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Advances in the understanding and exploitation of carbohydrate-active enzymes 在了解和利用碳水化合物活性酶方面取得的进展
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2024-04-23 DOI: 10.1016/j.cbpa.2024.102457
Rajneesh K. Bains , Seyed Amirhossein Nasseri , Jacob F. Wardman , Stephen G. Withers
{"title":"Advances in the understanding and exploitation of carbohydrate-active enzymes","authors":"Rajneesh K. Bains ,&nbsp;Seyed Amirhossein Nasseri ,&nbsp;Jacob F. Wardman ,&nbsp;Stephen G. Withers","doi":"10.1016/j.cbpa.2024.102457","DOIUrl":"https://doi.org/10.1016/j.cbpa.2024.102457","url":null,"abstract":"<div><p>Carbohydrate-active enzymes (CAZymes) are responsible for the biosynthesis, modification and degradation of all glycans in Nature. Advances in genomic and metagenomic methodologies, in conjunction with lower cost gene synthesis, have provided access to a steady stream of new CAZymes with both well-established and novel mechanisms. At the same time, increasing access to cryo-EM has resulted in exciting new structures, particularly of transmembrane glycosyltransferases of various sorts. This improved understanding has resulted in widespread progress in applications of CAZymes across diverse fields, including therapeutics, organ transplantation, foods, and biofuels. Herein, we highlight a few of the many important advances that have recently been made in the understanding and applications of CAZymes.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"80 ","pages":"Article 102457"},"PeriodicalIF":7.8,"publicationDate":"2024-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1367593124000334/pdfft?md5=6d0859c5becaa91bba0bea262cdd097f&pid=1-s2.0-S1367593124000334-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140633184","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}
引用次数: 0
Recent advances in the synthesis of extensive libraries of heparan sulfate oligosaccharides for structure–activity relationship studies 用于结构-活性关系研究的大量硫酸肝素寡糖库合成的最新进展
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2024-04-17 DOI: 10.1016/j.cbpa.2024.102455
Sherif Ramadan , Morgan Mayieka , Nicola L.B. Pohl , Jian Liu , Linda C. Hsieh-Wilson , Xuefei Huang
{"title":"Recent advances in the synthesis of extensive libraries of heparan sulfate oligosaccharides for structure–activity relationship studies","authors":"Sherif Ramadan ,&nbsp;Morgan Mayieka ,&nbsp;Nicola L.B. Pohl ,&nbsp;Jian Liu ,&nbsp;Linda C. Hsieh-Wilson ,&nbsp;Xuefei Huang","doi":"10.1016/j.cbpa.2024.102455","DOIUrl":"https://doi.org/10.1016/j.cbpa.2024.102455","url":null,"abstract":"<div><p>Heparan sulfate (HS) is a linear, sulfated and highly negatively-charged polysaccharide that plays important roles in many biological events. As a member of the glycosaminoglycan (GAG) family, HS is commonly found on mammalian cell surfaces and within the extracellular matrix. The structural complexities of natural HS polysaccharides have hampered the comprehension of their biological functions and structure–activity relationships (SARs). Although the sulfation patterns and backbone structures of HS can be major determinants of their biological activities, obtaining significant amounts of pure HS from natural sources for comprehensive SAR studies is challenging. Chemical and enzyme-based synthesis can aid in the production of structurally well-defined HS oligosaccharides. In this review, we discuss recent innovations enabling the syntheses of large libraries of HS and how these libraries can provide insights into the structural preferences of various HS binding proteins.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"80 ","pages":"Article 102455"},"PeriodicalIF":7.8,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140558086","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}
引用次数: 0
Advances in understanding and exploiting Siglec–glycan interactions 在理解和利用 Siglec-聚糖相互作用方面取得的进展
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2024-04-16 DOI: 10.1016/j.cbpa.2024.102454
Zeinab Jame-Chenarboo , Taylor E. Gray , Matthew S. Macauley
{"title":"Advances in understanding and exploiting Siglec–glycan interactions","authors":"Zeinab Jame-Chenarboo ,&nbsp;Taylor E. Gray ,&nbsp;Matthew S. Macauley","doi":"10.1016/j.cbpa.2024.102454","DOIUrl":"https://doi.org/10.1016/j.cbpa.2024.102454","url":null,"abstract":"<div><p>Sialic-acid-binding immunoglobulin-type lectins (Siglecs) are a family of cell-surface immunomodulatory receptors that recognize sialic-acid-containing glycans. The majority of Siglecs have an inhibitory motif in their intercellular domain and can regulate the cellular activation of immune cells. Importantly, the immunomodulatory role of Siglecs is regulated by engagement with distinct sialoglycan ligands. However, there are still many unanswered questions about the precise ligand(s) recognized by individual Siglec family members. New tools and approaches to study Siglec-ligand interactions are rapidly filling this knowledge gap. This review provides an overview of recent advances in discovering Siglec ligands as well as the development of approaches to modulate the function of Siglecs. In both aspects, chemical biology approaches are emphasized with a discussion on how these are complementing biochemical and genetic strategies.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"80 ","pages":"Article 102454"},"PeriodicalIF":7.8,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1367593124000309/pdfft?md5=cd791a4182d02e767f01f9a1108a7461&pid=1-s2.0-S1367593124000309-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140555451","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}
引用次数: 0
Chemical biology tools to probe bacterial glycans 探究细菌聚糖的化学生物学工具
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2024-04-05 DOI: 10.1016/j.cbpa.2024.102453
Daniel Calles-Garcia, Danielle H. Dube
{"title":"Chemical biology tools to probe bacterial glycans","authors":"Daniel Calles-Garcia,&nbsp;Danielle H. Dube","doi":"10.1016/j.cbpa.2024.102453","DOIUrl":"https://doi.org/10.1016/j.cbpa.2024.102453","url":null,"abstract":"<div><p>Bacterial cells are covered by a complex carbohydrate coat of armor that allows bacteria to thrive in a range of environments. As a testament to the importance of bacterial glycans, effective and heavily utilized antibiotics including penicillin and vancomycin target and disrupt the bacterial glycocalyx. Despite their importance, the study of bacterial glycans lags far behind their eukaryotic counterparts. Bacterial cells use a large palette of monosaccharides to craft glycans, leading to molecules that are significantly more complex than eukaryotic glycans and that are refractory to study. Fortunately, chemical tools designed to probe bacterial glycans have yielded insights into these molecules, their structures, their biosynthesis, and their functions.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"80 ","pages":"Article 102453"},"PeriodicalIF":7.8,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1367593124000292/pdfft?md5=5dc5c419e38b4491df61cf9fd077d1a0&pid=1-s2.0-S1367593124000292-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140351985","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}
引用次数: 0
Chemical toolbox to interrogate Heparanase-1 activity 研究肝素酶-1 活性的化学工具箱
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2024-03-30 DOI: 10.1016/j.cbpa.2024.102452
Zachary M. Rabinowitz, Johnathan Somers, Zhishen Wang, Lina Cui
{"title":"Chemical toolbox to interrogate Heparanase-1 activity","authors":"Zachary M. Rabinowitz,&nbsp;Johnathan Somers,&nbsp;Zhishen Wang,&nbsp;Lina Cui","doi":"10.1016/j.cbpa.2024.102452","DOIUrl":"https://doi.org/10.1016/j.cbpa.2024.102452","url":null,"abstract":"<div><p>The development of a robust chemical toolbox to interrogate the activity of heparanase-1 (HPSE-1), an endo-β-<span>d</span>-glucuronidase and the only known enzyme that cleaves heparan sulfate (HS), has become critically important. The primary function of HPSE-1, cleaving HS side chains from heparan sulfate proteoglycans (HSPGs), regulates the integrity of the extracellular matrix (ECM) and the bioavailability of active, heparan sulfate-binding partners such as enzymes, growth factors, chemokines, and cytokines. HPSE-1 enzymatic activity is strictly regulated and has been found to play fundamental roles in pathophysiological processes. HPSE-1 is significantly overexpressed under various conditions including cancer, metastasis, angiogenesis, and inflammation, making HPSE-1 a promising therapeutic and diagnostic target. Chemical tools that can detect and image HPSE-1 activity <em>in vitro</em> and/or <em>in vivo</em> can help drive the discovery of novel and efficacious anti-HPSE-1 drugs, investigate the basic biology of HPSE-1, and help serve as a diagnostic tool in clinical applications. Here, we will give an overview of the common chemical tools to detect HPSE-1 activity and highlight the novel heparanase probes recently developed in our lab.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"80 ","pages":"Article 102452"},"PeriodicalIF":7.8,"publicationDate":"2024-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140328147","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}
引用次数: 0
Fluorogenic polymethine dyes by intramolecular cyclization 通过分子内环化作用生成含氟聚甲基染料
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2024-03-23 DOI: 10.1016/j.cbpa.2024.102444
Annabell Martin , Pablo Rivera-Fuentes
{"title":"Fluorogenic polymethine dyes by intramolecular cyclization","authors":"Annabell Martin ,&nbsp;Pablo Rivera-Fuentes","doi":"10.1016/j.cbpa.2024.102444","DOIUrl":"https://doi.org/10.1016/j.cbpa.2024.102444","url":null,"abstract":"<div><p>Fluorescence imaging plays a pivotal role in the study of biological processes, and cell-permeable fluorogenic dyes are crucial to visualize intracellular structures with high specificity. Polymethine dyes are vitally important fluorophores in single-molecule localization microscopy and <em>in vivo</em> imaging, but their use in live cells has been limited by high background fluorescence and low membrane permeability. In this review, we summarize recent advances in the development of fluorogenic polymethine dyes <em>via</em> intramolecular cyclization. Finally, we offer an outlook on the prospects of fluorogenic polymethine dyes for bioimaging.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"80 ","pages":"Article 102444"},"PeriodicalIF":7.8,"publicationDate":"2024-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1367593124000206/pdfft?md5=4c69f98d22908c5110c6e62e2fce389f&pid=1-s2.0-S1367593124000206-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140190568","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}
引用次数: 0
Sortase-mediated labeling: Expanding frontiers in site-specific protein functionalization opens new research avenues 分类酶介导的标记：拓展特定位点蛋白质功能化的前沿，开辟新的研究途径
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2024-03-19 DOI: 10.1016/j.cbpa.2024.102443
Nayara Braga Emidio, Ross W. Cheloha
{"title":"Sortase-mediated labeling: Expanding frontiers in site-specific protein functionalization opens new research avenues","authors":"Nayara Braga Emidio,&nbsp;Ross W. Cheloha","doi":"10.1016/j.cbpa.2024.102443","DOIUrl":"https://doi.org/10.1016/j.cbpa.2024.102443","url":null,"abstract":"<div><p>New applications for biomolecules demand novel approaches for their synthesis and modification. Traditional methods for modifying proteins and cells using non-specific labeling chemistry are insufficiently precise to rigorously interrogate the mechanistic biological and physiological questions at the forefront of biomedical science. Site-specific catalytic modification of proteins promises to meet these challenges. Here, we describe recent applications of the enzyme sortase A in facilitating precise biomolecule labeling. We focus on describing new chemistries to broaden the scope of sortase-mediated labeling (sortagging), the development of new probes for imaging via enzymatic labeling, and the modulation of biological systems using probes and reactions mediated by sortase.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"80 ","pages":"Article 102443"},"PeriodicalIF":7.8,"publicationDate":"2024-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140160306","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}
引用次数: 0
Site-specific protein labeling strategies for super-resolution microscopy 用于超分辨率显微镜的特定位点蛋白质标记策略
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2024-03-14 DOI: 10.1016/j.cbpa.2024.102445
Made Budiarta , Marcel Streit , Gerti Beliu
{"title":"Site-specific protein labeling strategies for super-resolution microscopy","authors":"Made Budiarta ,&nbsp;Marcel Streit ,&nbsp;Gerti Beliu","doi":"10.1016/j.cbpa.2024.102445","DOIUrl":"https://doi.org/10.1016/j.cbpa.2024.102445","url":null,"abstract":"<div><p>Super-resolution microscopy (SRM) has transformed our understanding of proteins' subcellular organization and revealed cellular details down to nanometers, far beyond conventional microscopy. While localization precision is independent of the number of fluorophores attached to a biomolecule, labeling density is a decisive factor for resolving complex biological structures. The average distance between adjacent fluorophores should be less than half the desired spatial resolution for optimal clarity. While this was not a major limitation in recent decades, the success of modern microscopy approaching molecular resolution down to the single-digit nanometer range will depend heavily on advancements in fluorescence labeling. This review highlights recent advances and challenges in labeling strategies for SRM, focusing on site-specific labeling technologies. These advancements are crucial for improving SRM precision and expanding our understanding of molecular interactions.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"80 ","pages":"Article 102445"},"PeriodicalIF":7.8,"publicationDate":"2024-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1367593124000218/pdfft?md5=ec83e73c1a4b24d2d5b6a634493a448c&pid=1-s2.0-S1367593124000218-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140123036","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}
引用次数: 0
Advancing mass spectrometry–based glycoproteomic software tools for comprehensive site-specific glycoproteome analysis 推进基于质谱技术的糖蛋白组软件工具，以进行全面的特定位点糖蛋白组分析
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2024-03-08 DOI: 10.1016/j.cbpa.2024.102442
Weiqian Cao
{"title":"Advancing mass spectrometry–based glycoproteomic software tools for comprehensive site-specific glycoproteome analysis","authors":"Weiqian Cao","doi":"10.1016/j.cbpa.2024.102442","DOIUrl":"https://doi.org/10.1016/j.cbpa.2024.102442","url":null,"abstract":"<div><p>Glycoproteome analysis at a site-specific level and proteome scale stands out as a highly promising approach for gaining insights into the intricate roles of glycans in biological systems. Recent years have witnessed an upsurge in the development of innovative methodologies tailored for precisely this purpose. Breakthroughs in mass spectrometry–based glycoproteomic techniques, enabling the identification, quantification, and systematic exploration of site-specific glycans, have significantly enhanced our capacity to comprehensively and thoroughly characterize glycoproteins. In this short review, we delve into novel tools in advancing site-specific glycoproteomic analysis and summarize pertinent studies published in the past two years. Lastly, we discuss the ongoing challenges and outline future prospects in the field, considering both the analytical strategies of mass spectrometry and the tools employed for data interpretation.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"80 ","pages":"Article 102442"},"PeriodicalIF":7.8,"publicationDate":"2024-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140066765","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}
引用次数: 0
Recent advances in ratiometric fluorescence imaging of enzyme activity in vivo 体内酶活性比率荧光成像的最新进展
IF 7.8 2区 生物学
Current Opinion in Chemical Biology Pub Date : 2024-03-07 DOI: 10.1016/j.cbpa.2024.102441
Emily D. Cosco , Matthew Bogyo
{"title":"Recent advances in ratiometric fluorescence imaging of enzyme activity in vivo","authors":"Emily D. Cosco ,&nbsp;Matthew Bogyo","doi":"10.1016/j.cbpa.2024.102441","DOIUrl":"https://doi.org/10.1016/j.cbpa.2024.102441","url":null,"abstract":"<div><p>Among molecular imaging modalities that can monitor enzyme activity <em>in vivo,</em> optical imaging provides sensitive, molecular-level information at low-cost using safe and non-ionizing wavelengths of light. Yet, obtaining quantifiable optical signals <em>in vivo</em> poses significant challenges. Benchmarking using ratiometric signals can overcome dependence on dosing, illumination variability, and pharmacokinetics to provide quantitative <em>in vivo</em> optical data. This review highlights recent advances using fluorescent probes that are processed by enzymes to induce photophysical changes that can be monitored by ratiometric imaging. These diverse strategies include caged fluorophores that change photophysical properties upon enzymatic cleavage, as well as multi-fluorophore systems that are triggered by enzymatic cleavage to alter optical outputs in one or more fluorescent channels. The strategies discussed here have great potential for further development as well as potential broad applications for targeting diverse enzymes important for a wide range of human diseases.</p></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"80 ","pages":"Article 102441"},"PeriodicalIF":7.8,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140052106","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}
引用次数: 0
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