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Trends in Biochemical Sciences最新文献

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Inventories invite independence.
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2024-12-11 DOI: 10.1016/j.tibs.2024.11.003
Kayleigh Robichaux, Taylor Billings, Christina Marie Termini
{"title":"Inventories invite independence.","authors":"Kayleigh Robichaux, Taylor Billings, Christina Marie Termini","doi":"10.1016/j.tibs.2024.11.003","DOIUrl":"https://doi.org/10.1016/j.tibs.2024.11.003","url":null,"abstract":"<p><p>In this piece, we use an antibody inventory system to exemplify the potential benefits of laboratory organization in research environments. We highlight how inventories can support resource accessibility and strengthen a sense of independence for scientists, especially those new to research environments.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142816889","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}
引用次数: 0
Confronting PFAS persistence: enzymes catalyzing C-F bond cleavage.
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2024-12-05 DOI: 10.1016/j.tibs.2024.11.001
Lawrence P Wackett
{"title":"Confronting PFAS persistence: enzymes catalyzing C-F bond cleavage.","authors":"Lawrence P Wackett","doi":"10.1016/j.tibs.2024.11.001","DOIUrl":"https://doi.org/10.1016/j.tibs.2024.11.001","url":null,"abstract":"<p><p>Studies of enzymes catalyzing carbon-fluorine (C-F) bond cleavage have focused largely on a limited number of native microbial hydrolases that are reactive with the natural product fluoroacetate. Driven by widespread interest in biodegrading commercial fluorinated compounds, many of which are known as per- and polyfluorinated alkyl substances (PFAS), it is necessary to identify and engineer new enzymes. For example, some hydrolases react with -CF<sub>2</sub>- moieties, a common functionality in PFAS. Additional enzymatic C-F cleaving mechanisms catalyzed by reductases, lyases, and oxygenases have been identified via screening. Screening and evolving PFAS defluorination in bacteria is inhibited by the obligate release of toxic fluoride from C-F cleavage. Engineering greater fluoride tolerance in bacteria is a problem that must be solved in tandem with enzyme improvement.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":""},"PeriodicalIF":11.6,"publicationDate":"2024-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142790894","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}
引用次数: 0
Exploring cross-α amyloids: from functional roles to design innovations. 探索交叉α淀粉样蛋白：从功能作用到设计创新。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2024-12-01 Epub Date: 2024-11-06 DOI: 10.1016/j.tibs.2024.10.004
Sukantha Dey, Rohit Kumar, Rajkumar Mishra, Santu Bera
{"title":"Exploring cross-α amyloids: from functional roles to design innovations.","authors":"Sukantha Dey, Rohit Kumar, Rajkumar Mishra, Santu Bera","doi":"10.1016/j.tibs.2024.10.004","DOIUrl":"10.1016/j.tibs.2024.10.004","url":null,"abstract":"<p><p>Amyloids are filamentous protein aggregates that have traditionally been associated with neurodegenerative diseases, although they are also known to play pivotal functional roles across diverse forms of life. Although the cross-β structure has represented the hallmark of amyloidal assemblies, a cross-α structure was recently characterized as a functional microbial amyloid, and further work has shown that de novo designed sequences also assemble into cross-α amyloids, emphasizing cross-α as an alternative paradigm for self-assembly into ordered aggregates. In this review, we summarize recent discoveries of cross-α amyloids both in nature and artificially designed systems, and we describe their fundamental structural organization, self-assembly mechanisms, and biological functions. Finally, we outline the future opportunities for research and development in this potential field.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":"1097-1110"},"PeriodicalIF":11.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142602327","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}
引用次数: 0
Structural diversity of the CE-clan proteases in bacteria to disarm host ubiquitin defenses. 细菌中解除宿主泛素防御的 CE 族蛋白酶的结构多样性。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2024-12-01 Epub Date: 2024-09-28 DOI: 10.1016/j.tibs.2024.09.001
Lucía Sánchez-Alba, Helena Borràs-Gas, Ge Huang, Nathalia Varejão, David Reverter
{"title":"Structural diversity of the CE-clan proteases in bacteria to disarm host ubiquitin defenses.","authors":"Lucía Sánchez-Alba, Helena Borràs-Gas, Ge Huang, Nathalia Varejão, David Reverter","doi":"10.1016/j.tibs.2024.09.001","DOIUrl":"10.1016/j.tibs.2024.09.001","url":null,"abstract":"<p><p>Ubiquitin (Ub) and ubiquitin-like (UbL) modifications are critical regulators of multiple cellular processes in eukaryotes. These modifications are dynamically controlled by proteases that balance conjugation and deconjugation. In eukaryotes, these proteases include deubiquitinases (DUBs), mostly belonging to the CA-clan of cysteine proteases, and ubiquitin-like proteases (ULPs), belonging to the CE-clan proteases. Intriguingly, infectious bacteria exploit the CE-clan protease fold to generate deubiquitinating activities to disarm the immune system and degradation defenses of the host during infection. In this review, we explore the substrate preferences encoded within the CE-clan proteases and the structural determinants in the protease fold behind its selectivity, in particular those from infectious bacteria and viruses. Understanding this protease family provides crucial insights into the molecular mechanisms underlying infection and transmission of pathogenic organisms.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":"1111-1123"},"PeriodicalIF":11.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338675","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}
引用次数: 0
Anything you can do, glycans do better: deglycosylation and noncanonical ubiquitination vie to rule the proteasome. 你能做的任何事情，聚糖都能做得更好：脱糖基化和非经典泛素化争夺蛋白酶体的统治权。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2024-12-01 Epub Date: 2024-10-16 DOI: 10.1016/j.tibs.2024.10.001
Nicolas Lehrbach
{"title":"Anything you can do, glycans do better: deglycosylation and noncanonical ubiquitination vie to rule the proteasome.","authors":"Nicolas Lehrbach","doi":"10.1016/j.tibs.2024.10.001","DOIUrl":"10.1016/j.tibs.2024.10.001","url":null,"abstract":"<p><p>The Nrf1/Nfe2L1 transcription factor is a master regulator of proteasome biogenesis. New work by Yoshida and colleagues reveals a surprising mechanism by which ubiquitination of N-glycosylated Nrf1 controls its function.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":"1033-1035"},"PeriodicalIF":11.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11624994/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142455176","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}
引用次数: 0
Eph receptor signaling complexes in the plasma membrane. 质膜中的 Eph 受体信号复合体
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2024-12-01 Epub Date: 2024-11-12 DOI: 10.1016/j.tibs.2024.10.002
Elena B Pasquale
{"title":"Eph receptor signaling complexes in the plasma membrane.","authors":"Elena B Pasquale","doi":"10.1016/j.tibs.2024.10.002","DOIUrl":"10.1016/j.tibs.2024.10.002","url":null,"abstract":"<p><p>Eph receptor tyrosine kinases, together with their cell surface-anchored ephrin ligands, constitute an important cell-cell communication system that regulates physiological and pathological processes in most cell types. This review focuses on the multiple mechanisms by which Eph receptors initiate signaling via the formation of protein complexes in the plasma membrane. Upon ephrin binding, Eph receptors assemble into oligomers that can further aggregate into large complexes. Eph receptors also mediate ephrin-independent signaling through interplay with intracellular kinases or other cell-surface receptors. The distinct characteristics of Eph receptor family members, as well as their conserved domain structure, provide a framework for understanding their functional differences and redundancies. Possible areas of interest for future investigations of Eph receptor signaling complexes are also highlighted.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":"1079-1096"},"PeriodicalIF":11.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611613","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}
引用次数: 0
Constructive neutral evolution of homodimer to heterodimer transition. 同源二聚体向异源二聚体过渡的建设性中性进化。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2024-12-01 Epub Date: 2024-10-23 DOI: 10.1016/j.tibs.2024.10.003
Lin Chou, Carly J Houghton, Aaron Wacholder, Anne-Ruxandra Carvunis
{"title":"Constructive neutral evolution of homodimer to heterodimer transition.","authors":"Lin Chou, Carly J Houghton, Aaron Wacholder, Anne-Ruxandra Carvunis","doi":"10.1016/j.tibs.2024.10.003","DOIUrl":"10.1016/j.tibs.2024.10.003","url":null,"abstract":"<p><p>Complexification of macrobiomolecules, such as homodimer to heterodimer transitions, are common during evolution. Is such complexification always adaptive? Using large-scale experiments and in-depth biochemical analyses, Després et al. recently demonstrated that an obligate heterodimer can evolve from a homodimer through neutral, nonadaptive events, and quantified key parameters required for such transitions.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":"1036-1038"},"PeriodicalIF":11.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492411","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}
引用次数: 0
Functionalized DNA secondary structures and nanostructures for specific protein modifications. 用于特定蛋白质修饰的功能化 DNA 二级结构和纳米结构。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2024-12-01 Epub Date: 2024-10-22 DOI: 10.1016/j.tibs.2024.09.003
Bauke Albada
{"title":"Functionalized DNA secondary structures and nanostructures for specific protein modifications.","authors":"Bauke Albada","doi":"10.1016/j.tibs.2024.09.003","DOIUrl":"10.1016/j.tibs.2024.09.003","url":null,"abstract":"<p><p>The development of non-biological applications of DNA has not only resulted in delicately shaped DNA-based nano-objects with complex functions but also spawned their use for novel catalytic applications. From the multitude of applications of DNAzymes that operate on a relatively simple substrate, we have witnessed the emergence of multifunctional catalytically active DNA-based nanostructures for one of the most challenging tasks known to a chemist: the controlled and precise modification of a wild-type protein in its natural environment. By incorporating various elements associated with post-translational modification (PTM) writer enzymes into complex nanostructures, it is now possible to chemically modify a specific protein in cell lysates under the influence of an externally added trigger, clearly illustrating the promising future for this approach.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":"1124-1135"},"PeriodicalIF":11.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492412","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}
引用次数: 0
A two-way relationship between histone acetylation and metabolism. 组蛋白乙酰化与新陈代谢之间的双向关系
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2024-12-01 Epub Date: 2024-11-07 DOI: 10.1016/j.tibs.2024.10.005
Evelina Charidemou, Antonis Kirmizis
{"title":"A two-way relationship between histone acetylation and metabolism.","authors":"Evelina Charidemou, Antonis Kirmizis","doi":"10.1016/j.tibs.2024.10.005","DOIUrl":"10.1016/j.tibs.2024.10.005","url":null,"abstract":"<p><p>A link between epigenetics and metabolism was initially recognized because the cellular metabolic state is communicated to the genome through the concentration of intermediary metabolites that are cofactors of chromatin-modifying enzymes. Recently, an additional interaction was postulated due to the capacity of the epigenome to store substantial amounts of metabolites that could become available again to cellular metabolite pools. Here, we focus on histone acetylation and review recent evidence illustrating this reciprocal relationship: in one direction, signaling-induced acetyl-coenzyme A (acetyl-CoA) changes influence histone acetylation levels to regulate genomic functions, and in the opposite direction histone acetylation acts as an acetate reservoir to directly affect downstream acetyl-CoA-mediated metabolism. This review highlights the current understanding, experimental challenges, and future perspectives of this bidirectional interplay.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":"1046-1062"},"PeriodicalIF":11.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611610","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}
引用次数: 0
Clues into Wnt cell surface signalosomes and its biogenesis. Wnt 细胞表面信号体及其生物生成的线索。
IF 11.6 1区 生物学
Trends in Biochemical Sciences Pub Date : 2024-12-01 Epub Date: 2024-10-22 DOI: 10.1016/j.tibs.2024.09.007
Philip Schmiege, Xiaochun Li
{"title":"Clues into Wnt cell surface signalosomes and its biogenesis.","authors":"Philip Schmiege, Xiaochun Li","doi":"10.1016/j.tibs.2024.09.007","DOIUrl":"10.1016/j.tibs.2024.09.007","url":null,"abstract":"<p><p>Wnt morphogens induce signaling via binding their extracellular receptors. Here, we discuss several recent structural studies showing how Wnts engage their receptors frizzled (FZD) and low-density lipoprotein receptor-related protein 5/6 (LRP5/6), how Cachd1 has been shown as an alternative initiator of Wnt signaling, and how lipidated Wnt may be produced and secreted from the cell.</p>","PeriodicalId":440,"journal":{"name":"Trends in Biochemical Sciences","volume":" ","pages":"1042-1045"},"PeriodicalIF":11.6,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11624986/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142492410","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}
引用次数: 0
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