Biochemistry Biochemistry最新文献_第7页

Active Site Plasticity of the Bacterial Sliding Clamp 细菌滑动钳活性部位的可塑性

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-03-19 DOI: 10.1021/acs.biochem.4c0068610.1021/acs.biochem.4c00686

Zahra Raza, Nehad S. El Salamouni, Andrew B. McElroy, Danielle Skropeta, Michael J. Kelso, Aaron J. Oakley, Nicholas E. Dixon and Haibo Yu*,

{"title":"Active Site Plasticity of the Bacterial Sliding Clamp","authors":"Zahra Raza, Nehad S. El Salamouni, Andrew B. McElroy, Danielle Skropeta, Michael J. Kelso, Aaron J. Oakley, Nicholas E. Dixon and Haibo Yu*, ","doi":"10.1021/acs.biochem.4c0068610.1021/acs.biochem.4c00686","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00686https://doi.org/10.1021/acs.biochem.4c00686","url":null,"abstract":"The rise of antibiotic resistance poses a severe global threat, specifically due to the emergence of multiresistant bacteria (ESKAPE pathogens), which are responsible for countless deaths globally. Consequently, the development of novel antibiotics is in dire need. Targeting proteins essential to DNA replication is a promising pathway, making the β-sliding clamp (β-SC) an attractive target. Currently, there are no antibiotics on the market that target the β-SC. However, numerous compounds are being investigated to create an antibiotic with high potency against a broad range of bacterial species. Interestingly, most proposed compounds do not bind to the entire active site, which may reduce their potential as high-potency inhibitors. This is due to the active site residue Met at position 362, adopting a “closed” conformation, preventing inhibitors access into Subsite II of the active site. This study explored the effect of key residues on the plasticity of the β-SC active site using molecular dynamics and metadynamics simulations under different physiological states. Our results show that the Met gate exhibits flexibility and both open and closed states are thermodynamically and kinetically accessible.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 8","pages":"1762–1769 1762–1769"},"PeriodicalIF":2.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143827810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Active Site Plasticity of the Bacterial Sliding Clamp. 细菌滑动钳活性部位的可塑性。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-03-19 DOI: 10.1021/acs.biochem.4c00686

Zahra Raza, Nehad S El Salamouni, Andrew B McElroy, Danielle Skropeta, Michael J Kelso, Aaron J Oakley, Nicholas E Dixon, Haibo Yu

{"title":"Active Site Plasticity of the Bacterial Sliding Clamp.","authors":"Zahra Raza, Nehad S El Salamouni, Andrew B McElroy, Danielle Skropeta, Michael J Kelso, Aaron J Oakley, Nicholas E Dixon, Haibo Yu","doi":"10.1021/acs.biochem.4c00686","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00686","url":null,"abstract":"The rise of antibiotic resistance poses a severe global threat, specifically due to the emergence of multiresistant bacteria (ESKAPE pathogens), which are responsible for countless deaths globally. Consequently, the development of novel antibiotics is in dire need. Targeting proteins essential to DNA replication is a promising pathway, making the β-sliding clamp (β-SC) an attractive target. Currently, there are no antibiotics on the market that target the β-SC. However, numerous compounds are being investigated to create an antibiotic with high potency against a broad range of bacterial species. Interestingly, most proposed compounds do not bind to the entire active site, which may reduce their potential as high-potency inhibitors. This is due to the active site residue Met at position 362, adopting a \"closed\" conformation, preventing inhibitors access into Subsite II of the active site. This study explored the effect of key residues on the plasticity of the β-SC active site using molecular dynamics and metadynamics simulations under different physiological states. Our results show that the Met gate exhibits flexibility and both open and closed states are thermodynamically and kinetically accessible.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":""},"PeriodicalIF":2.9,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143661718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Directed Evolution of a Macrolide-Sensing Transcription Factor Biosensor for the Detection of Macrolactone Aglycones via “Effector Walking” and Efflux Pump Deletion 大环内酯传感转录因子生物传感器的定向进化，通过“效应行走”和外排泵缺失检测大环内酯苷元

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-03-18 DOI: 10.1021/acs.biochem.4c0079510.1021/acs.biochem.4c00795

Lindsay C. La Fleur, Zhongtian Zhang, Christian McRoberts-Amador, Jayani Christopher, Megan Reed, Jianting Zheng, T. Ashton Cropp and Gavin J. Williams*,

{"title":"Directed Evolution of a Macrolide-Sensing Transcription Factor Biosensor for the Detection of Macrolactone Aglycones via “Effector Walking” and Efflux Pump Deletion","authors":"Lindsay C. La Fleur, Zhongtian Zhang, Christian McRoberts-Amador, Jayani Christopher, Megan Reed, Jianting Zheng, T. Ashton Cropp and Gavin J. Williams*, ","doi":"10.1021/acs.biochem.4c0079510.1021/acs.biochem.4c00795","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00795https://doi.org/10.1021/acs.biochem.4c00795","url":null,"abstract":"Glycosylated macrolactones (macrolides) often display broad and potent biological activities and are targets for drug development and discovery. The modular genetic organization of macrolide polyketide synthases (PKSs) and various polyketide tailoring enzymes has inspired the combinatorial biosynthesis of new-to-nature macrolides. However, most engineered PKS and macrolide biosynthetic pathways are ineffective and produce reduced or negligible product titers. Directed evolution could improve the activity of engineered PKSs and associated pathways but critically requires a high-throughput screen to identify active variants from large libraries. Transcription factor-based biosensors can be used for this purpose. However, the effector specificity of the only known macrolide-sensing transcription factor MphR is limited to macrolides modified with the sugar, desosamine. The potential applications of MphR are subsequently limited, ruling out the possibility of leveraging MphR to screen libraries of pathway variants that make macrolactones that lack sugars (i.e., macrolide aglycones) such as the direct products of PKSs. In this study, we aimed to engineer the effector specificity of the MphR biosensor strain for detecting macrolide aglycones. By developing an “effector walking” strategy coupled with efflux pump deletion, the effector profile of MphR was dramatically broadened to include several erythronolide macrolactones. This work sets the stage for applying directed evolution and other high-throughput screening approaches to various PKSs. Our results suggest a broadly applicable approach to developing biosensors that detect ligands that are very different in structure from the native effector.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 7","pages":"1560–1571 1560–1571"},"PeriodicalIF":2.9,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143737518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Fine-Tuned Deep Transfer Learning Models for Large Screenings of Safer Drugs Targeting Class A GPCRs. 针对A类gpcr的更安全药物的大规模筛选的微调深度迁移学习模型。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-03-18 Epub Date: 2025-03-08 DOI: 10.1021/acs.biochem.4c00832

Davide Provasi, Marta Filizola

{"title":"Fine-Tuned Deep Transfer Learning Models for Large Screenings of Safer Drugs Targeting Class A GPCRs.","authors":"Davide Provasi, Marta Filizola","doi":"10.1021/acs.biochem.4c00832","DOIUrl":"10.1021/acs.biochem.4c00832","url":null,"abstract":"G protein-coupled receptors (GPCRs) remain a focal point of research due to their critical roles in cell signaling and their prominence as drug targets. However, directly linking drug efficacy to the receptor-mediated activation of specific intracellular transducers and the resulting physiological outcomes remains challenging. It is unclear whether the enhanced therapeutic window of certain drugs─defined as the dose range that provides effective therapy with minimal side effects─stems from their low intrinsic efficacy across all signaling pathways or ligand bias, wherein specific transducer subtypes are preferentially activated in a given cellular system compared to a reference ligand. Accurately predicting safer compounds, through either low intrinsic efficacy or ligand bias, would greatly advance drug development. While AI models hold promise for such predictions, the development of deep learning models capable of reliably forecasting GPCR ligands with defined bioactivities remains challenging, largely due to the limited availability of high-quality data. To address this, we pretrained a model on receptor sequences and ligand data sets across all class A GPCRs and then refined it to predict low-efficacy compounds or biased agonists for individual class A GPCRs. This was achieved using transfer learning and a neural network incorporating natural language processing of target sequences and receptor mutation effects on signaling. These two fine-tuned models─one for low-efficacy agonists and one for biased agonists─are available on demand for each class A GPCR and enable virtual screening of large chemical libraries, thereby facilitating the discovery of compounds with potentially improved safety profiles.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1328-1337"},"PeriodicalIF":2.9,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143582139","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Disordered C-Terminus Plays a Critical Role in the Activity of the Small GTPase Ran. 紊乱的c端在小GTPase Ran的活性中起关键作用。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-03-18 Epub Date: 2025-02-25 DOI: 10.1021/acs.biochem.4c00484

Wenyuan Wei, Melissa Valerio, Ning Ma, Hyunjun Kang, Le Xuan Truong Nguyen, Guido Marcucci, Nagarajan Vaidehi

{"title":"Disordered C-Terminus Plays a Critical Role in the Activity of the Small GTPase Ran.","authors":"Wenyuan Wei, Melissa Valerio, Ning Ma, Hyunjun Kang, Le Xuan Truong Nguyen, Guido Marcucci, Nagarajan Vaidehi","doi":"10.1021/acs.biochem.4c00484","DOIUrl":"10.1021/acs.biochem.4c00484","url":null,"abstract":"Ran is a small GTPase of the Ras superfamily that governs nucleocytoplasmic transport, including that of miR-126, a microRNA that supports the homeostasis and expansion of leukemia stem cells (LSCs). Ran binds to Exportin 5 to facilitate the transport of precursor (pre)-miR-126 across the nuclear membrane for its maturation. Our goal is to inhibit Ran to prevent transport of pre-miR-126 to the cytoplasm. Like other Ras family proteins, targeting Ran with small molecules is challenging due to its relatively flat surface and lack of binding cavities. Ran's activity is regulated by a long and disordered C-terminus that provides opportunities for identifying cryptic binding pockets to target. We used a combination of molecular dynamics simulations and experiments and uncovered the critical role of the ensemble of the C-terminal conformations that enable the transition of Ran from the GTP-bound \"on state\" to its GDP-bound \"off-state\". We also showed that the Ran C-terminus allosterically modulates the conformations of residues in the nucleotide binding site and in the functionally relevant Switch 1 and 2 regions. Through computational deep mutational scans and experiments, we identified four residue hotspots L182, Y197, D200, and L201 at the core-C-terminus interface and four residue mutations V27A, E70D, N122A, and N122Y that mediate the allosteric communication between the core and switch regions. This information paves the way for our next step in the design of novel allosteric modulators for Ran.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1393-1404"},"PeriodicalIF":2.9,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143497459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A "Knob Switch" Model for the Phosphoregulatory Mechanism of KCC3 at the Carboxy-Terminal Domain. KCC3在羧基末端磷酸化调控机制的“旋钮开关”模型。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-03-18 Epub Date: 2025-02-26 DOI: 10.1021/acs.biochem.4c00523

Xiaoli Lu, Jing Xue, Qiang Zhou, Jing Huang

{"title":"A \"Knob Switch\" Model for the Phosphoregulatory Mechanism of KCC3 at the Carboxy-Terminal Domain.","authors":"Xiaoli Lu, Jing Xue, Qiang Zhou, Jing Huang","doi":"10.1021/acs.biochem.4c00523","DOIUrl":"10.1021/acs.biochem.4c00523","url":null,"abstract":"Phosphorylation is a reversible post-translational modification that can modulate protein function. For example, phosphorylation modifications of solute carrier family 12 (SLC12) proteins function as molecular switches that precisely regulate cation-chloride ion transport. Elucidating the phosphoregulatory mechanism of SLC12 at the carboxy-terminal domain (CTD) through structural determination approaches remains challenging due to the domain's disordered and flexible nature. In this study, molecular dynamics (MD) simulations and enhanced sampling techniques were employed to investigate the CTD phosphoregulatory mechanism of SLC12A6 (also known as KCC3). Atomistic MD and metadynamics simulations revealed that the dephosphorylation of residues T940 and T997 stabilizes CTD to a favorable state that \"switches on\" the solvent accessibility of the inward-facing pocket. Meanwhile, phosphorylation induces distinct orientations of the CTD, transitioning the dimer into another favorable state that \"switches off\" the solvent accessibility. The alteration of solvent accessibility in the inward-facing pocket influences the water and ion dynamics. Based on these findings, we propose a \"knob switch\" model to illustrate how CTD phosphorylation regulates ion transport in KCC3.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1405-1414"},"PeriodicalIF":2.9,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143513999","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Identification and Characterization of the Two Glycosyltransferases Required for the Polymerization of the HS:1 Serotype Capsular Polysaccharide of Campylobacter jejuni G1. 空肠弯曲杆菌G1血清型荚膜多糖HS:1聚合所需两种糖基转移酶的鉴定与表征

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-03-18 Epub Date: 2025-02-28 DOI: 10.1021/acs.biochem.4c00803

Ronnie Bourland, Tamari Narindoshvili, Frank M Raushel

{"title":"Identification and Characterization of the Two Glycosyltransferases Required for the Polymerization of the HS:1 Serotype Capsular Polysaccharide of Campylobacter jejuni G1.","authors":"Ronnie Bourland, Tamari Narindoshvili, Frank M Raushel","doi":"10.1021/acs.biochem.4c00803","DOIUrl":"10.1021/acs.biochem.4c00803","url":null,"abstract":"Campylobacter jejuni is a Gram-negative pathogenic bacterium commonly found in poultry and is the leading cause of gastrointestinal infections in the United States. Similar to other Gram-negative bacteria, C. jejuni possesses an extracellular carbohydrate-based capsular polysaccharide (CPS) composed of repeating units of monosaccharides bound via glycosidic linkages. The gene cluster for serotype 1 (HS:1) of C. jejuni contains 13 different genes required for the production and presentation of the CPS. Each repeating unit within the HS:1 CPS structure contains a backbone of glycerol phosphate and d-galactose. Here, the enzyme HS1.11 was shown to catalyze the formation of CDP-(2R)-glycerol from MgCTP and l-glycerol-3-phosphate. HS1.09 was found to be a multidomain protein that catalyzes the polymerization of l-glycerol-3-phosphate and d-galactose using UDP-d-galactose and CDP-(2R)-glycerol as substrates. The domain of HS1.09 that extends from residues 286 to 703 was shown to catalyze the transfer of l-glycerol-P from CDP-glycerol to the hydroxyl group at C4 of the d-galactose moiety at the nonreducing end of the growing oligosaccharide. The transfer of d-galactose to the C2 hydroxyl group of the glycerol-phosphate moiety was shown to be catalyzed with retention of configuration by the domain of HS1.09 that extends from residues 704 to 1095. Primers as short as a single d-galactoside were accepted as initial substrates. Oligosaccharide products were isolated by ion exchange chromatography and identified by high-resolution ESI-mass spectrometry and NMR spectroscopy.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1370-1379"},"PeriodicalIF":2.9,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11924219/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143527812","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrated Study of Fluorescence Enhancement in the Y176H Variant of Cyanobacterial Phytochrome Cph1. 蓝藻植物色素 Cph1 Y176H 变体的荧光增强综合研究

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-03-18 Epub Date: 2025-02-27 DOI: 10.1021/acs.biochem.4c00687

Soshichiro Nagano, Chen Song, Valentin Rohr, Megan J Mackintosh, Oanh Tu Hoang, Anastasia Kraskov, Yang Yang, Jon Hughes, Karsten Heyne, Maria-Andrea Mroginski, Igor Schapiro, Peter Hildebrandt

{"title":"Integrated Study of Fluorescence Enhancement in the Y176H Variant of Cyanobacterial Phytochrome Cph1.","authors":"Soshichiro Nagano, Chen Song, Valentin Rohr, Megan J Mackintosh, Oanh Tu Hoang, Anastasia Kraskov, Yang Yang, Jon Hughes, Karsten Heyne, Maria-Andrea Mroginski, Igor Schapiro, Peter Hildebrandt","doi":"10.1021/acs.biochem.4c00687","DOIUrl":"10.1021/acs.biochem.4c00687","url":null,"abstract":"Phytochromes are red-light-sensitive biliprotein photoreceptors that control a variety of physiological processes in plants, fungi, and bacteria. Lately, greater attention has been paid to these photoreceptors due to their potential as fluorescent probes for deep-tissue microscopy. Such fluorescing phytochromes have been generated by multiple amino acid substitutions in weakly fluorescent wild-type (WT) proteins. Remarkably, the single substitution of conserved Tyr176 by His in cyanobacterial phytochrome Cph1 increases the fluorescence quantum yield from 2.4 to 14.5%. In this work, we studied this Y176H variant by crystallography, MAS NMR, resonance Raman spectroscopy, and ultrafast absorption spectroscopy complemented by theoretical methods. Two factors were identified to account for the strong fluorescence increase. First, the equilibrium between the photoactive and fluorescent substates of WT Cph1 was shown to shift entirely to the fluorescent substate in Y176H. Second, structural flexibility of the chromophore is drastically reduced and the photoisomerization barrier is raised, thereby increasing the excited-state lifetime. The most striking finding, however, is that Y176H includes the structural properties of both the dark-adapted Pr and the light-activated Pfr state. While the chromophore adopts the Pr-typical ZZZssa configuration, the tongue segment of the protein adopts a Pfr-typical α-helical structure. This implies that Tyr176 plays a key role in coupling chromophore photoisomerization to the sheet-to-helix transition of the tongue and the final Pfr structure. This conclusion extends to plant phytochromes, where the homologous substitution causes light-independent signaling activity akin to that of Pfr.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1348-1358"},"PeriodicalIF":2.9,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11924222/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143522198","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Oxysterols Modulate Protein–Sterol Interactions to Impair CXCR4 Signaling in Aging Cells 氧化甾醇调节蛋白-甾醇相互作用损害衰老细胞中的CXCR4信号

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-03-18 DOI: 10.1021/acs.biochem.4c0061710.1021/acs.biochem.4c00617

Suramya Asthana, Anant Verma, Baivabi Bhattacharya, Arnab Nath, Nithin Sajeev, Kiran Maan, Raji R. Nair, K. Ganapathy Ayappa* and Deepak Kumar Saini*,

{"title":"Oxysterols Modulate Protein–Sterol Interactions to Impair CXCR4 Signaling in Aging Cells","authors":"Suramya Asthana, Anant Verma, Baivabi Bhattacharya, Arnab Nath, Nithin Sajeev, Kiran Maan, Raji R. Nair, K. Ganapathy Ayappa* and Deepak Kumar Saini*, ","doi":"10.1021/acs.biochem.4c0061710.1021/acs.biochem.4c00617","DOIUrl":"https://doi.org/10.1021/acs.biochem.4c00617https://doi.org/10.1021/acs.biochem.4c00617","url":null,"abstract":"Organismal aging is accompanied by the accumulation of senescent cells in the body, which drives tissue dysfunction. Senescent cells have a distinctive profile, including proliferation arrest, resistance to apoptosis, altered gene expression, and high inflammation. Despite global signaling and metabolic dysregulation during senescence, the underlying reasons for changes in signaling remain unclear. GPCRs are pivotal in cellular signaling, dynamically mediating the complex interplay between cells and their surrounding environment to maintain cellular homeostasis. The chemokine receptor CXCR4 plays a crucial role in modulating immune responses and inflammation. It has been shown that the expression of CXCR4 increases in cells undergoing senescence, which enhances inflammation postactivation. Here, we examine CXCR4 signaling in deeply senescent cells (aged cells), where cholesterol and its oxidized derivatives, oxysterols, affect receptor function. We report elevated oxysterol levels in senescent cells, which altered classical CXCL12-mediated CXCR4 signaling. Tail-oxidized sterols disrupted signaling more than ring-oxidized counterparts. Molecular dynamics simulations revealed that 27-hydroxycholesterol displaces cholesterol and binds strongly to alter the conformation of critical signaling residues, modifying the sterol–CXCR4 interaction landscape. Our study provides a molecular view of the observed mitigated GPCR signaling in the presence of oxysterols, which switched G-protein signaling from Gαi/o to Gαs class. Overall, we present an altered paradigm of GPCR signaling, where cholesterol oxidation alters the signaling outcome in aged cells.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":"64 7","pages":"1606–1623 1606–1623"},"PeriodicalIF":2.9,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143737517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Coupling Subunit-Specific States to Allosteric Regulation in Homodimeric Cyclooxygenase-2. 同型二聚体环氧化酶-2亚基特异性状态与变构调控的耦合。

IF 2.9 3区生物学

Biochemistry Biochemistry Pub Date : 2025-03-18 Epub Date: 2025-02-28 DOI: 10.1021/acs.biochem.4c00821

Liang Dong, Michael G Malkowski

{"title":"Coupling Subunit-Specific States to Allosteric Regulation in Homodimeric Cyclooxygenase-2.","authors":"Liang Dong, Michael G Malkowski","doi":"10.1021/acs.biochem.4c00821","DOIUrl":"10.1021/acs.biochem.4c00821","url":null,"abstract":"The homodimeric cyclooxygenase enzymes (COX-1 and COX-2) oxygenate arachidonic acid (AA) to generate prostaglandins. COX-2 behaves as a conformational heterodimer in solution comprised of allosteric (Eallo) and catalytic (Ecat) subunits that function cooperatively. We previously utilized 19F-nuclear magnetic resonance spectroscopy (19F-NMR) to show that the cyclooxygenase active site entrances in a COX-2 homodimer construct exhibited composite tightened and relaxed states that are dependent upon the type of ligand bound. A third state, hypothesized to represent the alteration of a loop comprised of residues 120-129, was also detected in the presence of ligands that allosterically potentiate activity. We report here studies that couple the use of 19F-NMR with COX-2 heterodimer constructs to characterize states arising in the individual subunits. Glycine and proline substitutions at Ser-121 were introduced to examine how these mutations alter the 120-129 loop. In the presence of AA, the subunits exhibited asymmetry, with tightened and relaxed states observed in Eallo and Ecat, respectively. Allosteric ligand binding resulted in a shift to equivalent symmetrical states, with tightened states observed in the presence of the allosteric inhibitor flurbiprofen and relaxed states observed in the presence of the allosteric potentiator palmitic acid. The S121P substitution results in a shift to equivalent relaxed states, as well as an alteration of the 120-129 loop in the absence of bound ligand. We put forth a model linking the observed differential states arising from allosteric ligand binding with structural transitions across the dimer interface that govern the regulation of cyclooxygenase activity.","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"1380-1392"},"PeriodicalIF":2.9,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143530872","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0