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Annual review of biochemistry最新文献

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Biochemistry, Cell Biology, and Pathophysiology of the Innate Immune cGAS-cGAMP-STING Pathway. 天然免疫cGAS cGAMP STING通路的生物化学、细胞生物学和病理生理学。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-02-14 DOI: 10.1146/annurev-biochem-040320-101629
C. Ritchie, Jacqueline A. Carozza, Lingyin Li
{"title":"Biochemistry, Cell Biology, and Pathophysiology of the Innate Immune cGAS-cGAMP-STING Pathway.","authors":"C. Ritchie, Jacqueline A. Carozza, Lingyin Li","doi":"10.1146/annurev-biochem-040320-101629","DOIUrl":"https://doi.org/10.1146/annurev-biochem-040320-101629","url":null,"abstract":"In the decade since the discovery of the innate immune cyclic GMP-AMP synthase (cGAS)- 2'3'-cyclic GMP-AMP (cGAMP)- stimulator of interferon genes (STING) pathway, its proper activation and dysregulation have been rapidly implicated in many aspects of human disease. Understanding the biochemical, cellular, and regulatory mechanisms of this pathway is critical to developing therapeutic strategies that either harness it to boost defense or inhibit it to prevent unwanted inflammation. In this review, we first discuss how the second messenger cGAMP is synthesized by cGAS in response to double-stranded DNA and cGAMP's subsequent activation of cell-type-dependent STING signaling cascades with differential physiological consequences. We then review how cGAMP as an immunotransmitter mediates tightly controlled cell-cell communication by being exported from producing cells and imported into responding cells via cell-type-specific transporters. Finally, we review mechanisms by which the cGAS-cGAMP-STING pathway responds to different sources of mislocalized double-stranded DNA in pathogen defense, cancer, and autoimmune diseases. 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":"2022-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49418859","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: 22
Influence of Nonspecific Interactions on Protein Associations: Implications for Biochemistry In Vivo. 非特异性相互作用对蛋白质关联的影响:体内生物化学的意义。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-02-14 DOI: 10.1146/annurev-biochem-040320-104151
G. Rivas, A. Minton
{"title":"Influence of Nonspecific Interactions on Protein Associations: Implications for Biochemistry In Vivo.","authors":"G. Rivas, A. Minton","doi":"10.1146/annurev-biochem-040320-104151","DOIUrl":"https://doi.org/10.1146/annurev-biochem-040320-104151","url":null,"abstract":"The cellular interior is composed of a variety of microenvironments defined by distinct local compositions and composition-dependent intermolecular interactions. We review the various types of nonspecific interactions between proteins and between proteins and other macromolecules and supramolecular structures that influence the state of association and functional properties of a given protein existing within a particular microenvironment at a particular point in time. The present state of knowledge is summarized, and suggestions for fruitful directions of research are offered. 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":"2022-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42327873","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: 17
Summing up. 总结。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2021-12-06 DOI: 10.2307/j.ctv6gqt8x.21
K. Bloch
{"title":"Summing up.","authors":"K. Bloch","doi":"10.2307/j.ctv6gqt8x.21","DOIUrl":"https://doi.org/10.2307/j.ctv6gqt8x.21","url":null,"abstract":"","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"56 1","pages":"1-19"},"PeriodicalIF":16.6,"publicationDate":"2021-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48208481","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
Molecular Epigenetics: Chemical Biology Tools Come of Age. 分子表观遗传学:化学生物学工具的成熟。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2021-06-20 DOI: 10.1146/annurev-biochem-080120-021109
John D Bagert, Tom W Muir
{"title":"Molecular Epigenetics: Chemical Biology Tools Come of Age.","authors":"John D Bagert,&nbsp;Tom W Muir","doi":"10.1146/annurev-biochem-080120-021109","DOIUrl":"https://doi.org/10.1146/annurev-biochem-080120-021109","url":null,"abstract":"<p><p>The field of epigenetics has exploded over the last two decades, revealing an astonishing level of complexity in the way genetic information is stored and accessed in eukaryotes. This expansion of knowledge, which is very much ongoing, has been made possible by the availability of evermore sensitive and precise molecular tools. This review focuses on the increasingly important role that chemistry plays in this burgeoning field. In an effort to make these contributions more accessible to the nonspecialist, we group available chemical approaches into those that allow the covalent structure of the protein and DNA components of chromatin to be manipulated, those that allow the activity of myriad factors that act on chromatin to be controlled, and those that allow the covalent structure and folding of chromatin to be characterized. The application of these tools is illustrated through a series of case studies that highlight how the molecular precision afforded by chemistry is being used to establish causal biochemical relationships at the heart of epigenetic regulation.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"90 ","pages":"287-320"},"PeriodicalIF":16.6,"publicationDate":"2021-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8284505/pdf/nihms-1718924.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10389631","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: 9
An Overview of Microcrystal Electron Diffraction (MicroED). 微晶电子衍射(MicroED)综述。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2021-06-20 DOI: 10.1146/annurev-biochem-081720-020121
Xuelang Mu, Cody Gillman, Chi Nguyen, Tamir Gonen
{"title":"An Overview of Microcrystal Electron Diffraction (MicroED).","authors":"Xuelang Mu,&nbsp;Cody Gillman,&nbsp;Chi Nguyen,&nbsp;Tamir Gonen","doi":"10.1146/annurev-biochem-081720-020121","DOIUrl":"https://doi.org/10.1146/annurev-biochem-081720-020121","url":null,"abstract":"<p><p>The bedrock of drug discovery and a key tool for understanding cellular function and drug mechanisms of action is the structure determination of chemical compounds, peptides, and proteins. The development of new structure characterization tools, particularly those that fill critical gaps in existing methods, presents important steps forward for structural biology and drug discovery. The emergence of microcrystal electron diffraction (MicroED) expands the application of cryo-electron microscopy to include samples ranging from small molecules and membrane proteins to even large protein complexes using crystals that are one-billionth the size of those required for X-ray crystallography. This review outlines the conception, achievements, and exciting future trajectories for MicroED, an important addition to the existing biophysical toolkit.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"90 ","pages":"431-450"},"PeriodicalIF":16.6,"publicationDate":"2021-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9974886/pdf/nihms-1782092.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10806362","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: 4
The Myosin Family of Mechanoenzymes: From Mechanisms to Therapeutic Approaches. 肌球蛋白机械酶家族：从机制到治疗方法。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 Epub Date: 2020-03-13 DOI: 10.1146/annurev-biochem-011520-105234
Darshan V Trivedi, Suman Nag, Annamma Spudich, Kathleen M Ruppel, James A Spudich
{"title":"The Myosin Family of Mechanoenzymes: From Mechanisms to Therapeutic Approaches.","authors":"Darshan V Trivedi, Suman Nag, Annamma Spudich, Kathleen M Ruppel, James A Spudich","doi":"10.1146/annurev-biochem-011520-105234","DOIUrl":"10.1146/annurev-biochem-011520-105234","url":null,"abstract":"<p><p>Myosins are among the most fascinating enzymes in biology. As extremely allosteric chemomechanical molecular machines, myosins are involved in myriad pivotal cellular functions and are frequently sites of mutations leading to disease phenotypes. Human β-cardiac myosin has proved to be an excellent target for small-molecule therapeutics for heart muscle diseases, and, as we describe here, other myosin family members are likely to be potentially unique targets for treating other diseases as well. The first part of this review focuses on how myosins convert the chemical energy of ATP hydrolysis into mechanical movement, followed by a description of existing therapeutic approaches to target human β-cardiac myosin. The next section focuses on the possibility of targeting nonmuscle members of the human myosin family for several diseases. We end the review by describing the roles of myosin in parasites and the therapeutic potential of targeting them to block parasitic invasion of their hosts.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"667-693"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8742983/pdf/nihms-1710843.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37734952","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
Zona Pellucida Proteins, Fibrils, and Matrix. 透明带蛋白、原纤维和基质。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 DOI: 10.1146/annurev-biochem-011520-105310
Eveline S Litscher, Paul M Wassarman
{"title":"Zona Pellucida Proteins, Fibrils, and Matrix.","authors":"Eveline S Litscher,&nbsp;Paul M Wassarman","doi":"10.1146/annurev-biochem-011520-105310","DOIUrl":"https://doi.org/10.1146/annurev-biochem-011520-105310","url":null,"abstract":"<p><p>The zona pellucida (ZP) is an extracellular matrix that surrounds all mammalian oocytes, eggs, and early embryos and plays vital roles during oogenesis, fertilization, and preimplantation development. The ZP is composed of three or four glycosylated proteins, ZP1-4, that are synthesized, processed, secreted, and assembled into long, cross-linked fibrils by growing oocytes. ZP proteins have an immunoglobulin-like three-dimensional structure and a ZP domain that consists of two subdomains, ZP-N and ZP-C, with ZP-N of ZP2 and ZP3 required for fibril assembly. A ZP2-ZP3 dimer is located periodically along ZP fibrils that are cross-linked by ZP1, a protein with a proline-rich N terminus. Fibrils in the inner and outer regions of the ZP are oriented perpendicular and parallel to the oolemma, respectively, giving the ZP a multilayered appearance. Upon fertilization of eggs, modification of ZP2 and ZP3 results in changes in the ZP's physical and biological properties that have important consequences. Certain structural features of ZP proteins suggest that they may be amyloid-like proteins.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"695-715"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-011520-105310","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38070731","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: 34
Dynamic Competition of Polycomb and Trithorax in Transcriptional Programming. 转录编程中多聚酶和三叉轴的动态竞争
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 Epub Date: 2020-01-13 DOI: 10.1146/annurev-biochem-120219-103641
Mitzi I Kuroda, Hyuckjoon Kang, Sandip De, Judith A Kassis
{"title":"Dynamic Competition of Polycomb and Trithorax in Transcriptional Programming.","authors":"Mitzi I Kuroda, Hyuckjoon Kang, Sandip De, Judith A Kassis","doi":"10.1146/annurev-biochem-120219-103641","DOIUrl":"10.1146/annurev-biochem-120219-103641","url":null,"abstract":"<p><p>Predicting regulatory potential from primary DNA sequences or transcription factor binding patterns is not possible. However, the annotation of the genome by chromatin proteins, histone modifications, and differential compaction is largely sufficient to reveal the locations of genes and their differential activity states. The Polycomb Group (PcG) and Trithorax Group (TrxG) proteins are the central players in this cell type-specific chromatin organization. PcG function was originally viewed as being solely repressive and irreversible, as observed at the homeotic loci in flies and mammals. However, it is now clear that modular and reversible PcG function is essential at most developmental genes. Focusing mainly on recent advances, we review evidence for how PcG and TrxG patterns change dynamically during cell type transitions. The ability to implement cell type-specific transcriptional programming with exquisite fidelity is essential for normal development.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"235-253"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7311296/pdf/nihms-1575141.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37533775","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
Standing on the Shoulders of Viruses. 站在病毒的肩膀上
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 DOI: 10.1146/annurev-biochem-011320-103928
Ari Helenius
{"title":"Standing on the Shoulders of Viruses.","authors":"Ari Helenius","doi":"10.1146/annurev-biochem-011320-103928","DOIUrl":"10.1146/annurev-biochem-011320-103928","url":null,"abstract":"<p><p>My coworkers and I have used animal viruses and their interaction with host cells to investigate cellular processes difficult to study by other means. This approach has allowed us to branch out in many directions, including membrane protein characterization, endocytosis, secretion, protein folding, quality control, and glycobiology. At the same time, our aim has been to employ cell biological approaches to expand the fundamental understanding of animal viruses and their pathogenic lifestyles. We have studied mechanisms of host cell entry and the uncoating of incoming viruses as well as the synthesis, folding, maturation, and intracellular movement of viral proteins and molecular assemblies. I have had the privilege to work in institutions in four different countries. The early years in Finland (the University of Helsinki) were followed by 6 years in Germany (European Molecular Biology Laboratory), 16 years in the United States (Yale School of Medicine), and 16 years in Switzerland (ETH Zurich).</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"21-43"},"PeriodicalIF":12.1,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38071304","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
Mitochondrial Proteases: Multifaceted Regulators of Mitochondrial Plasticity. 线粒体蛋白酶:线粒体可塑性的多方面调节因子。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2020-06-20 Epub Date: 2020-02-19 DOI: 10.1146/annurev-biochem-062917-012739
Soni Deshwal, Kai Uwe Fiedler, Thomas Langer
{"title":"Mitochondrial Proteases: Multifaceted Regulators of Mitochondrial Plasticity.","authors":"Soni Deshwal,&nbsp;Kai Uwe Fiedler,&nbsp;Thomas Langer","doi":"10.1146/annurev-biochem-062917-012739","DOIUrl":"https://doi.org/10.1146/annurev-biochem-062917-012739","url":null,"abstract":"<p><p>Mitochondria are essential metabolic hubs that dynamically adapt to physiological demands. More than 40 proteases residing in different compartments of mitochondria, termed mitoproteases, preserve mitochondrial proteostasis and are emerging as central regulators of mitochondrial plasticity. These multifaceted enzymes limit the accumulation of short-lived, regulatory proteins within mitochondria, modulate the activity of mitochondrial proteins by protein processing, and mediate the degradation of damaged proteins. Various signaling cascades coordinate the activity of mitoproteases to preserve mitochondrial homeostasis and ensure cell survival. Loss of mitoproteases severely impairs the functional integrity of mitochondria, is associated with aging, and causes pleiotropic diseases. Understanding the dual function of mitoproteases as regulatory and quality control enzymes will help unravel the role of mitochondrial plasticity in aging and disease.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"89 ","pages":"501-528"},"PeriodicalIF":16.6,"publicationDate":"2020-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biochem-062917-012739","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37656954","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: 101
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