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Annual review of biochemistry最新文献

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Encapsulins. 密封剂。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-06-21 DOI: 10.1146/annurev-biochem-040320-102858
Tobias W Giessen
{"title":"Encapsulins.","authors":"Tobias W Giessen","doi":"10.1146/annurev-biochem-040320-102858","DOIUrl":"https://doi.org/10.1146/annurev-biochem-040320-102858","url":null,"abstract":"<p><p>Subcellular compartmentalization is a defining feature of all cells. In prokaryotes, compartmentalization is generally achieved via protein-based strategies. The two main classes of microbial protein compartments are bacterial microcompartments and encapsulin nanocompartments. Encapsulins self-assemble into proteinaceous shells with diameters between 24 and 42 nm and are defined by the viral HK97-fold of their shell protein. Encapsulins have the ability to encapsulate dedicated cargo proteins, including ferritin-like proteins, peroxidases, and desulfurases. Encapsulation is mediated by targeting sequences present in all cargo proteins. Encapsulins are found in many bacterial and archaeal phyla and have been suggested to play roles in iron storage, stress resistance, sulfur metabolism, and natural product biosynthesis. Phylogenetic analyses indicate that they share a common ancestor with viral capsid proteins. Many pathogens encode encapsulins, and recent evidence suggests that they may contribute toward pathogenicity. The existing information on encapsulin structure, biochemistry, biological function, and biomedical relevance is reviewed here.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"91 ","pages":"353-380"},"PeriodicalIF":16.6,"publicationDate":"2022-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9944552/pdf/nihms-1869567.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10750512","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: 14
The Structural Dynamics of Translation. 翻译的结构动力学。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-06-21 DOI: 10.1146/annurev-biochem-071921-122857
Andrei A Korostelev
{"title":"The Structural Dynamics of Translation.","authors":"Andrei A Korostelev","doi":"10.1146/annurev-biochem-071921-122857","DOIUrl":"https://doi.org/10.1146/annurev-biochem-071921-122857","url":null,"abstract":"<p><p>Accurate protein synthesis (translation) relies on translation factors that rectify ribosome fluctuations into a unidirectional process. Understanding this process requires structural characterization of the ribosome and translation-factor dynamics. In the 2000s, crystallographic studies determined high-resolution structures of ribosomes stalled with translation factors, providing a starting point for visualizing translation. Recent progress in single-particle cryogenic electron microscopy (cryo-EM) has enabled near-atomic resolution of numerous structures sampled in heterogeneous complexes (ensembles). Ensemble and time-resolved cryo-EM have now revealed unprecedented views of ribosome transitions in the three principal stages of translation: initiation, elongation, and termination. This review focuses on how translation factors help achieve high accuracy and efficiency of translation by monitoring distinct ribosome conformations and by differentially shifting the equilibria of ribosome rearrangements for cognate and near-cognate substrates.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"91 ","pages":"245-267"},"PeriodicalIF":16.6,"publicationDate":"2022-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10389292/pdf/nihms-1920330.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9890319","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: 13
Lipoproteins in the Central Nervous System: From Biology to Pathobiology. 中枢神经系统中的脂蛋白：从生物学到病理生物学
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2022-06-21 Epub Date: 2022-03-18 DOI: 10.1146/annurev-biochem-032620-104801
Ana-Caroline Raulin, Yuka A Martens, Guojun Bu
{"title":"Lipoproteins in the Central Nervous System: From Biology to Pathobiology.","authors":"Ana-Caroline Raulin, Yuka A Martens, Guojun Bu","doi":"10.1146/annurev-biochem-032620-104801","DOIUrl":"10.1146/annurev-biochem-032620-104801","url":null,"abstract":"<p><p>The brain, as one of the most lipid-rich organs, heavily relies on lipid transport and distribution to maintain homeostasis and neuronal function. Lipid transport mediated by lipoprotein particles, which are complex structures composed of apolipoproteins and lipids, has been thoroughly characterized in the periphery. Although lipoproteins in the central nervous system (CNS) were reported over half a century ago, the identification of <i>APOE4</i> as the strongest genetic risk factor for Alzheimer's disease has accelerated investigation of the biology and pathobiology of lipoproteins in the CNS. This review provides an overview of the different components of lipoprotein particles, in particular apolipoproteins, and their involvements in both physiological functions and pathological mechanisms in the CNS.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"91 ","pages":"731-759"},"PeriodicalIF":12.1,"publicationDate":"2022-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9634960/pdf/nihms-1844218.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9743352","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
Kinetic Proofreading. 动能校对。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-04-01 DOI: 10.1146/annurev-biochem-040320-103630
Hinrich Boeger
{"title":"Kinetic Proofreading.","authors":"Hinrich Boeger","doi":"10.1146/annurev-biochem-040320-103630","DOIUrl":"https://doi.org/10.1146/annurev-biochem-040320-103630","url":null,"abstract":"Biochemistry and molecular biology rely on the recognition of structural complementarity between molecules. Molecular interactions must be both quickly reversible, i.e., tenuous, and specific. How the cell reconciles these conflicting demands is the subject of this article. The problem and its theoretical solution are discussed within the wider theoretical context of the thermodynamics of stochastic processes (stochastic thermodynamics). The solution-an irreversible reaction cycle that decreases internal error at the expense of entropy export into the environment-is shown to be widely employed by biological processes that transmit genetic and regulatory information. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42335189","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: 6
Validating Small Molecule Chemical Probes for Biological Discovery. 用于生物发现的小分子化学探针的验证。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-04-01 DOI: 10.1146/annurev-biochem-032620-105344
Victoria Vu, Magdalena M. Szewczyk, David Y. Nie, C. Arrowsmith, D. Barsyte-Lovejoy
{"title":"Validating Small Molecule Chemical Probes for Biological Discovery.","authors":"Victoria Vu, Magdalena M. Szewczyk, David Y. Nie, C. Arrowsmith, D. Barsyte-Lovejoy","doi":"10.1146/annurev-biochem-032620-105344","DOIUrl":"https://doi.org/10.1146/annurev-biochem-032620-105344","url":null,"abstract":"Small molecule chemical probes are valuable tools for interrogating protein biological functions and relevance as a therapeutic target. Rigorous validation of chemical probe parameters such as cellular potency and selectivity is critical to unequivocally linking biological and phenotypic data resulting from treatment with a chemical probe to the function of a specific target protein. A variety of modern technologies are available to evaluate cellular potency and selectivity, target engagement, and functional response biomarkers of chemical probe compounds. Here, we review these technologies and the rationales behind using them for the characterization and validation of chemical probes. In addition, large-scale phenotypic characterization of chemical probes through chemical genetic screening is increasingly leading to a wealth of information on the cellular pharmacology and disease involvement of potential therapeutic targets. Extensive compound validation approaches and integration of phenotypic information will lay foundations for further use of chemical probes in biological discovery. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47671355","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: 8
Metalloproteomics for Biomedical Research: Methodology and Applications. 生物医学研究的金属代谢组学：方法论和应用。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-02-18 DOI: 10.1146/annurev-biochem-040320-104628
Ying Zhou, Hongyan Li, Hongzhe Sun
{"title":"Metalloproteomics for Biomedical Research: Methodology and Applications.","authors":"Ying Zhou, Hongyan Li, Hongzhe Sun","doi":"10.1146/annurev-biochem-040320-104628","DOIUrl":"https://doi.org/10.1146/annurev-biochem-040320-104628","url":null,"abstract":"Metals are essential components in life processes and participate in many important biological processes. Dysregulation of metal homeostasis is correlated with many diseases. Metals are also frequently incorporated into diagnosis and therapeutics. Understanding of metal homeostasis under (patho)physiological conditions and the molecular mechanisms of action of metallodrugs in biological systems has positive impacts on human health. As an emerging interdisciplinary area of research, metalloproteomics involves investigating metal-protein interactions in biological systems at a proteome-wide scale, has received growing attention, and has been implemented into metal-related research. In this review, we summarize the recent advances in metalloproteomics methodologies and applications. We also highlight emerging single-cell metalloproteomics, including time-resolved inductively coupled plasma mass spectrometry, mass cytometry, and secondary ion mass spectrometry. Finally, we discuss future perspectives in metalloproteomics, aiming to attract more original research to develop more advanced methodologies, which could be utilized rapidly by biochemists or biologists to expand our knowledge of how metal functions in biology and medicine. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2022-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47684630","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: 13
MAPK-Activated Protein Kinases: Servant or Partner? MAPK活化蛋白激酶：仆人还是伴侣？
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-02-18 DOI: 10.1146/annurev-biochem-081720-114505
N. Ronkina, M. Gaestel
{"title":"MAPK-Activated Protein Kinases: Servant or Partner?","authors":"N. Ronkina, M. Gaestel","doi":"10.1146/annurev-biochem-081720-114505","DOIUrl":"https://doi.org/10.1146/annurev-biochem-081720-114505","url":null,"abstract":"Mitogen-activated protein kinase (MAPK)-activated protein kinases (MAPKAPKs) are defined by their exclusive activation by MAPKs. They can be activated by classical and atypical MAPKs that have been stimulated by mitogens and various stresses. Genetic deletions of MAPKAPKs and availability of highly specific small-molecule inhibitors have continuously increased our functional understanding of these kinases. MAPKAPKs cooperate in the regulation of gene expression at the level of transcription; RNA processing, export, and stability; and protein synthesis. The diversity of stimuli for MAPK activation, the cross talk between the different MAPKs and MAPKAPKs, and the specific substrate pattern of MAPKAPKs orchestrate immediate-early and inflammatory responses in space and time and ensure proper control of cell growth, differentiation, and cell behavior. Hence, MAPKAPKs are promising targets for cancer therapy and treatments for conditions of acute and chronic inflammation, such as cytokine storms and rheumatoid arthritis. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2022-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46702617","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: 36
DNA-Protein Crosslinks and Their Resolution. DNA-蛋白质交联及其解析。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-02-18 DOI: 10.1146/annurev-biochem-032620-105820
P. Weickert, Julian Stingele
{"title":"DNA-Protein Crosslinks and Their Resolution.","authors":"P. Weickert, Julian Stingele","doi":"10.1146/annurev-biochem-032620-105820","DOIUrl":"https://doi.org/10.1146/annurev-biochem-032620-105820","url":null,"abstract":"Covalent DNA-protein crosslinks (DPCs) are pervasive DNA lesions that interfere with essential chromatin processes such as transcription or replication. This review strives to provide an overview of the sources and principles of cellular DPC formation. DPCs are caused by endogenous reactive metabolites and various chemotherapeutic agents. However, in certain conditions DPCs also arise physiologically in cells. We discuss the cellular mechanisms resolving these threats to genomic integrity. Detection and repair of DPCs require not only the action of canonical DNA repair pathways but also the activity of specialized proteolytic enzymes-including proteases of the SPRTN/Wss1 family-to degrade the crosslinked protein. Loss of DPC repair capacity has dramatic consequences, ranging from genome instability in yeast and worms to cancer predisposition and premature aging in mice and humans. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2022-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42309813","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: 23
The Wnt Pathway: From Signaling Mechanisms to Synthetic Modulators. Wnt通路:从信号机制到合成调制剂。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-02-18 DOI: 10.1146/annurev-biochem-040320-103615
Ellen Youngsoo Rim, H. Clevers, R. Nusse
{"title":"The Wnt Pathway: From Signaling Mechanisms to Synthetic Modulators.","authors":"Ellen Youngsoo Rim, H. Clevers, R. Nusse","doi":"10.1146/annurev-biochem-040320-103615","DOIUrl":"https://doi.org/10.1146/annurev-biochem-040320-103615","url":null,"abstract":"The Wnt pathway is central to a host of developmental and disease-related processes. The remarkable conservation of this intercellular signaling cascade throughout metazoan lineages indicates that it coevolved with multicellularity to regulate the generation and spatial arrangement of distinct cell types. By regulating cell fate specification, mitotic activity, and cell polarity, Wnt signaling orchestrates development and tissue homeostasis, and its dysregulation is implicated in developmental defects, cancer, and degenerative disorders. We review advances in our understanding of this key pathway, from Wnt protein production and secretion to relay of the signal in the cytoplasm of the receiving cell. We discuss the evolutionary history of this pathway as well as endogenous and synthetic modulators of its activity. Finally, we highlight remaining gaps in our knowledge of Wnt signal transduction and avenues for future research. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2022-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46544285","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: 93
The Role of DEAD-Box ATPases in Gene Expression and the Regulation of RNA-Protein Condensates. DEAD-Box-ATP酶在基因表达中的作用及对RNA蛋白凝结物的调控。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-02-18 DOI: 10.1146/annurev-biochem-032620-105429
K. Weis, Maria Hondele
{"title":"The Role of DEAD-Box ATPases in Gene Expression and the Regulation of RNA-Protein Condensates.","authors":"K. Weis, Maria Hondele","doi":"10.1146/annurev-biochem-032620-105429","DOIUrl":"https://doi.org/10.1146/annurev-biochem-032620-105429","url":null,"abstract":"DEAD-box ATPases constitute a very large protein family present in all cells, often in great abundance. From bacteria to humans, they play critical roles in many aspects of RNA metabolism, and due to their widespread importance in RNA biology, they have been characterized in great detail at both the structural and biochemical levels. DEAD-box proteins function as RNA-dependent ATPases that can unwind short duplexes of RNA, remodel ribonucleoprotein (RNP) complexes, or act as clamps to promote RNP assembly. Yet, it often remains enigmatic how individual DEAD-box proteins mechanistically contribute to specific RNA-processing steps. Here, we review the role of DEAD-box ATPases in the regulation of gene expression and propose that one common function of these enzymes is in the regulation of liquid-liquid phase separation of RNP condensates. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2022-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45126621","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: 13
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