Annual Review of Biophysics最新文献_第9页

Bayesian Inference: The Comprehensive Approach to Analyzing Single-Molecule Experiments. 贝叶斯推断:分析单分子实验的综合方法。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 Epub Date: 2021-02-03 DOI: 10.1146/annurev-biophys-082120-103921

Colin D Kinz-Thompson, Korak Kumar Ray, Ruben L Gonzalez

{"title":"Bayesian Inference: The Comprehensive Approach to Analyzing Single-Molecule Experiments.","authors":"Colin D Kinz-Thompson, Korak Kumar Ray, Ruben L Gonzalez","doi":"10.1146/annurev-biophys-082120-103921","DOIUrl":"https://doi.org/10.1146/annurev-biophys-082120-103921","url":null,"abstract":"Biophysics experiments performed at single-molecule resolution provide exceptional insight into the structural details and dynamic behavior of biological systems. However, extracting this information from the corresponding experimental data unequivocally requires applying a biophysical model. In this review, we discuss how to use probability theory to apply these models to single-molecule data. Many current single-molecule data analysis methods apply parts of probability theory, sometimes unknowingly, and thus miss out on the full set of benefits provided by this self-consistent framework. The full application of probability theory involves a process called Bayesian inference that fully accounts for the uncertainties inherent to single-molecule experiments. Additionally, using Bayesian inference provides a scientifically rigorous method of incorporating information from multiple experiments into a single analysis and finding the best biophysical model for an experiment without the risk of overfitting the data. These benefits make the Bayesian approach ideal for analyzing any type of single-molecule experiment.","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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8238404/pdf/nihms-1708438.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25326862","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: 10

The Molecular Basis for Life in Extreme Environments. 极端环境下生命的分子基础。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 Epub Date: 2021-02-26 DOI: 10.1146/annurev-biophys-100120-072804

Nozomi Ando, Blanca Barquera, Douglas H Bartlett, Eric Boyd, Audrey A Burnim, Amanda S Byer, Daniel Colman, Richard E Gillilan, Martin Gruebele, George Makhatadze, Catherine A Royer, Everett Shock, A Joshua Wand, Maxwell B Watkins

{"title":"The Molecular Basis for Life in Extreme Environments.","authors":"Nozomi Ando, Blanca Barquera, Douglas H Bartlett, Eric Boyd, Audrey A Burnim, Amanda S Byer, Daniel Colman, Richard E Gillilan, Martin Gruebele, George Makhatadze, Catherine A Royer, Everett Shock, A Joshua Wand, Maxwell B Watkins","doi":"10.1146/annurev-biophys-100120-072804","DOIUrl":"https://doi.org/10.1146/annurev-biophys-100120-072804","url":null,"abstract":"Sampling and genomic efforts over the past decade have revealed an enormous quantity and diversity of life in Earth's extreme environments. This new knowledge of life on Earth poses the challenge of understandingits molecular basis in such inhospitable conditions, given that such conditions lead to loss of structure and of function in biomolecules from mesophiles. In this review, we discuss the physicochemical properties of extreme environments. We present the state of recent progress in extreme environmental genomics. We then present an overview of our current understanding of the biomolecular adaptation to extreme conditions. As our current and future understanding of biomolecular structure-function relationships in extremophiles requires methodologies adapted to extremes of pressure, temperature, and chemical composition, advances in instrumentation for probing biophysical properties under extreme conditions are presented. Finally, we briefly discuss possible future directions in extreme biophysics.","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":"25408719","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

Learning to Model G-Quadruplexes: Current Methods and Perspectives. 学习建模g -四层:当前的方法和观点。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 Epub Date: 2021-02-09 DOI: 10.1146/annurev-biophys-060320-091827

Iker Ortiz de Luzuriaga, Xabier Lopez, Adrià Gil

{"title":"Learning to Model G-Quadruplexes: Current Methods and Perspectives.","authors":"Iker Ortiz de Luzuriaga, Xabier Lopez, Adrià Gil","doi":"10.1146/annurev-biophys-060320-091827","DOIUrl":"https://doi.org/10.1146/annurev-biophys-060320-091827","url":null,"abstract":"G-quadruplexes have raised considerable interest during the past years for the development of therapies against cancer. These noncanonical structures of DNA may be found in telomeres and/or oncogene promoters, and it has been observed that the stabilization of such G-quadruplexes may disturb tumor cell growth. Nevertheless, the mechanisms leading to folding and stabilization of these G-quadruplexes are still not well established, and they are the focus of much current work in this field. In seminal works, stabilization was observed to be produced by cations. However, subsequent studies showed that different kinds of small molecules, from planar and nonplanar organic molecules to square-planar and octahedral metal complexes, may also lead to the stabilization of G-quadruplexes. Thus, the comprehension and rationalization of the interaction of these small molecules with G-quadruplexes are also important topics of current interest in medical applications. To shed light on the questions arising from the literature on the formation of G-quadruplexes, their stabilization, and their interaction with small molecules, synergies between experimental studies and computational works are needed. In this review, we mainly focus on in silico approaches and provide a broad compilation of different leading studies carried out to date by different computational methods. We divide these methods into twomain categories: (a) classical methods, which allow for long-timescale molecular dynamics simulations and the corresponding analysis of dynamical information, and (b) quantum methods (semiempirical, quantum mechanics/molecular mechanics, and density functional theory methods), which allow for the explicit simulation of the electronic structure of the system but, in general, are not capable of being used in long-timescale molecular dynamics simulations and, therefore, give a more static picture of the relevant processes.","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":"25348489","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

The Sliding Filament Theory Since Andrew Huxley: Multiscale and Multidisciplinary Muscle Research. Andrew Huxley以来的滑丝理论：多尺度和多学科肌肉研究。

IF 10.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 Epub Date: 2021-02-26 DOI: 10.1146/annurev-biophys-110320-062613

Joseph D Powers, Sage A Malingen, Michael Regnier, Thomas L Daniel

引用次数: 0

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 : 2021-05-06 Epub Date: 2021-03-01 DOI: 10.1146/annurev-biophys-101220-072829

Álvaro Sánchez, Jean C C Vila, Chang-Yu Chang, Juan Diaz-Colunga, Sylvie Estrela, María Rebolleda-Gomez

引用次数: 39

Protein Reconstitution Inside Giant Unilamellar Vesicles. 巨型单层囊泡内的蛋白质重构。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 Epub Date: 2021-03-05 DOI: 10.1146/annurev-biophys-100620-114132

Thomas Litschel, Petra Schwille

引用次数: 29

Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field. 生物分子建模与模拟:一个蓬勃发展的多学科领域。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 Epub Date: 2021-02-19 DOI: 10.1146/annurev-biophys-091720-102019

Tamar Schlick, Stephanie Portillo-Ledesma, Christopher G Myers, Lauren Beljak, Justin Chen, Sami Dakhel, Daniel Darling, Sayak Ghosh, Joseph Hall, Mikaeel Jan, Emily Liang, Sera Saju, Mackenzie Vohr, Chris Wu, Yifan Xu, Eva Xue

{"title":"Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field.","authors":"Tamar Schlick, Stephanie Portillo-Ledesma, Christopher G Myers, Lauren Beljak, Justin Chen, Sami Dakhel, Daniel Darling, Sayak Ghosh, Joseph Hall, Mikaeel Jan, Emily Liang, Sera Saju, Mackenzie Vohr, Chris Wu, Yifan Xu, Eva Xue","doi":"10.1146/annurev-biophys-091720-102019","DOIUrl":"10.1146/annurev-biophys-091720-102019","url":null,"abstract":"We reassess progress in the field of biomolecular modeling and simulation, following up on our perspective published in 2011. By reviewing metrics for the field's productivity and providing examples of success, we underscore the productive phase of the field, whose short-term expectations were overestimated and long-term effects underestimated. Such successes include prediction of structures and mechanisms; generation of new insights into biomolecular activity; and thriving collaborations between modeling and experimentation, including experiments driven by modeling. We also discuss the impact of field exercises and web games on the field's progress. Overall, we note tremendous success by the biomolecular modeling community in utilization of computer power; improvement in force fields; and development and application of new algorithms, notably machine learning and artificial intelligence. The combined advances are enhancing the accuracy andscope of modeling and simulation, establishing an exemplary discipline where experiment and theory or simulations are full partners.","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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8105287/pdf/nihms-1683765.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25384525","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: 24

Measuring Absolute Membrane Potential Across Space and Time. 跨时空测量绝对膜电位

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 Epub Date: 2021-03-02 DOI: 10.1146/annurev-biophys-062920-063555

Julia R Lazzari-Dean, Anneliese M M Gest, Evan W Miller

{"title":"Measuring Absolute Membrane Potential Across Space and Time.","authors":"Julia R Lazzari-Dean, Anneliese M M Gest, Evan W Miller","doi":"10.1146/annurev-biophys-062920-063555","DOIUrl":"10.1146/annurev-biophys-062920-063555","url":null,"abstract":"Membrane potential (Vmem) is a fundamental biophysical signal present in all cells. Vmem signals range in time from milliseconds to days, and they span lengths from microns to centimeters. Vmem affects many cellular processes, ranging from neurotransmitter release to cell cycle control to tissue patterning. However, existing tools are not suitable for Vmem quantification in many of these areas. In this review, we outline the diverse biology of Vmem, drafting a wish list of features for a Vmem sensing platform. We then use these guidelines to discuss electrode-based and optical platforms for interrogating Vmem. On the one hand, electrode-based strategies exhibit excellent quantification but are most effective in short-term, cellular recordings. On the other hand, optical strategies provide easier access to diverse samples but generally only detect relative changes in Vmem. By combining the respective strengths of these technologies, recent advances in optical quantification of absolute Vmem enable new inquiries into Vmem biology.","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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8327616/pdf/nihms-1728629.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25422528","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

How Physical Interactions Shape Bacterial Biofilms. 物理相互作用如何塑造细菌生物膜。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 Epub Date: 2021-02-26 DOI: 10.1146/annurev-biophys-062920-063646

Berenike Maier

引用次数: 26

Structure and Mechanics of Dynein Motors. 动力电机的结构与力学。

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2021-05-06 DOI: 10.1146/annurev-biophys-111020-101511

John T Canty, Ruensern Tan, Emre Kusakci, Jonathan Fernandes, Ahmet Yildiz

{"title":"Structure and Mechanics of Dynein Motors.","authors":"John T Canty, Ruensern Tan, Emre Kusakci, Jonathan Fernandes, Ahmet Yildiz","doi":"10.1146/annurev-biophys-111020-101511","DOIUrl":"https://doi.org/10.1146/annurev-biophys-111020-101511","url":null,"abstract":"Dyneins make up a family of AAA+ motors that move toward the minus end of microtubules. Cytoplasmic dynein is responsible for transporting intracellular cargos in interphase cells and mediating spindle assembly and chromosome positioning during cell division. Other dynein isoforms transport cargos in cilia and power ciliary beating. Dyneins were the least studied of the cytoskeletal motors due to challenges in the reconstitution of active dynein complexes in vitro and the scarcity of high-resolution methods for in-depth structural and biophysical characterization of these motors. These challenges have been recently addressed, and there have been major advances in our understanding of the activation, mechanism, and regulation of dyneins. This review synthesizes the results of structural and biophysical studies for each class of dynein motors. We highlight several outstanding questions about the regulation of bidirectional transport along microtubules and the mechanisms that sustain self-coordinated oscillations within motile cilia.","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":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8592121/pdf/nihms-1753597.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38956586","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: 31