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Annual Review of Biophysics最新文献

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High-Speed Atomic Force Microscopy for Filming Protein Molecules in Dynamic Action 高速原子力显微镜拍摄蛋白质分子的动态动作
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-12-07 DOI: 10.1146/annurev-biophys-030722-113353
Toshio Ando, Shingo Fukuda, Kien X. Ngo, Holger Flechsig
{"title":"High-Speed Atomic Force Microscopy for Filming Protein Molecules in Dynamic Action","authors":"Toshio Ando, Shingo Fukuda, Kien X. Ngo, Holger Flechsig","doi":"10.1146/annurev-biophys-030722-113353","DOIUrl":"https://doi.org/10.1146/annurev-biophys-030722-113353","url":null,"abstract":"Structural biology is currently undergoing a transformation into dynamic structural biology, which reveals the dynamic structure of proteins during their functional activity to better elucidate how they function. Among the various approaches in dynamic structural biology, high-speed atomic force microscopy (HS-AFM) is unique in the ability to film individual molecules in dynamic action, although only topographical information is acquirable. This review provides a guide to the use of HS-AFM for biomolecular imaging and showcases several examples, as well as providing information on up-to-date progress in HS-AFM technology. Finally, we discuss the future prospects of HS-AFM in the context of dynamic structural biology in the upcoming era.Expected final online publication date for the Annual Review of Biophysics, Volume 53 is May 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2023-12-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138556113","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
Structure and Mechanism of Human ABC Transporters. 人类ABC转运蛋白的结构和机制。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 Epub Date: 2023-02-03 DOI: 10.1146/annurev-biophys-111622-091232
Amer Alam, Kaspar P Locher
{"title":"Structure and Mechanism of Human ABC Transporters.","authors":"Amer Alam, Kaspar P Locher","doi":"10.1146/annurev-biophys-111622-091232","DOIUrl":"10.1146/annurev-biophys-111622-091232","url":null,"abstract":"<p><p>ABC transporters are essential for cellular physiology. Humans have 48 ABC genes organized into seven distinct families. Of these genes, 44 (in five distinct families) encode for membrane transporters, of which several are involved in drug resistance and disease pathways resulting from transporter dysfunction. Over the last decade, advances in structural biology have vastly expanded our mechanistic understanding of human ABC transporter function, revealing details of their molecular arrangement, regulation, and interactions, facilitated in large part by advances in cryo-EM that have rendered hitherto inaccessible targets amenable to high-resolution structural analysis. As a result, experimentally determined structures of multiple members of each of the five families of ABC transporters in humans are now available. Here we review this recent progress, highlighting the physiological relevance of human ABC transporters and mechanistic insights gleaned from their direct structure determination. We also discuss the impact and limitations of model systems and structure prediction methods in understanding human ABC transporters and discuss current challenges and future research directions.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9437904","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: 12
Hybrid Quantum Mechanical/Molecular Mechanical Methods For Studying Energy Transduction in Biomolecular Machines. 研究生物分子机械中能量转换的量子力学/分子机械混合方法。
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-111622-091140
T Kubař, M Elstner, Q Cui
{"title":"Hybrid Quantum Mechanical/Molecular Mechanical Methods For Studying Energy Transduction in Biomolecular Machines.","authors":"T Kubař, M Elstner, Q Cui","doi":"10.1146/annurev-biophys-111622-091140","DOIUrl":"10.1146/annurev-biophys-111622-091140","url":null,"abstract":"<p><p>Hybrid quantum mechanical/molecular mechanical (QM/MM) methods have become indispensable tools for the study of biomolecules. In this article, we briefly review the basic methodological details of QM/MM approaches and discuss their applications to various energy transduction problems in biomolecular machines, such as long-range proton transports, fast electron transfers, and mechanochemical coupling. We highlight the particular importance for these applications of balancing computational efficiency and accuracy. Using several recent examples, we illustrate the value and limitations of QM/MM methodologies for both ground and excited states, as well as strategies for calibrating them in specific applications. We conclude with brief comments on several areas that can benefit from further efforts to make QM/MM analyses more quantitative and applicable to increasingly complex biological problems.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10810093/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9444168","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
Assembly and Architecture of NLR Resistosomes and Inflammasomes. NLR抵抗体和炎性小体的组装和结构。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 DOI: 10.1146/annurev-biophys-092922-073050
Zehan Hu, Jijie Chai
{"title":"Assembly and Architecture of NLR Resistosomes and Inflammasomes.","authors":"Zehan Hu,&nbsp;Jijie Chai","doi":"10.1146/annurev-biophys-092922-073050","DOIUrl":"https://doi.org/10.1146/annurev-biophys-092922-073050","url":null,"abstract":"<p><p>Nucleotide-binding and leucine-rich repeat (NLR) proteins are critical intracellular immune receptors in both animals and plants. Perception of pathogen-derived or stress-associated signals induces NLR oligomerization to form multiprotein complexes called inflammasomes in animals or resistosomes in plants to mediate host immune response. Significant progress has been made during the past few years in our understanding of NLR biology, particularly the structural perspective of these two types of NLR-containing complexes. In this article, we review the latest advances in our structural knowledge of how NLR inflammasomes and resistosomes are activated and assembled and how the structural information provides insight into their distinct mechanisms of action. Commonalities and differences between NLR inflammasomes and resistosomes are also discussed.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9814899","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: 4
Ball-and-Chain Inactivation in Potassium Channels. 钾离子通道的球链失活。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 DOI: 10.1146/annurev-biophys-100322-072921
Nattakan Sukomon, Chen Fan, Crina M Nimigean
{"title":"Ball-and-Chain Inactivation in Potassium Channels.","authors":"Nattakan Sukomon,&nbsp;Chen Fan,&nbsp;Crina M Nimigean","doi":"10.1146/annurev-biophys-100322-072921","DOIUrl":"https://doi.org/10.1146/annurev-biophys-100322-072921","url":null,"abstract":"Carefully orchestrated opening and closing of ion channels controls the diffusion of ions across cell membranes, generating the electrical signals required for fast transmission of information throughout the nervous system. Inactivation is a parsimonious means for channels to restrict ion conduction without the need to remove the activating stimulus. Voltage-gated channel inactivation plays crucial physiological roles, such as controlling action potential duration and firing frequency in neurons. The ball-and-chain moniker applies to a type of inactivation proposed first for sodium channels and later shown to be a universal mechanism. Still, structural evidence for this mechanism remained elusive until recently. We review the ball-and-chain inactivation research starting from its introduction as a crucial component of sodium conductance during electrical signaling in the classical Hodgkin and Huxley studies, through the discovery of its simple intuitive mechanism in potassium channels during the molecular cloning era, to the eventual elucidation of a potassium channel structure in a ball-and-chain inactivated state. Expected final online publication date for the Annual Review of Biophysics, Volume 52 is May 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9814900","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
The Expanded Central Dogma: Genome Resynthesis, Orthogonal Biosystems, Synthetic Genetics. 扩展的中心法则:基因组再合成，正交生物系统，合成遗传学。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 DOI: 10.1146/annurev-biophys-111622-091203
Karola Gerecht, Niklas Freund, Wei Liu, Yang Liu, Maximilian J L J Fürst, Philipp Holliger
{"title":"The Expanded Central Dogma: Genome Resynthesis, Orthogonal Biosystems, Synthetic Genetics.","authors":"Karola Gerecht,&nbsp;Niklas Freund,&nbsp;Wei Liu,&nbsp;Yang Liu,&nbsp;Maximilian J L J Fürst,&nbsp;Philipp Holliger","doi":"10.1146/annurev-biophys-111622-091203","DOIUrl":"https://doi.org/10.1146/annurev-biophys-111622-091203","url":null,"abstract":"<p><p>Synthetic biology seeks to probe fundamental aspects of biological form and function by construction [i.e., (re)synthesis] rather than deconstruction (analysis). In this sense, biological sciences now follow the lead given by the chemical sciences. Synthesis can complement analytic studies but also allows novel approaches to answering fundamental biological questions and opens up vast opportunities for the exploitation of biological processes to provide solutions for global problems. In this review, we explore aspects of this synthesis paradigm as applied to the chemistry and function of nucleic acids in biological systems and beyond, specifically, in genome resynthesis, synthetic genetics (i.e., the expansion of the genetic alphabet, of the genetic code, and of the chemical make-up of genetic systems), and the elaboration of orthogonal biosystems and components.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7614659/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9636415","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: 1
Next-Gen Biophysics: Look to the Forest, Beyond the Trees. 新一代生物物理学：透过树木看森林。
IF 12.4 1区 生物学
Annual Review of Biophysics Pub Date : 2023-05-09 DOI: 10.1146/annurev-bb-52-030923-100001
Jeremy Schmit, Ken A Dill
{"title":"Next-Gen Biophysics: Look to the Forest, Beyond the Trees.","authors":"Jeremy Schmit, Ken A Dill","doi":"10.1146/annurev-bb-52-030923-100001","DOIUrl":"10.1146/annurev-bb-52-030923-100001","url":null,"abstract":"","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2023-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9501369","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
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":null,"pages":null},"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":null,"pages":null},"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":null,"pages":null},"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
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