{"title":"Mechanisms of General Anesthesia.","authors":"Scott B Hansen","doi":"10.1146/annurev-biochem-030222-121430","DOIUrl":"https://doi.org/10.1146/annurev-biochem-030222-121430","url":null,"abstract":"<p><p>Anesthetics are a chemically diverse collection of molecules that dictate neuronal excitability and form the basis of modern medicine. Their molecular mechanism of action is fundamental to understanding nerve excitability, mood, consciousness, and psychiatric disease. Sites of anesthetic action are located within ion channels and the plasma membrane. In the membrane, palmitate, a 16-carbon lipid covalently links proteins and binds a lipid site to allow anesthetic sensitivity. In ion channels, anesthetics bind within an allosteric conduction pathway or compete for binding of regulatory lipids. Mechanisms of action arising from these binding sites share structural and functional characteristics with the classic anesthetic site in the enzyme luciferase. An update on the Meyer-Overton correlation is reviewed relative to each mechanism and placed in historical context with early theories. The review ends with a discussion of unresolved questions, including questions concerning endogenous anesthetics, anesthetic stereoselectivity, and aspects of a chain-length cutoff.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":""},"PeriodicalIF":12.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762805","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":"Essential Biology of Lipid Droplets.","authors":"Robert V Farese, Tobias C Walther","doi":"10.1146/annurev-biochem-091724-013733","DOIUrl":"https://doi.org/10.1146/annurev-biochem-091724-013733","url":null,"abstract":"<p><p>Lipid droplets (LDs), long overlooked as inert cellular storage organelles, are now recognized for their complex and rich biology as membraneless organelles integral to cell metabolism. Significant advances have revealed that LDs are crucial for cellular processes that include the storage and retrieval of lipids for metabolic energy and membrane synthesis and the detoxification of lipids by sequestering them in the organelle's core. Here, we review current key aspects of LD biology, emphasizing insights into fundamental mechanisms of their formation, the mechanisms of protein targeting, new insights into LD turnover, and how LDs integrate into cellular metabolism. Where possible, we describe how these processes are important in physiology and how alterations in LD biology can lead to metabolic disease. We highlight unresolved questions and key challenges to be addressed for further advancing our understanding of LD biology and its implications for health and disease.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":""},"PeriodicalIF":12.1,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762801","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":"Paternal Effects in Mammals: Challenges and Opportunities.","authors":"Chih-Hsiang Yang, Oliver J Rando","doi":"10.1146/annurev-biochem-072924-013858","DOIUrl":"https://doi.org/10.1146/annurev-biochem-072924-013858","url":null,"abstract":"<p><p>Once considered heretical, the idea that environmental conditions experienced in one generation can influence traits in future generations is now increasingly accepted. In particular, hundreds of studies in mammals have documented effects of various paternal exposures on offspring metabolism, behavior, and disease susceptibility. While the core claim that a father's experiences can modulate offspring health and disease is now well-established, the mechanistic basis for paternal effects in mammals remains obscure despite nearly two decades of intensive investigation. Here, we briefly review the phenomenology of mammalian paternal effects in broad strokes, focusing on common themes across the literature. We then critically explore our current understanding of the sperm epigenome and discuss challenges to the dominant mechanistic hypotheses proposed in the paternal effects literature.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":""},"PeriodicalIF":12.1,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750784","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":"Biochemical Mechanisms of Genetic Recombination and DNA Repair.","authors":"Vivek B Raina, Aidan Jessop, Eric C Greene","doi":"10.1146/annurev-biochem-083024-113931","DOIUrl":"https://doi.org/10.1146/annurev-biochem-083024-113931","url":null,"abstract":"<p><p>Genetic recombination involves the exchange of genetic material between homologous sequences of DNA. It is employed during meiosis in sexually reproducing organisms or in somatic cells to accurately repair toxic DNA lesions like double-strand breaks and stalled replication forks. In these separate roles, recombination drives genetic diversity by enabling reshuffling of parental genetic information while also serving as a molecular safeguard against the deleterious effects of gross chromosomal rearrangements or mutagenic insults arising for either endogenous or exogenous reasons. In both cases, efficient recombination ensures faithful transmission of genetic information to subsequent generations. In this review, we provide an exploration of the biochemical mechanisms driving genetic recombination, elucidating the molecular intricacies of fundamental processes involved therein with a focus on mechanistic insights gained into these processes using biochemical and single-molecule techniques.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":""},"PeriodicalIF":12.1,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143735580","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}
Sarah R Pope, Molly J McBride, Mrutyunjay A Nair, Xavier E Salas-Solá, Carsten Krebs, J Martin Bollinger, Amie K Boal
{"title":"Heme Oxygenase-Like Metalloenzymes.","authors":"Sarah R Pope, Molly J McBride, Mrutyunjay A Nair, Xavier E Salas-Solá, Carsten Krebs, J Martin Bollinger, Amie K Boal","doi":"10.1146/annurev-biochem-030122-043608","DOIUrl":"https://doi.org/10.1146/annurev-biochem-030122-043608","url":null,"abstract":"<p><p>Heme oxygenase (HO)-like metalloenzymes are an emerging protein superfamily diverse in reaction outcome and mechanism. Found primarily in bacterial biosynthetic pathways, members conserve a flexible protein scaffold shared with the heme catabolic enzyme, HO, and a set of metal-binding residues. Most HO-like metalloenzymes assemble a diiron cluster, although manganese-iron and mononuclear iron cofactors can also be accommodated. In the canonical HO-like diiron oxygenases/oxidases (HDOs), an Fe<sub>2</sub>(II/II) complex reacts with O<sub>2</sub> to form a peroxo-Fe<sub>2</sub>(III/III) intermediate (<b>P</b>), common to all HDOs studied to date. The HO-like scaffold confers both distinctive metal-binding properties, allowing for dynamic cofactor assembly and disassembly, and unusual reactivity to its associated metallocofactor. These features may prove to be important in HDO-mediated catalysis of the fragmentation and rearrangement reactions that remain unprecedented among other dinuclear iron enzymes. Much of the sequence space in the HO-like metalloenzyme superfamily remains unexplored, offering exciting opportunities for the discovery of new mechanisms and reactivities.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":""},"PeriodicalIF":12.1,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143727519","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}
Alejandro Gomez Toledo, Gregory J Golden, Richard D Cummings, Johan Malmström, Jeffrey D Esko
{"title":"Endothelial Glycocalyx Turnover in Vascular Health and Disease: Rethinking Endothelial Dysfunction.","authors":"Alejandro Gomez Toledo, Gregory J Golden, Richard D Cummings, Johan Malmström, Jeffrey D Esko","doi":"10.1146/annurev-biochem-032620-104745","DOIUrl":"https://doi.org/10.1146/annurev-biochem-032620-104745","url":null,"abstract":"<p><p>The endothelial glycocalyx, a glycan-rich layer on the luminal surface of endothelial cells lining blood and lymphatic vessels, plays a crucial role in vascular homeostasis by regulating vascular permeability, immune cell trafficking, and vascular tone. Dysregulated endothelial glycocalyx turnover-whether through altered synthesis, intracellular degradation, or shedding-contributes to endothelial dysfunction in conditions such as sepsis, ischemic events, and chronic inflammatory disorders including diabetes and atherosclerosis. In this review, we examine the structure, function, and turnover of the endothelial glycocalyx, emphasizing how pathological changes in its turnover drive vascular dysfunction. We also highlight diagnostic approaches to evaluate dysregulated endothelial glycocalyx turnover in connection with vascular diseases and discuss therapeutic strategies aimed at preventing endothelial glycocalyx degradation and restoring endothelial function.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":""},"PeriodicalIF":12.1,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143708246","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}
Meagan N Esbin, Trinity Cookis, Sathvik Anantakrishnan, Abrar A Abidi, Jonathan Karr, Claudia Cattoglio, Xavier Darzacq, Robert Tjian
{"title":"Assembly and Dynamics of Transcription Initiation Complexes.","authors":"Meagan N Esbin, Trinity Cookis, Sathvik Anantakrishnan, Abrar A Abidi, Jonathan Karr, Claudia Cattoglio, Xavier Darzacq, Robert Tjian","doi":"10.1146/annurev-biochem-072324-035226","DOIUrl":"https://doi.org/10.1146/annurev-biochem-072324-035226","url":null,"abstract":"<p><p>Gene expression is essential for life and development, allowing the cell to modulate mRNA production in response to intrinsic and extracellular cues. Initiation of gene transcription requires a highly regulated molecular process to assemble multisubunit complexes into the preinitiation complex (PIC). Attempts to visualize these processes have been driven largely by electron microscopy, with near atomic-level resolution producing static snapshots complemented by low-resolution fluorescence cell imaging. Here, we review how new advances in superresolution single-molecule imaging in live cells can track transcription across vast spatiotemporal scales. We discuss how recent imaging research has fundamentally recast our understanding of PIC assembly from a stable, ordered process to one constantly in flux, dominated by multivalent weak interactions. We also discuss future advancements that will further expand our ability to measure PIC assembly in concert with cellular behavior, predict complex interactions computationally, and target undruggable transcription factors to treat human disease.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":""},"PeriodicalIF":12.1,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143708186","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}
Sophie A S Lawrence, Andrew Dolan, Maya M Miller, Carol V Robinson
{"title":"Membrane Protein Complexity Revealed Through Native Mass Spectrometry.","authors":"Sophie A S Lawrence, Andrew Dolan, Maya M Miller, Carol V Robinson","doi":"10.1146/annurev-biochem-081424-044501","DOIUrl":"https://doi.org/10.1146/annurev-biochem-081424-044501","url":null,"abstract":"<p><p>In all living organisms, membrane proteins play a crucial role in governing essential biological functions, such as cellular signaling and molecular transport. These functions rely on intricate interactions with a variety of biomolecules, including substrates, proteins, metabolites, and lipids. Any disruption or alteration to these interactions often results in disease. Therefore, comprehending the complex assemblies of membrane proteins, and their intrinsic interactions, is crucial for unraveling the mechanisms of cellular regulation and has implications in disease pathology. Over the past three decades, native mass spectrometry (MS) has emerged as a pivotal tool for investigating the structure and dynamics of proteins, including membrane protein complexes. In this review, we discuss recent developments in instrumentation that advance our ability to characterize membrane proteins in their native context. As we transition toward increasingly complex eukaryotic systems, we show how this information is translated into an understanding of disease. We also highlight preliminary studies in which native MS has been used to sequence and localize membrane protein complexes within endogenous tissue. This level of detail offers the promise of informing about the molecular mechanisms of disease states.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":""},"PeriodicalIF":12.1,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699386","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":"Structural Mechanisms of Topoisomerase-Targeting Drugs.","authors":"Anthony C O'Donnell, James M Berger","doi":"10.1146/annurev-biochem-030122-043917","DOIUrl":"https://doi.org/10.1146/annurev-biochem-030122-043917","url":null,"abstract":"<p><p>Topoisomerases are enzymes responsible for recognizing and resolving superhelical crossings and topological tangles in DNA. Topoisomerases also serve as valuable established targets for numerous clinically used antibacterial and antitumor agents; small-molecule antagonists not only have an ability to disrupt essential cellular functions but also convert these enzymes into DNA-damaging agents. Here, we review biochemical and structural data that explain how current therapeutics target eukaryotic and prokaryotic topoisomerases at a molecular level. New and highly promising agents that showcase the continued utility of targeting topoisomerases for clinical benefit are also discussed.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":""},"PeriodicalIF":12.1,"publicationDate":"2025-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699387","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":"Exploiting Covalent Chemical Labeling with Self-Labeling Proteins.","authors":"Nicola Porzberg, Klara Gries, Kai Johnsson","doi":"10.1146/annurev-biochem-030222-121016","DOIUrl":"https://doi.org/10.1146/annurev-biochem-030222-121016","url":null,"abstract":"<p><p>The visualization and manipulation of proteins in live cells are critical for studying complex biological processes. Self-labeling proteins do so by enabling the specific and covalent attachment of synthetic probes, offering unprecedented flexibility in the chemical labeling of proteins in live cells and in vivo. By combining the excellent photophysical properties of synthetic dyes with genetic targetability, these tags provide a modular and innovative toolbox for live-cell and high-resolution fluorescence imaging. In this review, we explore the development and diverse applications of the key self-labeling protein technologies, HaloTag7, SNAP-tag, and CLIP-tag, as well as the covalent trimethoprim (TMP)-tag. We discuss recent innovations in both protein engineering and substrate design that have introduced new functionalities to enable multiplexed imaging, super-resolution microscopy, and the design of novel biosensors and recorders.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":""},"PeriodicalIF":12.1,"publicationDate":"2025-03-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143662109","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}
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