seasons and during COVID-19 restrictions in Taiwan. The experiments revealed significant seasonal variations in metal and polycyclic aromatic hydrocarbons (PAHs) content in PM2.5, with summer having the highest metal levels and winter the highest PAHs. Exposure to PM2.5 increased cell biotoxicity, correlating with higher PM2.5 concentrations. Further analysis showed that PM2.5 exposure polarized macrophages into the M1 type, triggering inflammatory cytokines, increased ROS levels, cell growth arrest, and apoptosis. Notably, PM2.5 from summer exhibited the highest biotoxicity. The study also identified four metals (Fe, Ti, Co, Sb) as key contributors to biotoxicity. PM2.5 collected during COVID-19 Level 2 Alert showed higher concentrations of these metals, resulting in greater toxicity to macrophages. This research underscores how seasonal changes and human activities influence PM2.5's impact on the immune system, contributing to air pollution control efforts.</p>","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144850017","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bacillus subtilis 6S-1 RNA regulates transcription of genes related to surfactin biosynthesis. 枯草芽孢杆菌6S-1 RNA调控表面素生物合成相关基因的转录。
IF 3
Biochimie Pub Date : 2025-08-11 DOI: 10.1016/j.biochi.2025.08.008
V S Trefilov, E Y Lindin, D E Elkina, M I Zvereva, V A Alferova, M A C Schlüter, R K Hartmann, E A Kubareva, O Y Burenina
{"title":"Bacillus subtilis 6S-1 RNA regulates transcription of genes related to surfactin biosynthesis.","authors":"V S Trefilov, E Y Lindin, D E Elkina, M I Zvereva, V A Alferova, M A C Schlüter, R K Hartmann, E A Kubareva, O Y Burenina","doi":"10.1016/j.biochi.2025.08.008","DOIUrl":"10.1016/j.biochi.2025.08.008","url":null,"abstract":"<p><p>The biosurfactant surfactin is a cyclic lipopeptide produced by different representatives of the genus Bacillus. It has a large surface activity and is considered as a prospective biodegradable detergent. In the present study, we investigated the impact of non-coding 6S-1 RNA - a global transcription regulator in bacteria - on surfactin biosynthesis in the undomesticated B. subtilis strain NCIB 3610. It was found by RT-qPCR that a 6S-1 RNA knockout (KO) (ΔbsrA, ΔA) leads to increase of mRNA levels of several genes positively affecting surfactin biosynthesis, in particular the surfactin synthetase operon srfA. However, the lack of 6S-1 RNA did not result in an increase of surfactin amounts secreted by NCIB 3610 cells, as was shown by colorimetric and HPLC methods. Likewise, expression analysis of a GFP reporter construct provided no evidence that elevated transcript levels derived from the srfA promoter are paralleled by higher levels of translation products in the ΔA strain. We further identified a number of key factors also dysregulated in the ΔA strain, including a 20-fold increased level of rocG mRNA encoding glutamate dehydrogenase, an enzyme that may deplete the building block L-glutamate required for surfactin synthesis. Here we present the first study that evaluates the role of 6S-1 RNA in surfactin biosynthesis. We demonstrated that the absence of the riboregulator 6S-1 RNA profoundly destabilizes mRNA levels of genes, related to surfactin biosynthesis, in the undomesticated B. subtilis NCIB 3610.</p>","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144850016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A 25-year journey with protein blocks: Unveiling the versatility of a structural alphabet. 25年的蛋白质块之旅:揭示结构字母表的多功能性。
IF 3
Biochimie Pub Date : 2025-08-09 DOI: 10.1016/j.biochi.2025.08.007
Bernard Offmann, Alexandre G de Brevern
{"title":"A 25-year journey with protein blocks: Unveiling the versatility of a structural alphabet.","authors":"Bernard Offmann, Alexandre G de Brevern","doi":"10.1016/j.biochi.2025.08.007","DOIUrl":"10.1016/j.biochi.2025.08.007","url":null,"abstract":"<p><p>Protein Blocks (PBs) represent a widely used structural alphabet that enables the approximation and analysis of local protein conformations through 16 prototype fragments defined by dihedral angles. Initially developed to overcome the limitations of classical secondary structure definitions, PBs provide a powerful tool for understanding protein structure, dynamics, and function. Their applications span structural annotation, protein fold superimposition and recognition, sequence-based prediction and molecular dynamics analysis. Notably, PBs facilitate the distinction between rigid, flexible, and disordered regions via an entropy-based index (N<sub>eq</sub>), offering insights into protein flexibility and intrinsic disorder. Their integration with deep learning has dramatically improved predictive performance, and their utility has been demonstrated in diverse contexts such as integrin polymorphisms, V<sub>H</sub>H variability and AlphaFold structure analysis. As a robust and adaptable framework, PBs remain central in modern structural bioinformatics.</p>","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144823413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Liver glycogen catabolism in young adult Goto-Kakizaki rats. 年轻成年后藤- kakizaki大鼠肝糖原分解代谢。
IF 3
Biochimie Pub Date : 2025-08-09 DOI: 10.1016/j.biochi.2025.08.013
Isabele G Frasson-Uemura, Franciele P Dall'Aqua, Lunna U Bosquetti, Otávio Vinícius C Jorge, Thais T Braga, Maria F Siqueira, Manoel O E Favaro, Vania G M Mattaraia, Rui Curi, Roberto B Bazotte, Priscila Cassolla, Gisele Lopes Bertolini
{"title":"Liver glycogen catabolism in young adult Goto-Kakizaki rats.","authors":"Isabele G Frasson-Uemura, Franciele P Dall'Aqua, Lunna U Bosquetti, Otávio Vinícius C Jorge, Thais T Braga, Maria F Siqueira, Manoel O E Favaro, Vania G M Mattaraia, Rui Curi, Roberto B Bazotte, Priscila Cassolla, Gisele Lopes Bertolini","doi":"10.1016/j.biochi.2025.08.013","DOIUrl":"10.1016/j.biochi.2025.08.013","url":null,"abstract":"<p><p>Liver glycogen catabolism was investigated in young adult Goto-Kakizaki rats (GK group) and compared with non-diabetic Wistar rats (Control group). The diabetic condition of GK rats was confirmed by hyperglycemia and insulin resistance. Glycogen catabolism was intensified during the infusion of epinephrine (10 μM, 20 μM, and 40 μM), phenylephrine (2 μM, 4 μM, and 6 μM), and glucagon (1 nM) in both Control and GK livers. The degree of glycogen catabolism during these infusions was similar in Control and GK rats, despite the higher liver glycogen content observed in the GK rats. However, a diminished intensification of hepatic glucose production was observed in GK rats during the infusion of isoproterenol (10 μM, 20 μM, and 40 μM). To further investigate this difference, the effect of cAMP, the intracellular mediator of isoproterenol, on liver glycogen catabolism was examined. Livers from GK rats showed no response to 3 μM and 5 μM cAMP but displayed a similar intensification of glycogen catabolism at 7 μM and 9 μM cAMP as the Control group. Interestingly, a higher intensification of glycogen catabolism was observed in GK livers during the infusion of 3 μM dibutyryl-cAMP, a phosphodiesterase-resistant cAMP analog, suggesting that cAMP inactivation by phosphodiesterases might be increased in GK livers. While these findings suggest a possible involvement of phosphodiesterases in the reduced response to isoproterenol, the evidence is insufficient to conclusively establish this mechanism. It can be concluded that liver glycogenolysis does not contribute to the hyperglycemia and glucose intolerance observed in young adult GK rats and that cAMP-mediated intracellular signaling appears to be attenuated in the livers of these animals.</p>","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144823415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Hypothyroidism impacts mammary tumor-associated adipose tissue and breast cancer epithelial cell dialogue. 甲状腺功能减退影响乳腺肿瘤相关脂肪组织和乳腺癌上皮细胞对话。
IF 3
Biochimie Pub Date : 2025-08-09 DOI: 10.1016/j.biochi.2025.08.012
Leila E Zyla, Flavia A Bruna, Flavia E Santiano, Silvina E Gómez, Rocío Cano, Mariángeles Ávila Maniero, Elisa O Pietrobon, Paula M Ginevro, Fernando D Cuello-Carrión, Virginia Pistone-Creydt, Rubén W Carón, Constanza M López Fontana
{"title":"Hypothyroidism impacts mammary tumor-associated adipose tissue and breast cancer epithelial cell dialogue.","authors":"Leila E Zyla, Flavia A Bruna, Flavia E Santiano, Silvina E Gómez, Rocío Cano, Mariángeles Ávila Maniero, Elisa O Pietrobon, Paula M Ginevro, Fernando D Cuello-Carrión, Virginia Pistone-Creydt, Rubén W Carón, Constanza M López Fontana","doi":"10.1016/j.biochi.2025.08.012","DOIUrl":"10.1016/j.biochi.2025.08.012","url":null,"abstract":"<p><p>Thyroid hormones play a key role in adipose tissue development and function. Hypothyroidism (HypoT) can delay mammary tumor development in rats, possibly by altering mammary adipose tissue (MAT) and its interaction with epithelial cells. To explore this hypothesis, we evaluated the effects of conditioned media derived from mammary adipose tissue (MAT-CMs) of hypothyroid (HypoT) and euthyroid (EUT) rats, with and without mammary tumors, on the behavior of mammary epithelial cells. Specifically, we assessed cell viability, proliferation, apoptosis, adhesion, and migration in tumorigenic (MCF-7, MDA-MB-231) and non-tumorigenic (MCF-10A) human mammary epithelial cell lines exposed to the MAT-CMs. Mammary tumors were induced in female Sprague-Dawley rats using 7,12-dimethylbenz[a]anthracene (15 mg/rat), and animals were randomly assigned to HypoT (0.01 % 6-N-propyl-2-thiouracil in drinking water; n = 30) or EUT (tap water; n = 30) groups. MAT fragments were incubated in M199 medium for 24 h, and the resulting CMs were collected and applied to cell cultures. In vivo, HypoT rats exhibited larger mammary fat pads, reduced tumor incidence, volume, and growth rate, and extended tumor-free survival. In vitro, non-tumor MAT-CMs from HypoT rats promoted apoptosis in MCF-10A cells, reduced viability and adhesion of MCF-7 cells, and increased proliferation while decreasing adhesion in MDA-MB-231 cells. Tumor MAT-CMs from HypoT rats stimulated proliferation in tumorigenic cells and inhibited apoptosis in MCF-10A cells. In conclusion, these findings indicate that HypoT modifies the secretory profile of MAT, with tumor MAT-CMs from HypoT potentially enhancing tumorigenic behaviors in mammary tumor cells.</p>","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144823414","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Exploring therapeutic targets with the HMM-SA structural alphabet: Methods, tools, and application to HIV-2 protease. 用HMM-SA结构字母表探索治疗靶点:方法、工具和对HIV-2蛋白酶的应用。
IF 3
Biochimie Pub Date : 2025-08-08 DOI: 10.1016/j.biochi.2025.08.001
Anne-Claude Camproux, Marine Baillif, Léa Dufay, Leslie Regad
{"title":"Exploring therapeutic targets with the HMM-SA structural alphabet: Methods, tools, and application to HIV-2 protease.","authors":"Anne-Claude Camproux, Marine Baillif, Léa Dufay, Leslie Regad","doi":"10.1016/j.biochi.2025.08.001","DOIUrl":"10.1016/j.biochi.2025.08.001","url":null,"abstract":"<p><p>The rapid expansion of available three-dimensional protein structures-derived from both experimental techniques and bioinformatic predictions-offers unprecedented opportunities for drug discovery, particularly for targets that have historically been difficult to characterize. However, the effective analysis of these increasingly complex and voluminous structural datasets remains a major challenge. Efficient representations of protein conformations are essential to facilitate large-scale comparison, structural classification, and functional interpretation in therapeutic contexts. The concept of structural alphabets, introduced by Pr S. Hazout in 1999, provides a robust and scalable framework to represent local protein backbone conformations using a limited set of recurring structural motifs. This representation enables a one-dimensional encoding of three-dimensional protein structures that retains essential geometric features beyond secondary structure, while allowing systematic and interpretable analyses. In this review, we focus on HMM-SA, a structural alphabet constructed using a hidden Markov model. HMM-SA defines 27 structural motifs, including 18 regions specifically dedicated to loops, and captures the statistical dependencies between them. We present a detailed overview of the HMM-SA framework, and of the computational tools derived from this structural alphabet, developed to explore protein function, conformational variability, and the structural determinants of molecular recognition. The utility of HMM-SA is illustrated through a case study on HIV-2 protease (PR2), a critical enzyme in antiretroviral drug development. By analyzing PR2 structural asymmetry, ligand-induced conformational changes, and mutation-driven alterations, we highlight the ability of HMM-SA-based methods to identify key structural features involved in ligand specificity and resistance mechanisms, thereby advancing therapeutic target analysis.</p>","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144818644","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
In memoriam of professor Serge Hazout (1950-2005) - a bioinformatics pioneer in France. 纪念法国生物信息学先驱塞尔日·哈佐特教授(1950 - 2005)。
IF 3
Biochimie Pub Date : 2025-08-08 DOI: 10.1016/j.biochi.2025.08.005
Alexandre G de Brevern
{"title":"In memoriam of professor Serge Hazout (1950-2005) - a bioinformatics pioneer in France.","authors":"Alexandre G de Brevern","doi":"10.1016/j.biochi.2025.08.005","DOIUrl":"10.1016/j.biochi.2025.08.005","url":null,"abstract":"<p><p>Professor Serge Hazout, or Serge, as his friends and colleagues knew him, passed away on April 24, 2005 in Paris, France. Serge was a leading pioneer in the field of Bioinformatics in France. His work stretched over 30 years beginning with his graduate studies in 1975, and he impacted a large number of researches in this field. This in memoriam outlines both his professional career and personal life; highlighting his impact on bioinformatics at the training level in France and his numerous scientific contributions which both continue to flourish today.</p>","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":" ","pages":""},"PeriodicalIF":3.0,"publicationDate":"2025-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144818645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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