Annual Review of Biophysics最新文献_第10页

Molecular Force Measurement with Tension Sensors. 张力传感器分子力测量。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 Epub Date: 2021-03-12 DOI: 10.1146/annurev-biophys-101920-064756

Lisa S Fischer, Srishti Rangarajan, Tanmay Sadhanasatish, Carsten Grashoff

{"title":"Molecular Force Measurement with Tension Sensors.","authors":"Lisa S Fischer, Srishti Rangarajan, Tanmay Sadhanasatish, Carsten Grashoff","doi":"10.1146/annurev-biophys-101920-064756","DOIUrl":"https://doi.org/10.1146/annurev-biophys-101920-064756","url":null,"abstract":"The ability of cells to generate mechanical forces, but also to sense, adapt to, and respond to mechanical signals, is crucial for many developmental, postnatal homeostatic, and pathophysiological processes. However, the molecular mechanisms underlying cellular mechanotransduction have remained elusive for many decades, as techniques to visualize and quantify molecular forces across individual proteins in cells were missing. The development of genetically encoded molecular tension sensors now allows the quantification of piconewton-scale forces that act upon distinct molecules in living cells and even whole organisms. In this review, we discuss the physical principles, advantages, and limitations of this increasingly popular method. By highlighting current examples from the literature, we demonstrate how molecular tension sensors can be utilized to obtain access to previously unappreciated biophysical parameters that define the propagation of mechanical forces on molecular scales. We discuss how the methodology can be further developed and provide a perspective on how the technique could be applied to uncover entirely novel aspects of mechanobiology in the future.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2021-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25469207","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

Cutting-Edge Single-Molecule Technologies Unveil New Mechanics in Cellular Biochemistry. 尖端的单分子技术揭示了细胞生物化学的新机制。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 Epub Date: 2021-03-01 DOI: 10.1146/annurev-biophys-090420-083836

Souradeep Banerjee, Soham Chakraborty, Abhijit Sreepada, Devshuvam Banerji, Shashwat Goyal, Yajushi Khurana, Shubhasis Haldar

{"title":"Cutting-Edge Single-Molecule Technologies Unveil New Mechanics in Cellular Biochemistry.","authors":"Souradeep Banerjee, Soham Chakraborty, Abhijit Sreepada, Devshuvam Banerji, Shashwat Goyal, Yajushi Khurana, Shubhasis Haldar","doi":"10.1146/annurev-biophys-090420-083836","DOIUrl":"https://doi.org/10.1146/annurev-biophys-090420-083836","url":null,"abstract":"Single-molecule technologies have expanded our ability to detect biological events individually, in contrast to ensemble biophysical technologies, where the result provides averaged information. Recent developments in atomic force microscopy have not only enabled us to distinguish the heterogeneous phenomena of individual molecules, but also allowed us to view up to the resolution of a single covalent bond. Similarly, optical tweezers, due to their versatility and precision, have emerged as a potent technique to dissect a diverse range of complex biological processes, from the nanomechanics of ClpXP protease-dependent degradation to force-dependent processivity of motor proteins. Despite the advantages of optical tweezers, the time scales used in this technology were inconsistent with physiological scenarios, which led to the development of magnetic tweezers, where proteins are covalently linked with the glass surface, which in turn increases the observation window of a single biomolecule from minutes to weeks. Unlike optical tweezers, magnetic tweezers use magnetic fields to impose torque, which makes them convenient for studying DNA topology and topoisomerase functioning. Using modified magnetic tweezers, researchers were able to discover the mechanical role of chaperones, which support their substrate proteinsby pulling them during translocation and assist their native folding as a mechanical foldase. In this article, we provide a focused review of many of these new roles of single-molecule technologies, ranging from single bond breaking to complex chaperone machinery, along with the potential to design mechanomedicine, which would be a breakthrough in pharmacological interventions against many diseases.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2021-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25423932","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

Structure of Phycobilisomes. 藻胆体的结构。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 DOI: 10.1146/annurev-biophys-062920-063657

Sen-Fang Sui

引用次数: 22

The Phasor Plot: A Universal Circle to Advance Fluorescence Lifetime Analysis and Interpretation. 相量图:推进荧光寿命分析和解释的通用循环。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 DOI: 10.1146/annurev-biophys-062920-063631

Leonel Malacrida, Suman Ranjit, David M Jameson, Enrico Gratton

{"title":"The Phasor Plot: A Universal Circle to Advance Fluorescence Lifetime Analysis and Interpretation.","authors":"Leonel Malacrida, Suman Ranjit, David M Jameson, Enrico Gratton","doi":"10.1146/annurev-biophys-062920-063631","DOIUrl":"https://doi.org/10.1146/annurev-biophys-062920-063631","url":null,"abstract":"The phasor approach to fluorescence lifetime imaging has become a common method to analyze complicated fluorescence signals from biological samples. The appeal of the phasor representation of complex fluorescence decays in biological systems is that a visual representation of the decay of entire cells or tissues can be used to easily interpret fundamental biological states related to metabolism and oxidative stress. Phenotyping based on autofluorescence provides new avenues for disease characterization and diagnostics. The phasor approach is a transformation of complex fluorescence decays that does not use fits to model decays and therefore has the same information content as the original data. The phasor plot is unique for a given system, is highly reproducible, and provides a robust method to evaluate the existence of molecular interactions such as Förster resonance energy transfer or the response of ion indicators. Recent advances permitquantification of multiple components from phasor plots in fluorescence lifetime imaging microscopy, which is not presently possible using data fitting methods, especially in biological systems.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2021-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38956583","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: 46

Recent Developments in the Field of Intrinsically Disordered Proteins: Intrinsic Disorder-Based Emergence in Cellular Biology in Light of the Physiological and Pathological Liquid-Liquid Phase Transitions. 内在无序蛋白领域的新进展:从生理和病理的液-液相变看细胞生物学中基于内在无序的出现

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 Epub Date: 2021-01-27 DOI: 10.1146/annurev-biophys-062920-063704

Vladimir N Uversky

引用次数: 41

Directed Evolution of Microbial Communities. 微生物群落的定向进化。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2020-07-28 DOI: 10.32942/osf.io/gsz7j

Álvaro Sánchez, Jean C. C. Vila, Chang-Yu Chang, Juan Díaz-Colunga, Sylvie Estrela, María Rebolleda-Gómez

{"title":"Directed Evolution of Microbial Communities.","authors":"Álvaro Sánchez, Jean C. C. Vila, Chang-Yu Chang, Juan Díaz-Colunga, Sylvie Estrela, María Rebolleda-Gómez","doi":"10.32942/osf.io/gsz7j","DOIUrl":"https://doi.org/10.32942/osf.io/gsz7j","url":null,"abstract":"Directed evolution is a form of artificial selection that has been used for decades to find biomolecules and organisms with new or enhanced functional traits. Directed evolution can be conceptualized as a guided exploration of the genotype-phenotype map, where genetic variants with desirable phenotypes are first selected and then mutagenized to search the genotype space for an even better mutant. In recent years, the idea of applying artificial selection to microbial communities has gained momentum. In this article, we review the main limitations of artificial selection when applied to large and diverse collectives of asexually dividing microbes and discuss how the tools of directed evolution may be deployed to engineer communities from the top down. We conceptualize directed evolution of microbial communities as a guided exploration of an ecological structure-function landscape and propose practical guidelines for navigating these ecological landscapes. Expected final online publication date for the Annual Review of Biophysics, Volume 50 is May 2021. 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":"2020-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44829334","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: 43

The Physics of Cellular Decision Making During Epithelial-Mesenchymal Transition. 上皮-间质转化过程中细胞决策的物理学。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2020-05-06 Epub Date: 2020-01-08 DOI: 10.1146/annurev-biophys-121219-081557

Shubham Tripathi, Herbert Levine, Mohit Kumar Jolly

{"title":"The Physics of Cellular Decision Making During Epithelial-Mesenchymal Transition.","authors":"Shubham Tripathi, Herbert Levine, Mohit Kumar Jolly","doi":"10.1146/annurev-biophys-121219-081557","DOIUrl":"https://doi.org/10.1146/annurev-biophys-121219-081557","url":null,"abstract":"The epithelial-mesenchymal transition (EMT) is a process by which cells lose epithelial traits, such as cell-cell adhesion and apico-basal polarity, and acquire migratory and invasive traits. EMT is crucial to embryonic development and wound healing. Misregulated EMT has been implicated in processes associated with cancer aggressiveness, including metastasis. Recent experimental advances such as single-cell analysis and temporal phenotypic characterization have established that EMT is a multistable process wherein cells exhibit and switch among multiple phenotypic states. This is in contrast to the classical perception of EMT as leading to a binary choice. Mathematical modeling has been at the forefront of this transformation for the field, not only providing a conceptual framework to integrate and analyze experimental data, but also making testable predictions. In this article, we review the key features and characteristics of EMT dynamics, with a focus on the mathematical modeling approaches that have been instrumental to obtaining various useful insights.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2020-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biophys-121219-081557","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37522435","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: 62

Physical Principles Underlying the Complex Biology of Intracellular Phase Transitions. 细胞内相变复杂生物学的物理原理。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2020-05-06 Epub Date: 2020-01-31 DOI: 10.1146/annurev-biophys-121219-081629

Jeong-Mo Choi, Alex S Holehouse, Rohit V Pappu

引用次数: 438

Predicting Evolution Using Regulatory Architecture. 利用监管架构预测进化。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2020-05-06 Epub Date: 2020-02-04 DOI: 10.1146/annurev-biophys-070317-032939

Philippe Nghe, Marjon G J de Vos, Enzo Kingma, Manjunatha Kogenaru, Frank J Poelwijk, Liedewij Laan, Sander J Tans

引用次数: 7

Gene Regulation in and out of Equilibrium. 平衡内外的基因调控。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2020-05-06 DOI: 10.1146/annurev-biophys-121219-081542

Felix Wong, Jeremy Gunawardena

{"title":"Gene Regulation in and out of Equilibrium.","authors":"Felix Wong, Jeremy Gunawardena","doi":"10.1146/annurev-biophys-121219-081542","DOIUrl":"https://doi.org/10.1146/annurev-biophys-121219-081542","url":null,"abstract":"Determining whether and how a gene is transcribed are two of the central processes of life. The conceptual basis for understanding such gene regulation arose from pioneering biophysical studies in eubacteria. However, eukaryotic genomes exhibit vastly greater complexity, which raises questions not addressed by this bacterial paradigm. First, how is information integrated from many widely separated binding sites to determine how a gene is transcribed? Second, does the presence of multiple energy-expending mechanisms, which are absent from eubacterial genomes, indicate that eukaryotes are capable of improved forms of genetic information processing? An updated biophysical foundation is needed to answer such questions. We describe the linear framework, a graph-based approach to Markov processes, and show that it can accommodate many previous studies in the field. Under the assumption of thermodynamic equilibrium, we introduce a language of higher-order cooperativities and show how it can rigorously quantify gene regulatory properties suggested by experiment. We point out that fundamental limits to information processing arise at thermodynamic equilibrium and can only be bypassed through energy expenditure. Finally, we outline some of the mathematical challenges that must be overcome to construct an improved biophysical understanding of gene regulation.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":null,"pages":null},"PeriodicalIF":12.4,"publicationDate":"2020-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1146/annurev-biophys-121219-081542","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37907373","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