RSC Chemical Biology最新文献_第10页

Carbohydrate-active enzyme (CAZyme) discovery and engineering via (Ultra)high-throughput screening 通过（超）高通量筛选发现和设计碳水化合物活性酶 (CAZyme)

IF 4.2

RSC Chemical Biology Pub Date : 2024-05-23 DOI: 10.1039/D4CB00024B

Jacob F. Wardman and Stephen G. Withers

引用次数: 0

Chemical tools for profiling the intracellular ADP-ribosylated proteome† 剖析细胞内 ADP 核糖基化蛋白质组的化学工具

IF 4.2

RSC Chemical Biology Pub Date : 2024-05-22 DOI: 10.1039/D4CB00043A

Simeon D. Draganov, Michael J. Gruet, Daniel Conole, Cristina Balcells, Alexandros P. Siskos, Hector C. Keun, Dorian O. Haskard and Edward W. Tate

{"title":"Chemical tools for profiling the intracellular ADP-ribosylated proteome†","authors":"Simeon D. Draganov, Michael J. Gruet, Daniel Conole, Cristina Balcells, Alexandros P. Siskos, Hector C. Keun, Dorian O. Haskard and Edward W. Tate","doi":"10.1039/D4CB00043A","DOIUrl":"10.1039/D4CB00043A","url":null,"abstract":"The post-translational modification (PTM) ADP-ribosylation plays an important role in cell signalling and regulating protein function and has been implicated in the development of multiple diseases, including breast and ovarian cancers. Studying the underlying mechanisms through which this PTM contributes towards disease development, however, has been hampered by the lack of appropriate tools for reliable identification of physiologically relevant ADP-ribosylated proteins in a live-cell environment. Herein, we explore the application of an alkyne-tagged proprobe, 6Yn-ProTide-Ad (6Yn-Pro) as a chemical tool for the identification of intracellular ADP-ribosylated proteins through metabolic labelling. We applied targeted metabolomics and chemical proteomics in HEK293T cells treated with 6Yn-Pro to demonstrate intracellular metabolic conversion of the probe into ADP-ribosylation cofactor 6Yn-NAD+, and subsequent labelling and enrichment of PARP1 and multiple known ADP-ribosylated proteins in cells under hydrogen peroxide-induced stress. We anticipate that the approach and methodology described here will be useful for future identification of novel intracellular ADP-ribosylated proteins.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 7","pages":" 640-651"},"PeriodicalIF":4.2,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d4cb00043a?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141148779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A minimal RNA substrate with dual fluorescent probes enables rapid kinetics and provides insight into bacterial RNase P active site interactions 带有双荧光探针的最低限度 RNA 底物可实现快速动力学，并有助于深入了解细菌 RNase P 活性位点的相互作用

IF 4.2

RSC Chemical Biology Pub Date : 2024-05-17 DOI: 10.1039/D4CB00049H

Tong Huang, Alexandra Chamberlain, Jiaqiang Zhu and Michael E. Harris

{"title":"A minimal RNA substrate with dual fluorescent probes enables rapid kinetics and provides insight into bacterial RNase P active site interactions","authors":"Tong Huang, Alexandra Chamberlain, Jiaqiang Zhu and Michael E. Harris","doi":"10.1039/D4CB00049H","DOIUrl":"10.1039/D4CB00049H","url":null,"abstract":"Bacterial ribonuclease P (RNase P) is a tRNA processing endonuclease that occurs primarily as a ribonucleoprotein with a catalytic RNA subunit (P RNA). As one of the first ribozymes discovered, P RNA is a well-studied model system for understanding RNA catalysis and substrate recognition. Extensive structural and biochemical studies have revealed the structure of RNase P bound to precursor tRNA (ptRNA) and product tRNA. These studies also helped to define active site residues and propose the molecular interactions that are involved in substrate binding and catalysis. However, a detailed quantitative model of the reaction cycle that includes the structures of intermediates and the process of positioning active site metal ions for catalysis is lacking. To further this goal, we used a chemically modified minimal RNA duplex substrate (MD1) to establish a kinetic framework for measuring the functional effects of P RNA active site mutations. Substitution of U69, a critical nucleotide involved in active site Mg2+ binding, was found to reduce catalysis >500-fold as expected, but had no measurable effect on ptRNA binding kinetics. In contrast, the same U69 mutations had little effect on catalysis in Ca2+ compared to reactions containing native Mg2+ ions. CryoEM structures and SHAPE mapping suggested increased flexibility of U69 and adjacent nucleotides in Ca2+ compared to Mg2+. These results support a model in which slow catalysis in Ca2+ is due to inability to engage U69. These studies establish a set of experimental tools to analyze RNase P kinetics and mechanism and can be expanded to gain new insights into the assembly of the active RNase P–ptRNA complex.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 7","pages":" 652-668"},"PeriodicalIF":4.2,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d4cb00049h?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141062035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Insights into docking in megasynthases from the investigation of the toblerol trans-AT polyketide synthase: many α-helical means to an end† 通过对 toblerol 反式-AT 多酮类合成酶的研究，深入了解巨合成酶的对接：实现目的的多种 α 螺旋手段

IF 4.2

RSC Chemical Biology Pub Date : 2024-05-16 DOI: 10.1039/D4CB00075G

Serge Scat, Kira J. Weissman and Benjamin Chagot

{"title":"Insights into docking in megasynthases from the investigation of the toblerol trans-AT polyketide synthase: many α-helical means to an end†","authors":"Serge Scat, Kira J. Weissman and Benjamin Chagot","doi":"10.1039/D4CB00075G","DOIUrl":"10.1039/D4CB00075G","url":null,"abstract":"The fidelity of biosynthesis by modular polyketide synthases (PKSs) depends on specific moderate affinity interactions between successive polypeptide subunits mediated by docking domains (DDs). These sequence elements are notably portable, allowing their transplantation into alternative biosynthetic and metabolic contexts. Herein, we use integrative structural biology to characterize a pair of DDs from the toblerol trans-AT PKS. Both are intrinsically disordered regions (IDRs) that fold into a 3 α-helix docking complex of unprecedented topology. The C-terminal docking domain (CDD) resembles the 4 α-helix type (4HB) CDDs, which shows that the same type of DD can be redeployed to form complexes of distinct geometry. By carefully re-examining known DD structures, we further extend this observation to type 2 docking domains, establishing previously unsuspected structural relations between DD types. Taken together, these data illustrate the plasticity of α-helical DDs, which allow the formation of a diverse topological spectrum of docked complexes. The newly identified DDs should also find utility in modular PKS genetic engineering.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 7","pages":" 669-683"},"PeriodicalIF":4.2,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d4cb00075g?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141062141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

[68Ga]Ga-THP-tetrazine for bioorthogonal click radiolabelling: pretargeted PET imaging of liposomal nanomedicines† 用于生物正交点击放射性标记的[68Ga]Ga-THP-四嗪：脂质体纳米药物的前靶向 PET 成像

IF 4.2

RSC Chemical Biology Pub Date : 2024-05-14 DOI: 10.1039/D4CB00039K

Aishwarya Mishra, Amaia Carrascal-Miniño, Jana Kim and Rafael T. M. de Rosales

{"title":"[68Ga]Ga-THP-tetrazine for bioorthogonal click radiolabelling: pretargeted PET imaging of liposomal nanomedicines†","authors":"Aishwarya Mishra, Amaia Carrascal-Miniño, Jana Kim and Rafael T. M. de Rosales","doi":"10.1039/D4CB00039K","DOIUrl":"10.1039/D4CB00039K","url":null,"abstract":"Pretargeted PET imaging using bioorthogonal chemistry is a leading strategy for the tracking of long-circulating agents such as antibodies and nanoparticle-drug delivery systems with short-lived isotopes. Here, we report the synthesis, characterisation and in vitro/vivo evaluation of a new 68Ga-based radiotracer [68Ga]Ga-THP-Tetrazine ([68Ga]Ga-THP-Tz) for bioorthogonal click radiochemistry and in vivo labelling of agents with slow pharmacokinetics. THP-tetrazine (THP-Tz) can be radiolabelled to give [68/67Ga]Ga-THP-Tz at room temperature in less than 15 minutes with excellent radiochemical stability in vitro and in vivo. [68Ga]Ga-THP-Tz was tested in vitro and in vivo for pretargeted imaging of stealth PEGylated liposomes, chosen as a leading clinically-approved platform of nanoparticle-based drug delivery, and for their known long-circulating properties. To achieve this, PEGylated liposomes were functionalised with a synthesised transcyclooctene (TCO) modified phospholipid. Radiolabelling of TCO-PEG-liposomes with [68/67Ga]Ga-THP-Tz was demonstrated in vitro in human serum, and in vivo using both healthy mice and in a syngeneic cancer murine model (WEHI-164 fibrosarcoma). Interestingly in vivo data revealed that [68Ga]Ga-THP-Tz was able to in vivo radiolabel liposomes present in the liver and spleen, and not those in the blood pool or in the tumour. Overall, these results demonstrate the potential of [68Ga]Ga-THP-Tz for pretargeted imaging/therapy but also some unexpected limitations of this system.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 7","pages":" 622-639"},"PeriodicalIF":4.2,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d4cb00039k?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140937007","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mining proteomes for zinc finger persulfidation† 为锌指过硫化挖掘蛋白质组

IF 4.1

RSC Chemical Biology Pub Date : 2024-05-13 DOI: 10.1039/D3CB00106G

Haoju Li, Andrew T. Stoltzfus and Sarah L. J. Michel

{"title":"Mining proteomes for zinc finger persulfidation†","authors":"Haoju Li, Andrew T. Stoltzfus and Sarah L. J. Michel","doi":"10.1039/D3CB00106G","DOIUrl":"10.1039/D3CB00106G","url":null,"abstract":"Hydrogen sulfide (H2S) is an endogenous gasotransmitter that signals via persulfidation. There is evidence that the cysteine residues of certain zinc finger (ZF) proteins, a common type of cysteine rich protein, are modified to persulfides by H2S. To determine how frequently ZF persulfidation occurs in cells and identify the types of ZFs that are persulfidated, persulfide specific proteomics data were evaluated. 22 datasets from 16 studies were analyzed via a meta-analysis approach. Persulfidated ZFs were identified in a range of eukaryotic species, including Homo sapiens, Mus musculus, Rattus norvegicus, Arabidopsis thaliana, and Emiliania huxley (single-celled phytoplankton). The types of ZFs identified for each species encompassed all three common ZF ligand sets (4-cysteine, 3-cysteine-1-histidine, and 2-cysteine-2-hisitidine), indicating that persulfidation of ZFs is broad. Overlap analysis between different species identified several common ZFs. GO and KEGG analysis identified pathway enrichment for ubiquitin-dependent protein catabolic process and viral carcinogenesis. These collective findings support ZF persulfidation as a wide-ranging PTM that impacts all classes of ZFs.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 6","pages":" 572-585"},"PeriodicalIF":4.1,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d3cb00106g?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140936829","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Introduction to “Chemical biology of metals” 金属化学生物学 "简介

IF 4.1

RSC Chemical Biology Pub Date : 2024-05-10 DOI: 10.1039/D4CB90017K

Angela Casini, Hui Chao, Hongzhe Sun and Christopher J. Chang

引用次数: 0

Target identification of usnic acid in bacterial and human cells† 细菌和人体细胞中的鸟苷酸靶标鉴定

IF 4.2

RSC Chemical Biology Pub Date : 2024-05-07 DOI: 10.1039/D4CB00040D

Stuart A. Ruddell, Dietrich Mostert and Stephan A. Sieber

引用次数: 0

Recent advances in chemical biology tools for protein and RNA profiling of extracellular vesicles 用于细胞外囊泡蛋白质和 RNA 分析的化学生物学工具的最新进展

IF 4.1

RSC Chemical Biology Pub Date : 2024-04-30 DOI: 10.1039/D3CB00200D

Woojeong Lim, Soyeon Lee, Minseob Koh, Ala Jo and Jongmin Park

{"title":"Recent advances in chemical biology tools for protein and RNA profiling of extracellular vesicles","authors":"Woojeong Lim, Soyeon Lee, Minseob Koh, Ala Jo and Jongmin Park","doi":"10.1039/D3CB00200D","DOIUrl":"10.1039/D3CB00200D","url":null,"abstract":"Extracellular vesicles (EVs) are nano-sized vesicles secreted by cells that contain various cellular components such as proteins, nucleic acids, and lipids from the parent cell. EVs are abundant in body fluids and can serve as circulating biomarkers for a variety of diseases or as a regulator of various biological processes. Considering these characteristics of EVs, analysis of the EV cargo has been spotlighted for disease diagnosis or to understand biological processes in biomedical research. Over the past decade, technologies for rapid and sensitive analysis of EVs in biofluids have evolved, but detection and isolation of targeted EVs in complex body fluids is still challenging due to the unique physical and biological properties of EVs. Recent advances in chemical biology provide new opportunities for efficient profiling of the molecular contents of EVs. A myriad of chemical biology tools have been harnessed to enhance the analytical performance of conventional assays for better understanding of EV biology. In this review, we will discuss the improvements that have been achieved using chemical biology tools.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 6","pages":" 483-499"},"PeriodicalIF":4.1,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d3cb00200d?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140837624","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","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 synthesis of grafted cyclotides using a “plug and play” approach† 采用 "即插即用 "方法化学合成接枝环苷酸

IF 4.1

RSC Chemical Biology Pub Date : 2024-04-29 DOI: 10.1039/D4CB00008K

Johannes Koehbach, Edin Muratspahić, Zakaria M Ahmed, Andrew M White, Nataša Tomašević, Thomas Durek, Richard J Clark, Christian W Gruber and David J Craik

{"title":"Chemical synthesis of grafted cyclotides using a “plug and play” approach†","authors":"Johannes Koehbach, Edin Muratspahić, Zakaria M Ahmed, Andrew M White, Nataša Tomašević, Thomas Durek, Richard J Clark, Christian W Gruber and David J Craik","doi":"10.1039/D4CB00008K","DOIUrl":"10.1039/D4CB00008K","url":null,"abstract":"Cyclotides are a diverse class of plant-derived cyclic, disulfide-rich peptides with a unique cyclic cystine knot topology. Their remarkable structural stability and resistance to proteolytic degradation can lead to improved pharmacokinetics and oral activity as well as selectivity and high enzymatic stability. Thus, cyclotides have emerged as powerful scaffold molecules for designing peptide-based therapeutics. The chemical engineering of cyclotides has generated novel peptide ligands of G protein-coupled receptors (GPCRs), today's most exploited drug targets. However key challenges potentially limit the widespread use of cyclotides in molecular grafting applications. Folding of cyclotides containing bioactive epitopes remains a major bottleneck in cyclotide synthesis. Here we present a modular ‘plug and play’ approach that effectively bypasses problems associated with the oxidative folding of cyclotides. By grafting onto a pre-formed acyclic cyclotide-like scaffold we show that difficult-to-graft sequences can be easily obtained and can target GPCRs with nanomolar affinities and potencies. We further show the suitability of this new method to graft other complex epitopes including structures with additional disulfide bonds that are not readily available via currently employed chemical methods, thus fully unlocking cyclotides to be used in drug design applications.","PeriodicalId":40691,"journal":{"name":"RSC Chemical Biology","volume":" 6","pages":" 567-571"},"PeriodicalIF":4.1,"publicationDate":"2024-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.rsc.org/en/content/articlepdf/2024/cb/d4cb00008k?page=search","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140811682","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0