Pub Date : 2025-12-01Epub Date: 2025-11-19DOI: 10.1016/j.cbpa.2025.102640
Jing Yang, Wenqing Shui
{"title":"Editorial Overview: Converging innovations in chemical proteomics","authors":"Jing Yang, Wenqing Shui","doi":"10.1016/j.cbpa.2025.102640","DOIUrl":"10.1016/j.cbpa.2025.102640","url":null,"abstract":"","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"89 ","pages":"Article 102640"},"PeriodicalIF":6.1,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145561937","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}
Pub Date : 2025-10-01Epub Date: 2025-09-11DOI: 10.1016/j.cbpa.2025.102629
Ting Dang , Wenqing Shui
Proximity labeling (PL), with its capability to resolve spatiotemporal dynamics of biomolecular interactions, has become a pivotal technology for interrogating protein–protein interaction networks, subcellular proteomics, and intercellular communication. This review focuses on the breakthrough developments in PL from 2023 to 2025, highlighting three major frontiers: (1) catalytic system innovation, including the development of new enzymes, cascade reactions, and environment-responsive labeling systems, which collectively lead to increased spatiotemporal resolution and enhanced in vivo applicability; (2) new strategies to address endogenous targets, facilitating interactome mapping in native tissues and live animals; and (3) determination of the labeling radius for different PL tools using super-resolution imaging or DNA nanostructures. We also briefly discuss the desired innovation in the next-generation PL research.
{"title":"Evolving advances of proximity labeling in capturing biomolecular interactions","authors":"Ting Dang , Wenqing Shui","doi":"10.1016/j.cbpa.2025.102629","DOIUrl":"10.1016/j.cbpa.2025.102629","url":null,"abstract":"<div><div>Proximity labeling (PL), with its capability to resolve spatiotemporal dynamics of biomolecular interactions, has become a pivotal technology for interrogating protein–protein interaction networks, subcellular proteomics, and intercellular communication. This review focuses on the breakthrough developments in PL from 2023 to 2025, highlighting three major frontiers: (1) catalytic system innovation, including the development of new enzymes, cascade reactions, and environment-responsive labeling systems, which collectively lead to increased spatiotemporal resolution and enhanced <em>in vivo</em> applicability; (2) new strategies to address endogenous targets, facilitating interactome mapping in native tissues and live animals; and (3) determination of the labeling radius for different PL tools using super-resolution imaging or DNA nanostructures. We also briefly discuss the desired innovation in the next-generation PL research.</div></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"88 ","pages":"Article 102629"},"PeriodicalIF":6.1,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145044511","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}
Pub Date : 2025-10-01Epub Date: 2025-09-12DOI: 10.1016/j.cbpa.2025.102630
Jing Chen , Qun Zhao , Yukui Zhang , Lihua Zhang
In vivo chemical cross-linking mass spectrometry (XL-MS) has emerged as a powerful technique for high-throughput, proteome-wide mapping of intramolecular conformations and intermolecular interactions of protein complexes in living cells. By providing distance constraints between specific residues, XL-MS enables the characterization of protein conformations and interaction networks under near-physiological conditions, greatly facilitating the analysis of biomacromolecular functions and regulatory mechanisms. The information obtained from cross-linking is particularly valuable at the systems level, and its value continues to increase with improvements in the density of cross-link identification, the precision of distance constraints, and the spatiotemporal resolution. In recent years, advances in cross-linker design, cross-linked peptide enrichment methods, mass spectrometry analysis, and artificial intelligence-assisted data analysis have significantly expanded the capabilities of in vivo XL-MS. This article systematically reviews the latest progress in in vivo XL-MS for protein conformation and interaction network analysis, highlights its unique advantages, discusses current technical challenges, and explores further development.
{"title":"In vivo cross-linking mass spectrometry: Advances and challenges in decoding protein conformational dynamics and complex regulatory networks in living cells","authors":"Jing Chen , Qun Zhao , Yukui Zhang , Lihua Zhang","doi":"10.1016/j.cbpa.2025.102630","DOIUrl":"10.1016/j.cbpa.2025.102630","url":null,"abstract":"<div><div><em>In vivo</em> chemical cross-linking mass spectrometry (XL-MS) has emerged as a powerful technique for high-throughput, proteome-wide mapping of intramolecular conformations and intermolecular interactions of protein complexes in living cells. By providing distance constraints between specific residues, XL-MS enables the characterization of protein conformations and interaction networks under near-physiological conditions, greatly facilitating the analysis of biomacromolecular functions and regulatory mechanisms. The information obtained from cross-linking is particularly valuable at the systems level, and its value continues to increase with improvements in the density of cross-link identification, the precision of distance constraints, and the spatiotemporal resolution. In recent years, advances in cross-linker design, cross-linked peptide enrichment methods, mass spectrometry analysis, and artificial intelligence-assisted data analysis have significantly expanded the capabilities of <em>in vivo</em> XL-MS. This article systematically reviews the latest progress in <em>in vivo</em> XL-MS for protein conformation and interaction network analysis, highlights its unique advantages, discusses current technical challenges, and explores further development.</div></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"88 ","pages":"Article 102630"},"PeriodicalIF":6.1,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145044512","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}
Pub Date : 2025-10-01Epub Date: 2025-07-24DOI: 10.1016/j.cbpa.2025.102622
Wensi Zhao , Jun Zhang , Kaifeng Chen , Jian Yuan , Linhui Zhai , Minjia Tan
Histone post-translational modifications (PTMs) play critical roles in regulating chromatin dynamics and gene expression. Increasing evidence demonstrates that the dysregulation of histone PTMs is closely associated with the pathogenesis of various diseases. Traditional methods for detecting histone PTMs, such as western blot (WB) and chromatin immunoprecipitation sequencing (ChIP-seq), are often limited by their dependence on specific antibodies and relatively low analytical throughput. Mass spectrometry (MS)-based proteomics offers a powerful and unbiased approach for comprehensive characterization of histone PTMs. This review focuses on the advanced development of MS-based strategies for characterizing histone PTMs. These strategies include histone extraction, enzymatic digestion, labeling, enrichment, and MS-based detection. These techniques not only enable comprehensive identification and quantitative analysis of classical modifications, such as acetylation and methylation, but also substantially facilitate the discovery of less-characterized histone PTMs, including succinylation, lactylation, crotonylation, and monoaminylation. Consequently, these findings significantly enhance the complexity of histone code. Collectively, MS-based approaches have profoundly advanced our understanding of histone PTM landscapes and their potential epigenetic regulatory mechanisms in both physiology and pathology contexts.
组蛋白翻译后修饰（PTMs）在调节染色质动力学和基因表达中起着至关重要的作用。越来越多的证据表明，组蛋白ptm的失调与多种疾病的发病密切相关。检测组蛋白ptm的传统方法，如western blot （WB）和染色质免疫沉淀测序（ChIP-seq），往往受其依赖于特异性抗体和相对较低的分析通量的限制。基于质谱（MS）的蛋白质组学为组蛋白ptm的全面表征提供了一种强大而公正的方法。本文综述了基于ms的组蛋白ptm表征策略的最新进展。这些策略包括组蛋白提取、酶消化、标记、富集和质谱检测。这些技术不仅能够对经典修饰（如乙酰化和甲基化）进行全面的鉴定和定量分析，而且还极大地促进了发现较少表征的组蛋白PTMs，包括琥珀酰化、乳酸化、巴豆酰化和单胺化。因此，这些发现显著提高了组蛋白编码的复杂性。总的来说，基于ms的方法深刻地推进了我们对组蛋白PTM景观及其在生理和病理背景下潜在的表观遗传调控机制的理解。
{"title":"Mass spectrometry-based characterization of histone post-translational modification","authors":"Wensi Zhao , Jun Zhang , Kaifeng Chen , Jian Yuan , Linhui Zhai , Minjia Tan","doi":"10.1016/j.cbpa.2025.102622","DOIUrl":"10.1016/j.cbpa.2025.102622","url":null,"abstract":"<div><div>Histone post-translational modifications (PTMs) play critical roles in regulating chromatin dynamics and gene expression. Increasing evidence demonstrates that the dysregulation of histone PTMs is closely associated with the pathogenesis of various diseases. Traditional methods for detecting histone PTMs, such as western blot (WB) and chromatin immunoprecipitation sequencing (ChIP-seq), are often limited by their dependence on specific antibodies and relatively low analytical throughput. Mass spectrometry (MS)-based proteomics offers a powerful and unbiased approach for comprehensive characterization of histone PTMs. This review focuses on the advanced development of MS-based strategies for characterizing histone PTMs. These strategies include histone extraction, enzymatic digestion, labeling, enrichment, and MS-based detection. These techniques not only enable comprehensive identification and quantitative analysis of classical modifications, such as acetylation and methylation, but also substantially facilitate the discovery of less-characterized histone PTMs, including succinylation, lactylation, crotonylation, and monoaminylation. Consequently, these findings significantly enhance the complexity of histone code. Collectively, MS-based approaches have profoundly advanced our understanding of histone PTM landscapes and their potential epigenetic regulatory mechanisms in both physiology and pathology contexts.</div></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"88 ","pages":"Article 102622"},"PeriodicalIF":6.9,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144697031","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}
Pub Date : 2025-08-01Epub Date: 2025-06-27DOI: 10.1016/j.cbpa.2025.102618
Jefferson Chan, Martin J. Schnermann
{"title":"Editorial overview: Editorial of molecular imaging","authors":"Jefferson Chan, Martin J. Schnermann","doi":"10.1016/j.cbpa.2025.102618","DOIUrl":"10.1016/j.cbpa.2025.102618","url":null,"abstract":"","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"87 ","pages":"Article 102618"},"PeriodicalIF":6.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144502449","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}
Pub Date : 2025-08-01Epub Date: 2025-04-18DOI: 10.1016/j.cbpa.2025.102598
Jay E. Cournoyer , Bidhan C. De , Angad P. Mehta
Mitochondria and chloroplasts evolved through the transformation of bacterial endosymbionts established within the host cells. Studies on these organelles have provided several phylogenetic and biochemical insights related to this remarkable evolutionary transformation. Additionally, comparative studies between naturally existing endosymbionts and present-day organelles have allowed us to identify important common features of endosymbiotic evolution. In this review, we discuss hallmarks of photosynthetic endosymbiotic systems, particularly focusing on some of the fascinating molecular changes that occur in the endosymbiont and the host as the endosymbiont/host chimera evolves and transforms endosymbionts into organelles; these include the following: (i) endosymbiont genome minimization and host/endosymbiont gene transfer, (ii) protein import/export systems, (iii) metabolic crosstalk between the endosymbiont, (iv) alterations to the endosymbiont peptidoglycan, and (v) host-controlled replication of endosymbionts/organelles. We discuss these hallmarks in the context of naturally existing photosynthetic endosymbiotic systems and present-day chloroplasts. Further, we also briefly discuss laboratory efforts to engineer endosymbiosis between photosynthetic bacteria and host cells, the lessons learned from these studies, future directions of these studies, and their implications on evolutionary biology and synthetic biology.
{"title":"Molecular and biochemical insights from natural and engineered photosynthetic endosymbiotic systems","authors":"Jay E. Cournoyer , Bidhan C. De , Angad P. Mehta","doi":"10.1016/j.cbpa.2025.102598","DOIUrl":"10.1016/j.cbpa.2025.102598","url":null,"abstract":"<div><div>Mitochondria and chloroplasts evolved through the transformation of bacterial endosymbionts established within the host cells. Studies on these organelles have provided several phylogenetic and biochemical insights related to this remarkable evolutionary transformation. Additionally, comparative studies between naturally existing endosymbionts and present-day organelles have allowed us to identify important common features of endosymbiotic evolution. In this review, we discuss hallmarks of photosynthetic endosymbiotic systems, particularly focusing on some of the fascinating molecular changes that occur in the endosymbiont and the host as the endosymbiont/host chimera evolves and transforms endosymbionts into organelles; these include the following: (i) endosymbiont genome minimization and host/endosymbiont gene transfer, (ii) protein import/export systems, (iii) metabolic crosstalk between the endosymbiont, (iv) alterations to the endosymbiont peptidoglycan, and (v) host-controlled replication of endosymbionts/organelles. We discuss these hallmarks in the context of naturally existing photosynthetic endosymbiotic systems and present-day chloroplasts. Further, we also briefly discuss laboratory efforts to engineer endosymbiosis between photosynthetic bacteria and host cells, the lessons learned from these studies, future directions of these studies, and their implications on evolutionary biology and synthetic biology.</div></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"87 ","pages":"Article 102598"},"PeriodicalIF":6.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143848300","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}
Pub Date : 2025-08-01Epub Date: 2025-06-28DOI: 10.1016/j.cbpa.2025.102619
Mia L. Huang, Peng Wu
{"title":"Editorial overview: Glycobiology (2024)","authors":"Mia L. Huang, Peng Wu","doi":"10.1016/j.cbpa.2025.102619","DOIUrl":"10.1016/j.cbpa.2025.102619","url":null,"abstract":"","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"87 ","pages":"Article 102619"},"PeriodicalIF":6.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144502448","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}
The integration of proximity labeling (PL) and advanced mass spectrometry-based proteomics is a robust framework for mapping protein–protein interaction (PPI) networks and local protein inventories in the crowded multimolecular environment of live cells. Over the last decade, numerous PL technologies such as biotin identification (BioID), ascorbate peroxidase (APEX) etc. using engineered enzymes or synthetic photocatalysts have been developed and successfully used in cell-based experiments. However, the application of such technologies beyond cultured cells, (i.e. in more complicated tissues or in vivo) remains challenging. In this review, we summarize the current issues in applying PL methods in vivo and highlight recent studies that could provide breakthroughs to overcome the existing limitations and expand the application of PL to tissues and in vivo.
{"title":"Recent advances in proximity labeling for chemical proteomics: Paving the way for in vivo applications","authors":"Fátima Yuri Tanimura Valor, Tomonori Tamura, Itaru Hamachi","doi":"10.1016/j.cbpa.2025.102620","DOIUrl":"10.1016/j.cbpa.2025.102620","url":null,"abstract":"<div><div>The integration of proximity labeling (PL) and advanced mass spectrometry-based proteomics is a robust framework for mapping protein–protein interaction (PPI) networks and local protein inventories in the crowded multimolecular environment of live cells. Over the last decade, numerous PL technologies such as biotin identification (BioID), ascorbate peroxidase (APEX) etc. using engineered enzymes or synthetic photocatalysts have been developed and successfully used in cell-based experiments. However, the application of such technologies beyond cultured cells, (i.e. in more complicated tissues or <em>in vivo</em>) remains challenging. In this review, we summarize the current issues in applying PL methods <em>in vivo</em> and highlight recent studies that could provide breakthroughs to overcome the existing limitations and expand the application of PL to tissues and <em>in vivo</em>.</div></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"87 ","pages":"Article 102620"},"PeriodicalIF":6.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144548597","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}
Pub Date : 2025-08-01Epub Date: 2025-05-23DOI: 10.1016/j.cbpa.2025.102601
Zih-Jheng Lin, Cheng-Yu Fang, Tsung-Shing Andrew Wang
Siderophores are iron chelators secreted by microorganisms to scavenge iron from the environment. Natural siderophores have gained remarkable importance because their conjugates can be applied as antibiotics and diagnostic imaging agents. By utilizing the iron uptake system of microorganisms, functional molecules such as antibiotics or imaging agents can be delivered into cells. Notably, artificial siderophores have also been developed to increase stability and broaden metal chelating diversity. Various strategies, including backbone fine-tuning, artificial chelation moieties, and direct metal swapping, can be employed. Therefore, artificial siderophores can bind biorelated metals or radioactive isotopes, expanding their biological and medical applications. The aim of this review is to introduce recent advances in natural and artificial siderophore applications and highlight future challenges in this area of research.
{"title":"Natural and artificial siderophores: Iron-based applications and beyond","authors":"Zih-Jheng Lin, Cheng-Yu Fang, Tsung-Shing Andrew Wang","doi":"10.1016/j.cbpa.2025.102601","DOIUrl":"10.1016/j.cbpa.2025.102601","url":null,"abstract":"<div><div>Siderophores are iron chelators secreted by microorganisms to scavenge iron from the environment. Natural siderophores have gained remarkable importance because their conjugates can be applied as antibiotics and diagnostic imaging agents. By utilizing the iron uptake system of microorganisms, functional molecules such as antibiotics or imaging agents can be delivered into cells. Notably, artificial siderophores have also been developed to increase stability and broaden metal chelating diversity. Various strategies, including backbone fine-tuning, artificial chelation moieties, and direct metal swapping, can be employed. Therefore, artificial siderophores can bind biorelated metals or radioactive isotopes, expanding their biological and medical applications. The aim of this review is to introduce recent advances in natural and artificial siderophore applications and highlight future challenges in this area of research.</div></div>","PeriodicalId":291,"journal":{"name":"Current Opinion in Chemical Biology","volume":"87 ","pages":"Article 102601"},"PeriodicalIF":6.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144114946","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}
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