{"title":"Two hearts beat as one: the debate over RAS dimers continues","authors":"Andrew G. Stephen","doi":"10.1016/j.tibs.2024.09.005","DOIUrl":"10.1016/j.tibs.2024.09.005","url":null,"abstract":"<div><div>A recent report by <span><span>Yun <em>et al.</em></span><svg><path></path></svg></span> describes the detection of RAS dimers using intact mass spectrometry and investigates the role that membrane lipids, nucleotide state, and binding partners have in their formation.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"49 11","pages":"Pages 933-935"},"PeriodicalIF":11.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11560542/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142363886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Advancing sustainable biotechnology through protein engineering","authors":"Amelia R. Bergeson , Hal S. Alper","doi":"10.1016/j.tibs.2024.07.006","DOIUrl":"10.1016/j.tibs.2024.07.006","url":null,"abstract":"<div><div>The push for industrial sustainability benefits from the use of enzymes as a replacement for traditional chemistry. Biological catalysts, especially those that have been engineered for increased activity, stability, or novel function, and are often greener than alternative chemical approaches. This Review highlights the role of engineered enzymes (and identifies directions for further engineering efforts) in the application areas of greenhouse gas sequestration, fuel production, bioremediation, and degradation of plastic wastes.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"49 11","pages":"Pages 955-968"},"PeriodicalIF":11.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142131555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Advisory Board and Contents","authors":"","doi":"10.1016/S0968-0004(24)00238-X","DOIUrl":"10.1016/S0968-0004(24)00238-X","url":null,"abstract":"","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"49 11","pages":"Pages i-ii"},"PeriodicalIF":11.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142651063","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Seyun Kim , Rashna Bhandari , Charles A. Brearley , Adolfo Saiardi
{"title":"The inositol phosphate signalling network in physiology and disease","authors":"Seyun Kim , Rashna Bhandari , Charles A. Brearley , Adolfo Saiardi","doi":"10.1016/j.tibs.2024.08.005","DOIUrl":"10.1016/j.tibs.2024.08.005","url":null,"abstract":"<div><div>Combinatorial substitution of phosphate groups on the inositol ring gives rise to a plethora of inositol phosphates (InsPs) and inositol pyrophosphates (PP-InsPs). These small molecules constitute an elaborate metabolic and signalling network that influences nearly every cellular function. This review delves into the knowledge accumulated over the past decades regarding the biochemical principles and significance of InsP metabolism. We focus on the biological actions of InsPs in mammals, with an emphasis on recent findings regarding specific target proteins. We further discuss the roles of InsP metabolism in contributing to physiological homeostasis and pathological conditions. A deeper understanding of InsPs and their metabolic pathways holds the potential to address unresolved questions and propel advances towards therapeutic applications.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"49 11","pages":"Pages 969-985"},"PeriodicalIF":11.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bocheng Wu , Angela N. Koehler , Peter M.K. Westcott
{"title":"New opportunities to overcome T cell dysfunction: the role of transcription factors and how to target them","authors":"Bocheng Wu , Angela N. Koehler , Peter M.K. Westcott","doi":"10.1016/j.tibs.2024.08.002","DOIUrl":"10.1016/j.tibs.2024.08.002","url":null,"abstract":"<div><div>Immune checkpoint blockade (ICB) therapies, which block inhibitory receptors on T cells, can be efficacious in reinvigorating dysfunctional T cell responses. However, most cancers do not respond to these therapies and even in those that respond, tumors can acquire resistance. New strategies are needed to rescue and recruit T cell responses across patient populations and disease states. In this review, we define mechanisms of T cell dysfunction, focusing on key transcription factor (TF) networks. We discuss the complex and sometimes contradictory roles of core TFs in both T cell function and dysfunction. Finally, we review strategies to target TFs using small molecule modulators, which represent a challenging but highly promising opportunity to tune the T cell response toward sustained immunity.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"49 11","pages":"Pages 1014-1029"},"PeriodicalIF":11.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142278406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Wenqiang Chen , Valdemar Brimnes Ingemann Johansen , Cristina Legido-Quigley
{"title":"Bridging brain insulin resistance to Alzheimer’s pathogenesis","authors":"Wenqiang Chen , Valdemar Brimnes Ingemann Johansen , Cristina Legido-Quigley","doi":"10.1016/j.tibs.2024.09.004","DOIUrl":"10.1016/j.tibs.2024.09.004","url":null,"abstract":"<div><div>Emerging evidence links type 2 diabetes mellitus (T2DM) and Alzheimer’s disease (AD), with brain insulin resistance (BIR) as a key factor. In a recent study, <span><span>Lanzillotta <em>et al.</em></span><svg><path></path></svg></span> reveal that reduced biliverdin reductase-A (BVR-A) impairs glycogen synthase kinase 3β (GSK3β) phosphorylation, causing mitochondrial dysfunction and exacerbating brain insulin resistance in the progression of both T2DM and AD.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"49 11","pages":"Pages 939-941"},"PeriodicalIF":11.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142363885","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Suzanne A. Weijers , Michiel Vermeulen , Katarzyna W. Kliza
{"title":"The quest to identify ADP-ribosylation readers: methodological advances","authors":"Suzanne A. Weijers , Michiel Vermeulen , Katarzyna W. Kliza","doi":"10.1016/j.tibs.2024.08.006","DOIUrl":"10.1016/j.tibs.2024.08.006","url":null,"abstract":"<div><div>ADP-ribosylation regulates numerous fundamental cellular processes in health and disease. However, the limited availability of suitable tools and methods prevents the identification and characterization of certain components of the ADP-ribosylation signaling network and, consequently, efficient utilization of their biomedical potential. Identification of ADP-ribose (ADPr) readers has been particularly impeded by challenges associated with the development of ADPr-based enrichment probes. These difficulties were finally overcome in several recent studies describing various approaches to identifying ADPr readers in an unbiased, proteome-wide manner. In this review we discuss these different strategies and their limitations, benefits and drawbacks, and summarize how these technologies contribute to a dissection of ADP-ribosylation signaling networks. We also address unmet technological needs and future directions to investigate interactions with ADPr linkages.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"49 11","pages":"Pages 1000-1013"},"PeriodicalIF":11.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142278407","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The expanding landscape of canonical and non-canonical protein phosphorylation","authors":"Thibault Houles , Sang-Oh Yoon , Philippe P. Roux","doi":"10.1016/j.tibs.2024.08.004","DOIUrl":"10.1016/j.tibs.2024.08.004","url":null,"abstract":"<div><div>Protein phosphorylation is a crucial regulatory mechanism in cell signaling, acting as a molecular switch that modulates protein function. Catalyzed by protein kinases and reversed by phosphoprotein phosphatases, it is essential in both normal physiological and pathological states. Recent advances have uncovered a vast and intricate landscape of protein phosphorylation that include histidine phosphorylation and more unconventional events, such as pyrophosphorylation and polyphosphorylation. Many questions remain about the true size of the phosphoproteome and, more importantly, its site-specific functional relevance. The involvement of unconventional actors such as pseudokinases and pseudophosphatases adds further complexity to be resolved. This review explores recent discoveries and ongoing challenges, highlighting the need for continued research to fully elucidate the roles and regulation of protein phosphorylation.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"49 11","pages":"Pages 986-999"},"PeriodicalIF":11.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142267667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Surfaces as frameworks for intracellular organization","authors":"Germán Rivas , Allen P. Minton","doi":"10.1016/j.tibs.2024.07.007","DOIUrl":"10.1016/j.tibs.2024.07.007","url":null,"abstract":"<div><div>A large fraction of soluble protein within the interior of living cells may reversibly associate with structural elements, including proteinaceous fibers and phospholipid membranes. In this opinion, we present theoretical and experimental evidence that many of these associations are due to nonspecific attraction between the protein and the surface of the fiber or membrane, and that such associations may lead to substantial changes in the association state of the adsorbed proteins, the biological function of the adsorbed proteins, and the distribution of these proteins between the many microenvironments existing within the cell.</div></div>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":"49 11","pages":"Pages 942-954"},"PeriodicalIF":11.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387123","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}