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High-resolution Single-molecule Magnetic Tweezers. 高分辨率单分子磁性镊子。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-02-14 DOI: 10.1146/annurev-biochem-032620-104637
Hyun-Kyu Choi, Hyun Gyu Kim, M. Shon, Tae-Young Yoon
{"title":"High-resolution Single-molecule Magnetic Tweezers.","authors":"Hyun-Kyu Choi, Hyun Gyu Kim, M. Shon, Tae-Young Yoon","doi":"10.1146/annurev-biochem-032620-104637","DOIUrl":"https://doi.org/10.1146/annurev-biochem-032620-104637","url":null,"abstract":"Single-molecule magnetic tweezers deliver magnetic force and torque to single target molecules, permitting the study of dynamic changes in biomolecular structures and their interactions. Because the magnetic tweezer setups can generate magnetic fields that vary slowly over tens of millimeters-far larger than the nanometer scale of the single molecule events being observed-this technique can maintain essentially constant force levels during biochemical experiments while generating a biologically meaningful force on the order of 1-100 pN. When using bead-tether constructs to pull on single molecules, smaller magnetic beads and shorter submicrometer tethers improve dynamic response times and measurement precision. In addition, employing high-speed cameras, stronger light sources, and a graphics programming unit permits true high-resolution single-molecule magnetic tweezers that can track nanometer changes in target molecules on a millisecond or even submillisecond time scale. The unique force-clamping capacity of the magnetic tweezer technique provides a way to conduct measurements under near-equilibrium conditions and directly map the energy landscapes underlying various molecular phenomena. High-resolution single-molecule magnetic tweezers can thus be used to monitor crucial conformational changes in single-protein molecules, including those involved in mechanotransduction and protein folding. 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":"48194579","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: 10
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
Preparing Better Samples for Cryo-Electron Microscopy: Biochemical Challenges Do Not End with Isolation and Purification. 制备更好的样品冷冻电子显微镜:生化挑战不结束与分离和纯化。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2021-06-20 Epub Date: 2021-02-08 DOI: 10.1146/annurev-biochem-072020-020231
Robert M Glaeser
{"title":"Preparing Better Samples for Cryo-Electron Microscopy: Biochemical Challenges Do Not End with Isolation and Purification.","authors":"Robert M Glaeser","doi":"10.1146/annurev-biochem-072020-020231","DOIUrl":"https://doi.org/10.1146/annurev-biochem-072020-020231","url":null,"abstract":"<p><p>The preparation of extremely thin samples, which are required for high-resolution electron microscopy, poses extreme risk of damaging biological macromolecules due to interactions with the air-water interface. Although the rapid increase in the number of published structures initially gave little indication that this was a problem, the search for methods that substantially mitigate this hazard is now intensifying. The two main approaches under investigation are (<i>a</i>) immobilizing particles onto structure-friendly support films and (<i>b</i>) reducing the length of time during which such interactions may occur. While there is little possibility of outrunning diffusion to the interface, intentional passivation of the interface may slow the process of adsorption and denaturation. In addition, growing attention is being given to gaining more effective control of the thickness of the sample prior to vitrification.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":"451-474"},"PeriodicalIF":16.6,"publicationDate":"2021-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25344763","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: 21
Repair of DNA Double-Strand Breaks by the Nonhomologous End Joining Pathway. 非同源末端连接途径修复DNA双链断裂。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2021-06-20 Epub Date: 2021-02-08 DOI: 10.1146/annurev-biochem-080320-110356
Benjamin M Stinson, Joseph J Loparo
{"title":"Repair of DNA Double-Strand Breaks by the Nonhomologous End Joining Pathway.","authors":"Benjamin M Stinson,&nbsp;Joseph J Loparo","doi":"10.1146/annurev-biochem-080320-110356","DOIUrl":"https://doi.org/10.1146/annurev-biochem-080320-110356","url":null,"abstract":"<p><p>DNA double-strand breaks pose a serious threat to genome stability. In vertebrates, these breaks are predominantly repaired by nonhomologous end joining (NHEJ), which pairs DNA ends in a multiprotein synaptic complex to promote their direct ligation. NHEJ is a highly versatile pathway that uses an array of processing enzymes to modify damaged DNA ends and enable their ligation. The mechanisms of end synapsis and end processing have important implications for genome stability. Rapid and stable synapsis is necessary to limit chromosome translocations that result from the mispairing of DNA ends. Furthermore, end processing must be tightly regulated to minimize mutations at the break site. Here, we review our current mechanistic understanding of vertebrate NHEJ, with a particular focus on end synapsis and processing.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":"137-164"},"PeriodicalIF":16.6,"publicationDate":"2021-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8899865/pdf/nihms-1679445.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25344765","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: 56
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
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