ACS Chemical Biology最新文献

{"title":"Probing the Signal Transduction Mechanism of the Light-Activated Adenylate Cyclase OaPAC Using Unnatural Amino Acid Mutagenesis.","authors":"Samruddhi S Jewlikar, Jinnette Tolentino Collado, Madeeha I Ali, Aya Sabbah, YongLe He, James N Iuliano, Christopher R Hall, Katrin Adamczyk, Gregory M Greetham, Andras Lukacs, Stephen R Meech, Peter J Tonge","doi":"10.1021/acschembio.4c00627","DOIUrl":"10.1021/acschembio.4c00627","url":null,"abstract":"<p><p>OaPAC, the photoactivated adenylyl cyclase from <i>Oscillatoria acuminata</i>, is composed of a blue light using FAD (BLUF) domain fused to an adenylate cyclase (AC) domain. Since both the BLUF and AC domains are part of the same protein, OaPAC is a model for understanding how the ultrafast modulation of the chromophore binding pocket caused by photoexcitation results in the activation of the output domain on the μs-s time scale. In the present work, we use unnatural amino acid mutagenesis to identify specific sites in the protein that are involved in transducing the signal from the FAD binding site to the ATP binding site. To provide insight into site-specific structural dynamics, we replaced W90 which is close to the chromophore pocket, F103 which interacts with W90 across the dimer interface, and F180 in the central core of the AC domain, with the infrared probe azido-Phe (AzPhe). Using ultrafast IR, we show that AzPhe at position 90 responds on multiple time scales following photoexcitation. In contrast, the light minus dark IR spectrum of AzPhe103 shows only a minor perturbation in environment between the dark and light states, while replacement of F180 with AzPhe resulted in a protein with no catalytic activity. We also replaced Y125, which hydrogen bonds with N256 across the dimer interface, with fluoro-Tyr residues. All the fluoro-Tyr substituted proteins retained the light-induced red shift in the flavin absorption spectrum; however, only the 3-FY125 OaPAC retained photoinduced catalytic activity. The loss of activity in 3,5-F₂Y125 and 2,3,5-F₃Y125 OaPAC, which potentially increase the acidity of the Y125 phenol by more than 1000-fold, suggests that deprotonation of Y125 disrupts the signal transduction pathway from the BLUF to the AC domain.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"369-377"},"PeriodicalIF":3.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021284","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chemoproteomic Profiling of Clickable Fumarate Probes for Target Identification and Mechanism of Action Studies.","authors":"Lu Zhang, Jeffrey G Martin, Benbo Gao, Weike Zeng, Shalise Couvertier, Douglas S Johnson","doi":"10.1021/acschembio.4c00617","DOIUrl":"10.1021/acschembio.4c00617","url":null,"abstract":"<p><p>Dimethyl fumarate (DMF) is an established oral therapy for multiple sclerosis worldwide. Although the clinical efficacy of these fumarate esters has been extensively investigated, the mode of action and pharmacokinetics of fumarates have not been fully elucidated due to their broad-spectrum reactivity and complex metabolism in vivo. To better understand the mechanism of action of DMF and its active metabolite, monomethyl fumarate (MMF), we designed and utilized clickable probes to visualize and enrich probe-modified proteins. We further perform quantitative chemoproteomics analysis for proteome-wide target identification and validate several unique and shared targets of DMF and MMF, which provide insight into the reactivity, selectivity, and target engagement of fumarates.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"340-356"},"PeriodicalIF":3.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143057497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tools for Intersectional Optical and Chemical Tagging on Cell Surfaces.","authors":"Sarah Innes-Gold, Hanzeng Cheng, Luping Liu, Adam E Cohen","doi":"10.1021/acschembio.4c00756","DOIUrl":"10.1021/acschembio.4c00756","url":null,"abstract":"<p><p>We present versatile tools for intersectional optical and chemical tagging of live cells. Photocaged tetrazines serve as \"photo-click\" adapters between recognition groups on the cell surface and diverse chemical payloads. We describe two new functionalized photocaged tetrazine structures which add a light-gating step to three common cell-targeting chemical methods: HaloTag/chloroalkane labeling, nonspecific primary amine labeling, and antibody labeling. We demonstrate light-gated versions of these three techniques in live cultured cells. We then explore two applications: monitoring tissue flows on the surface of developing zebrafish embryos, and combinatorial multicolor labeling and sorting of optically defined groups of cells. Photoclick adapters add optical control to cell tagging schemes, with modularity in both tag and cell attachment chemistry.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"455-463"},"PeriodicalIF":3.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142995970","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Photoactivatable Plant Hormone-Based Chemical Inducers of Proximity for <i>In Vivo</i> Applications.","authors":"Philipp Pöschko, Caroline M Berrou, Kaisa Pakari, Michael J Ziegler, Christoph Kern, Birgit Koch, Joachim Wittbrodt, Richard Wombacher","doi":"10.1021/acschembio.4c00592","DOIUrl":"10.1021/acschembio.4c00592","url":null,"abstract":"<p><p>Protein interactions play a crucial role in regulating cellular mechanisms, highlighting the need for effective methods to control these processes. In this regard, chemical inducers of proximity (CIPs) offer a promising approach to precisely manipulate protein-protein interactions in live cells and <i>in vivo</i>. In this study, we introduce pMandi, a photocaged version of the plant hormone-based CIP mandipropamid (Mandi), which allows the use of light as an external trigger to induce protein proximity in live mammalian cells. Furthermore, we present opabactin (OP) as a new plant hormone-based CIP that is effective in live mammalian cells at low nanomolar concentration and in live medaka embryos at submicromolar concentration. Its photocaged derivative, pOP, enables the induction of protein proximity upon light exposure in individual cells, enhancing spatiotemporal control to the level of single-cell resolution. Additionally, we explored the use of both photocaged CIPs to promote protein proximity in live medaka embryos.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"332-339"},"PeriodicalIF":3.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11851429/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143044865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Understanding the Glycosylation Pathways Involved in the Biosynthesis of the Sulfated Glycan Ligands for Siglecs.","authors":"Jaesoo Jung, Edward N Schmidt, Hua-Chien Chang, Zeinab Jame-Chenarboo, Jhon R Enterina, Kelli A McCord, Taylor E Gray, Lauren Kageler, Chris D St Laurent, Chao Wang, Ryan A Flynn, Peng Wu, Kay-Hooi Khoo, Matthew S Macauley","doi":"10.1021/acschembio.4c00677","DOIUrl":"10.1021/acschembio.4c00677","url":null,"abstract":"<p><p>Carbohydrate sulfation plays a pivotal role in modulating the strength of Siglec-glycan interactions. Recently, new aspects of Siglec binding to sulfated cell surface carbohydrates have been discovered, but the class of glycan presenting these sulfated Siglec ligands has not been fully elucidated. In this study, the contribution of different classes of glycans to <i>cis</i> and <i>trans</i> Siglec ligands was investigated within cells expressing the carbohydrate sulfotransferase 1 (CHST1) or CHST2. For some Siglecs, the glycan class mediating binding was clear, such as <i>O</i>-glycans for Siglec-7 and <i>N</i>-glycans for Siglec-2 and Siglec-9. Both <i>N</i>-glycans and mucin-type <i>O</i>-glycans contributed to ligands for Siglec-3, -5, -8, and -15. However, significant levels of Siglec-3 and -8 ligands remained in CHST1-expressing cells lacking complex <i>N</i>-glycans and mucin-type <i>O</i>-glycans. A combination of genetic, pharmacological, and enzymatic treatment strategies ruled out heparan sulfates and glycoRNA as contributors, although Siglec-8 did exhibit some binding to glycolipids. Genetic disruption of <i>O</i>-mannose glycans within CHST1-expressing cells had a small but significant impact on Siglec-3 and -8 binding, demonstrating that this class of glycans can present sulfated Siglec ligands. We also investigated the ability of sulfated <i>cis</i> ligands to mask Siglec-3 and Siglec-7. For Siglec-7, <i>cis</i> ligands were again found to be mucin-type <i>O</i>-glycans. While <i>N</i>-glycans were the major sulfated <i>trans</i> ligands for Siglec-3, disruption of complex mucin-type <i>O</i>-glycans had the largest impact on Siglec-3 masking. Overall, this study enhances our knowledge of the types of sulfated glycans that can serve as Siglec ligands.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"386-400"},"PeriodicalIF":3.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142995974","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptomics-Driven Discovery of New Meroterpenoid Rhynchospenes Involved in the Virulence of the Barley Pathogen <i>Rhynchosporium commune</i>.","authors":"Reynaldi Darma, Zhuo Shang, Joe Bracegirdle, Stephen Moggach, Megan C McDonald, Andrew M Piggott, Peter S Solomon, Yit-Heng Chooi","doi":"10.1021/acschembio.4c00731","DOIUrl":"10.1021/acschembio.4c00731","url":null,"abstract":"<p><p><i>Rhynchosporium commune</i>, the causal agent of barley scald disease, poses a major threat to global barley production. Despite its significant impact, the molecular mechanisms underlying <i>R. commune</i>'s infection process remain largely unexplored. To address this, we analyzed the differential gene expression data of <i>R. commune</i> WAI453 cultivated under both <i>in planta</i> and <i>in vitro</i> conditions, aiming to identify secondary metabolite biosynthetic gene clusters that are potentially involved in the pathogenicity of <i>R. commune</i>. Our analysis revealed increased expression of a polyketide-terpene gene cluster (the <i>rhy</i> cluster), containing a specific myeloblastosis (MYB)-type transcription factor gene <i>rhyM</i>, during <i>in planta</i> growth. Overexpression of <i>rhyM</i> in an axenic culture activated the expression of the <i>rhy</i> cluster, resulting in the production of a series of new meroterpenoid metabolites, which we named rhynchospenes A-E. Their structures were elucidated through a combination of spectroscopic methods and single crystal X-ray diffraction analysis. Infiltration of rhynchospenes into barley leaves resulted in strong necrosis, with rhynchospene B demonstrating the highest phytotoxicity and causing necrosis at a minimum concentration of 50 ppm. Silencing <i>rhyM</i> in <i>R. commune</i> WAI453 confirmed the role of rhynchospenes as virulence factors in barley disease. The resulting mutant showed significantly reduced expression of the <i>rhy</i> cluster <i>in planta</i> compared to the wild-type strain and decreased virulence in seedling pathogenicity assays on barley. The characterization of the <i>rhy</i> cluster and rhynchospenes provided insights into the role of secondary metabolites in <i>R. commune</i> virulence and barley scald disease development. The study also highlights the potential use of MYB-type transcription factor overexpression in uncovering cryptic SMs involved in pathogenicity and host adaptations.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"421-431"},"PeriodicalIF":3.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143397479","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"12/15-Lipoxygenase-Derived Electrophilic Lipid Modifications in Phagocytic Macrophages.","authors":"Kaiyuan Deng, Yosuke Isobe, Kazuya Tsumagari, Taiga Kato, Hiroyuki Arai, Koshi Imami, Makoto Arita","doi":"10.1021/acschembio.4c00624","DOIUrl":"10.1021/acschembio.4c00624","url":null,"abstract":"<p><p>Macrophages remove apoptotic cells via phagocytosis, also known as efferocytosis, during inflammation to maintain tissue homeostasis. This process is accompanied by various metabolic changes in macrophages including the production of lipid metabolites by fatty acid oxygenases. Among these, highly reactive metabolites, called lipid-derived electrophiles (LDEs), modify cysteines and other nucleophilic amino acids in intracellular proteins. However, the landscape and functions of the modifications by these electrophilic metabolites have been poorly characterized. In this study, we used activity-based protein profiling to quantitatively profile the cysteine reactivity landscape and identify the potential targets of endogenous LDE modification during efferocytosis in mouse peritoneal macrophages. Using this methodology, we identified multiple cysteine sites that are highly likely to be modified by LDEs generated by 12/15-lipoxygenase (12/15-LOX), an efferocytosis-related fatty acid oxygenase that is highly expressed in peritoneal macrophages. Among these, actin-depolymerizing protein Cofilin-1 was found to be a target of 12/15-LOX-derived LDEs. In vitro Cofilin-1 activity was attenuated by 12/15-LOX-derived LDEs, and intracellular actin stabilization and efferocytosis were substantially enhanced by the LDE treatment of mouse peritoneal macrophages. These results highlighted the role of intracellular LDE modification during efferocytosis in macrophages.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"357-368"},"PeriodicalIF":3.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11854370/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142995957","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of an <i>In Situ</i> G Protein-Coupled Receptor Fragment Molecule Screening Approach with High-Resolution Magic Angle Spinning Nuclear Magnetic Resonance.","authors":"Enzo Petracco, Guillaume Ferré, Ivo Kabelka, Flavio Ballante, Jens Carlsson, Emma Mulry, Arka P Ray, James Collins, Florent Allais, Matthew T Eddy","doi":"10.1021/acschembio.4c00686","DOIUrl":"10.1021/acschembio.4c00686","url":null,"abstract":"<p><p>Small molecules are essential for investigating the pharmacology of membrane proteins and remain the most common approach for therapeutically targeting them. However, most experimental small molecule screening methods require ligands containing radiolabels or fluorescent labels and often involve isolating proteins from their cellular environment. Additionally, most conventional screening methods are suited for identifying compounds with moderate to higher affinities (<i>K</i>_D < 1 μM) and are less effective at detecting lower affinity compounds, such as weakly binding molecular fragments. To address these limitations, we demonstrated a proof-of-concept application of high-resolution magic angle spinning nuclear magnetic resonance (HRMAS NMR) spectroscopy with small molecules that bind the human A_2A adenosine receptor (A_2AAR), a class A G protein-coupled receptor. Our approach leverages a streamlined workflow to prepare NMR samples with only milligrams of unpurified cell membranes containing ∼1 μM of A_2AAR. Utilizing saturation transfer difference NMR, we identified bound small molecules from spectra recorded within minutes and further derived information on ligand binding poses without the need for detailed structure determination. After establishing optimal criteria for which the HRMAS approach is most sensitive, we leveraged our HRMAS approach to identify and characterize molecular fragments not previously known to be ligands of A_2AAR. In molecular docking and simulations, we observed novel binding poses for these fragments, which revealed the potential to grow them into more complex ligands and confirmed HRMAS NMR as a valuable tool for lead compound identification in the context of fragment-based drug discovery.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"401-411"},"PeriodicalIF":3.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142995960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"European Robin Cryptochrome-4a Associates with Lipid Bilayers in an Ordered Manner, Fulfilling a Molecular-Level Condition for Magnetoreception","authors":"Marta Majewska,&nbsp;Maja Hanić,&nbsp;Rabea Bartölke,&nbsp;Jessica Schmidt,&nbsp;Justyna Bożek,&nbsp;Luca Gerhards,&nbsp;Henrik Mouritsen,&nbsp;Karl-Wilhelm Koch,&nbsp;Ilia A. Solov’yov* and Izabella Brand*,&nbsp;","doi":"10.1021/acschembio.4c0057610.1021/acschembio.4c00576","DOIUrl":"https://doi.org/10.1021/acschembio.4c00576https://doi.org/10.1021/acschembio.4c00576","url":null,"abstract":"<p >Since the middle of the 20th century, long-distance avian migration has been known to rely partly on geomagnetic field. However, the underlying sensory mechanism is still not fully understood. Cryptochrome-4a (ErCry4a), found in European robin (<i>Erithacus rubecula</i>), a night-migratory songbird, has been suggested to be a magnetic sensory molecule. It is sensitive to external magnetic fields via the so-called radical-pair mechanism. ErCry4a is primarily located in the outer segments of the double-cone photoreceptor cells in the eye, which contain stacked and highly ordered membranes that could facilitate the anisotropic attachment of ErCry4a needed for magnetic compass sensing. Here, we investigate possible interactions of ErCry4a with a model membrane that mimics the lipid composition of outer segments of vertebrate photoreceptor cells using experimental and computational approaches. Experimental results show that the attachment of ErCry4a to the membrane could be controlled by the physical state of lipid molecules (average area per lipid) in the outer leaflet of the lipid bilayer. Furthermore, polarization modulation infrared reflection absorption spectroscopy allowed us to determine the conformation, motional freedom, and average orientation of the α-helices in ErCry4a in a membrane-associated state. Atomistic molecular dynamics studies supported the experimental results. <i>A</i> ∼ 1000 kcal mol^–1 decrease in the interaction energy as a result of ErCry4a membrane binding was determined compared to cases where no protein binding to the membrane occurred. At the molecular level, the binding seems to involve negatively charged carboxylate groups of the phosphoserine lipids and the C-terminal residues of ErCry4a. Our study reveals a potential direct interaction of ErCry4a with the lipid membrane and discusses how this binding could be an essential step for ErCry4a to propagate a magnetic signal further and thus fulfill a role as a magnetoreceptor.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":"20 3","pages":"592–606 592–606"},"PeriodicalIF":3.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acschembio.4c00576","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143667018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mapping snoRNA Targets Transcriptome-Wide with snoKARR-seq.","authors":"Bei Liu","doi":"10.1021/acschembio.4c00813","DOIUrl":"10.1021/acschembio.4c00813","url":null,"abstract":"<p><p>Small nucleolar RNAs (snoRNAs) are noncoding RNAs primarily known for guiding chemical modifications of RNA, but their broader cellular roles and contributions to human diseases remain elusive. This In Focus article introduces the development of snoRNA-enriched kethoxal-assisted RNA-RNA sequencing (snoKARR-seq), a transcriptome-wide approach to uncover snoRNA targets with enhanced sensitivity and specificity. This method revealed an unexpected role for snoRNAs in protein translocation and secretion, expanding our understanding of their noncanonical functions.</p>","PeriodicalId":11,"journal":{"name":"ACS Chemical Biology","volume":" ","pages":"242-244"},"PeriodicalIF":3.5,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142981988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}