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Annual Review of Biophysics最新文献

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Fifty Years of Biophysics at the Membrane Frontier. 膜前沿生物物理学五十年。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 Epub Date: 2023-02-15 DOI: 10.1146/annurev-biophys-051622-112341
Stephen H White
{"title":"Fifty Years of Biophysics at the Membrane Frontier.","authors":"Stephen H White","doi":"10.1146/annurev-biophys-051622-112341","DOIUrl":"10.1146/annurev-biophys-051622-112341","url":null,"abstract":"<p><p>The author first describes his childhood in the South and the ways in which it fostered the values he has espoused throughout his life, his development of a keen fascination with science, and the influences that supported his progress toward higher education. His experiences in ROTC as a student, followed by two years in the US Army during the Vietnam War, honed his leadership skills. The bulk of the autobiography is a chronological journey through his scientific career, beginning with arrival at the University of California, Irvine in 1972, with an emphasis on the postdoctoral students and colleagues who have contributed substantially to each phase of his lab's progress. White's fundamental findings played a key role in the development of membrane biophysics, helping establish it as fertile ground for research. A story gradually unfolds that reveals the deeply collaborative and painstakingly executed work necessary for a successful career in science.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"52 ","pages":"21-67"},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9500207","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
Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes. 对蛋白质和蛋白质复合物三维结构预测方法的严格评估。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 Epub Date: 2023-01-10 DOI: 10.1146/annurev-biophys-102622-084607
Shoshana J Wodak, Sandor Vajda, Marc F Lensink, Dima Kozakov, Paul A Bates
{"title":"Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes.","authors":"Shoshana J Wodak, Sandor Vajda, Marc F Lensink, Dima Kozakov, Paul A Bates","doi":"10.1146/annurev-biophys-102622-084607","DOIUrl":"10.1146/annurev-biophys-102622-084607","url":null,"abstract":"<p><p>Advances in a scientific discipline are often measured by small, incremental steps. In this review, we report on two intertwined disciplines in the protein structure prediction field, modeling of single chains and modeling of complexes, that have over decades emulated this pattern, as monitored by the community-wide blind prediction experiments CASP and CAPRI. However, over the past few years, dramatic advances were observed for the accurate prediction of single protein chains, driven by a surge of deep learning methodologies entering the prediction field. We review the mainscientific developments that enabled these recent breakthroughs and feature the important role of blind prediction experiments in building up and nurturing the structure prediction field. We discuss how the new wave of artificial intelligence-based methods is impacting the fields of computational and experimental structural biology and highlight areas in which deep learning methods are likely to lead to future developments, provided that major challenges are overcome.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"52 ","pages":"183-206"},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10885158/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9855379","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
Theoretical and Practical Aspects of Multienzyme Organization and Encapsulation. 多酶组织和封装的理论和实践方面。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 Epub Date: 2023-02-28 DOI: 10.1146/annurev-biophys-092222-020832
Charlotte H Abrahamson, Brett J Palmero, Nolan W Kennedy, Danielle Tullman-Ercek
{"title":"Theoretical and Practical Aspects of Multienzyme Organization and Encapsulation.","authors":"Charlotte H Abrahamson, Brett J Palmero, Nolan W Kennedy, Danielle Tullman-Ercek","doi":"10.1146/annurev-biophys-092222-020832","DOIUrl":"10.1146/annurev-biophys-092222-020832","url":null,"abstract":"<p><p>The advent of biotechnology has enabled metabolic engineers to assemble heterologous pathways in cells to produce a variety of products of industrial relevance, often in a sustainable way. However, many pathways face challenges of low product yield. These pathways often suffer from issues that are difficult to optimize, such as low pathway flux and off-target pathway consumption of intermediates. These issues are exacerbated by the need to balance pathway flux with the health of the cell, particularly when a toxic intermediate builds up. Nature faces similar challenges and has evolved spatial organization strategies to increase metabolic pathway flux and efficiency. Inspired by these strategies, bioengineers have developed clever strategies to mimic spatial organization in nature. This review explores the use of spatial organization strategies, including protein scaffolding and protein encapsulation inside of proteinaceous shells, toward overcoming bottlenecks in metabolic engineering efforts.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"52 ","pages":"553-572"},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9440534","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: 1
Mechanisms of Protein Quality Control in the Endoplasmic Reticulum by a Coordinated Hsp40-Hsp70-Hsp90 System. Hsp40-Hsp70-Hsp90协同系统在内质网中蛋白质质量控制的机制
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 DOI: 10.1146/annurev-biophys-111622-091309
Judy L M Kotler, Timothy O Street
{"title":"Mechanisms of Protein Quality Control in the Endoplasmic Reticulum by a Coordinated Hsp40-Hsp70-Hsp90 System.","authors":"Judy L M Kotler,&nbsp;Timothy O Street","doi":"10.1146/annurev-biophys-111622-091309","DOIUrl":"https://doi.org/10.1146/annurev-biophys-111622-091309","url":null,"abstract":"<p><p>The Hsp40, Hsp70, and Hsp90 chaperone families are ancient, highly conserved, and critical to cellular protein homeostasis. Hsp40 chaperones can transfer their protein clients to Hsp70, and Hsp70 can transfer clients to Hsp90, but the functional benefits of these transfers are unclear. Recent structural and mechanistic work has opened up the possibility of uncovering how Hsp40, Hsp70, and Hsp90 work together as unified system. In this review, we compile mechanistic data on the ER J-domain protein 3 (ERdj3) (an Hsp40), BiP (an Hsp70), and Grp94 (an Hsp90) chaperones within the endoplasmic reticulum; what is known about how these chaperones work together; and gaps in this understanding. Using calculations, we examine how client transfer could impact the solubilization of aggregates, the folding of soluble proteins, and the triage decisions by which proteins are targeted for degradation. The proposed roles of client transfer among Hsp40-Hsp70-Hsp90 chaperones are new hypotheses, and we discuss potential experimental tests of these ideas.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"52 ","pages":"509-524"},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9466565","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: 1
Emerging Time-Resolved X-Ray Diffraction Approaches for Protein Dynamics. 蛋白质动力学的新兴时间分辨X射线衍射方法。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 DOI: 10.1146/annurev-biophys-111622-091155
Doeke R Hekstra
{"title":"Emerging Time-Resolved X-Ray Diffraction Approaches for Protein Dynamics.","authors":"Doeke R Hekstra","doi":"10.1146/annurev-biophys-111622-091155","DOIUrl":"10.1146/annurev-biophys-111622-091155","url":null,"abstract":"<p><p>Proteins guide the flows of information, energy, and matter that make life possible by accelerating transport and chemical reactions, by allosterically modulating these reactions, and by forming dynamic supramolecular assemblies. In these roles, conformational change underlies functional transitions. Time-resolved X-ray diffraction methods characterize these transitions either by directly triggering sequences of functionally important motions or, more broadly, by capturing the motions of which proteins are capable. To date, most successful have been experiments in which conformational change is triggered in light-dependent proteins. In this review, I emphasize emerging techniques that probe the dynamic basis of function in proteins lacking natively light-dependent transitions and speculate about extensions and further possibilities. In addition, I review how the weaker and more distributed signals in these data push the limits of the capabilities of analytical methods. Taken together, these new methods are beginning to establish a powerful paradigm for the study of the physics of protein function.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"52 ","pages":"255-274"},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10687665/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9642991","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: 2
Simulation of Complex Biomolecular Systems: The Ribosome Challenge. 复杂生物分子系统的模拟:核糖体挑战。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 DOI: 10.1146/annurev-biophys-111622-091147
Lars V Bock, Sara Gabrielli, Michal H Kolář, Helmut Grubmüller
{"title":"Simulation of Complex Biomolecular Systems: The Ribosome Challenge.","authors":"Lars V Bock,&nbsp;Sara Gabrielli,&nbsp;Michal H Kolář,&nbsp;Helmut Grubmüller","doi":"10.1146/annurev-biophys-111622-091147","DOIUrl":"https://doi.org/10.1146/annurev-biophys-111622-091147","url":null,"abstract":"<p><p>Large biomolecular systems are at the heart of many essential cellular processes. The dynamics and energetics of an increasing number of these systems are being studied by computer simulations. Pushing the limits of length- and timescales that can be accessed by current hard- and software has expanded the ability to describe biomolecules at different levels of detail. We focus in this review on the ribosome, which exemplifies the close interplay between experiment and various simulation approaches, as a particularly challenging and prototypic nanomachine that is pivotal to cellular biology due to its central role in translation. We sketch widely used simulation methods and demonstrate how the combination of simulations and experiments advances our understanding of the function of the translation apparatus based on fundamental physics.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"52 ","pages":"361-390"},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9446283","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: 2
HX and Me: Understanding Allostery, Folding, and Protein Machines. HX和我:理解变构、折叠和蛋白质机器。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 DOI: 10.1146/annurev-biophys-062122-093517
S Walter Englander
{"title":"HX and Me: Understanding Allostery, Folding, and Protein Machines.","authors":"S Walter Englander","doi":"10.1146/annurev-biophys-062122-093517","DOIUrl":"https://doi.org/10.1146/annurev-biophys-062122-093517","url":null,"abstract":"<p><p>My accidental encounter with protein hydrogen exchange (HX) at its very beginning and its continued development through my scientific career have led us to a series of advances in HX measurement, interpretation, and cutting edge biophysical applications. After some thoughts about how life brought me there, I take the opportunity to reflect on our early studies of allosteric structure and energy change in hemoglobin, the still-current protein folding problem, and our most recent forward-looking studies on protein machines.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"52 ","pages":"1-18"},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9499376","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: 1
Protein Diffusion Along Protein and DNA Lattices: Role of Electrostatics and Disordered Regions. 蛋白质沿蛋白质和DNA晶格扩散:静电和无序区域的作用。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 DOI: 10.1146/annurev-biophys-111622-091220
Lavi S Bigman, Yaakov Levy
{"title":"Protein Diffusion Along Protein and DNA Lattices: Role of Electrostatics and Disordered Regions.","authors":"Lavi S Bigman,&nbsp;Yaakov Levy","doi":"10.1146/annurev-biophys-111622-091220","DOIUrl":"https://doi.org/10.1146/annurev-biophys-111622-091220","url":null,"abstract":"<p><p>Diffusion is a pervasive process present in a broad spectrum of cellular reactions. Its mathematical description has existed for nearly two centuries and permits the construction of simple rules for evaluating the characteristic timescales of diffusive processes and some of their determinants. Although the term diffusion originally referred to random motions in three-dimensional (3D) media, several biological diffusion processes in lower dimensions have been reported. One-dimensional (1D) diffusions have been reported, for example, for translocations of various proteins along DNA or protein (e.g., microtubule) lattices and translation of helical peptides along the coiled-coil interface. Two-dimensional (2D) diffusion has been shown for dynamics of proteins along membranes. The microscopic mechanisms of these 1-3D diffusions may vary significantly depending on the nature of the diffusing molecules, the substrate, and the interactions between them. In this review, we highlight some key examples of 1-3D biomolecular diffusion processes and illustrate the roles that electrostatic interactions and intrinsic disorder may play in modulating these processes.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"52 ","pages":"463-486"},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9499388","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: 3
Prospects and Limitations of High-Resolution Single-Particle Cryo-Electron Microscopy. 高分辨率单粒子冷冻电子显微镜的前景与局限性。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 DOI: 10.1146/annurev-biophys-111622-091300
Ashwin Chari, Holger Stark
{"title":"Prospects and Limitations of High-Resolution Single-Particle Cryo-Electron Microscopy.","authors":"Ashwin Chari,&nbsp;Holger Stark","doi":"10.1146/annurev-biophys-111622-091300","DOIUrl":"https://doi.org/10.1146/annurev-biophys-111622-091300","url":null,"abstract":"<p><p>Single particle cryo-electron microscopy (cryo-EM) has matured into a robust method for the determination of biological macromolecule structures in the past decade, complementing X-ray crystallography and nuclear magnetic resonance. Constant methodological improvements in both cryo-EM hardware and image processing software continue to contribute to an exponential growth in the number of structures solved annually. In this review, we provide a historical view of the many steps that were required to make cryo-EM a successful method for the determination of high-resolution protein complex structures. We further discuss aspects of cryo-EM methodology that are the greatest pitfalls challenging successful structure determination to date. Lastly, we highlight and propose potential future developments that would improve the method even further in the near future.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"52 ","pages":"391-411"},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9501371","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: 2
Decoding and Recoding of mRNA Sequences by the Ribosome. 核糖体对mRNA序列的解码和再编码。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 DOI: 10.1146/annurev-biophys-101922-072452
Marina V Rodnina
{"title":"Decoding and Recoding of mRNA Sequences by the Ribosome.","authors":"Marina V Rodnina","doi":"10.1146/annurev-biophys-101922-072452","DOIUrl":"https://doi.org/10.1146/annurev-biophys-101922-072452","url":null,"abstract":"<p><p>Faithful translation of messenger RNA (mRNA) into protein is essential to maintain protein homeostasis in the cell. Spontaneous translation errors are very rare due to stringent selection of cognate aminoacyl transfer RNAs (tRNAs) and the tight control of the mRNA reading frame by the ribosome. Recoding events, such as stop codon readthrough, frameshifting, and translational bypassing, reprogram the ribosome to make intentional mistakes and produce alternative proteins from the same mRNA. The hallmark of recoding is the change of ribosome dynamics. The signals for recoding are built into the mRNA, but their reading depends on the genetic makeup of the cell, resulting in cell-specific changes in expression programs. In this review, I discuss the mechanisms of canonical decoding and tRNA-mRNA translocation; describe alternative pathways leading to recoding; and identify the links among mRNA signals, ribosome dynamics, and recoding.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"52 ","pages":"161-182"},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9501373","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
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