Annual Review of Biophysics最新文献

Soft Modes as a Predictive Framework for Low-Dimensional Biological Systems Across Scales. 软模式作为跨尺度低维生物系统的预测框架

IF 10.4 1区生物学

Annual Review of Biophysics Pub Date : 2025-02-19 DOI: 10.1146/annurev-biophys-081624-030543

Christopher Joel Russo, Kabir Husain, Arvind Murugan

引用次数: 0

Membrane Association of Intrinsically Disordered Proteins. 内在无序蛋白的膜结合。

IF 10.4 1区生物学

Annual Review of Biophysics Pub Date : 2025-02-14 DOI: 10.1146/annurev-biophys-070124-092816

Matthew MacAinsh, Fidha Nazreen Kunnath Muhammedkutty, Ramesh Prasad, Huan-Xiang Zhou

引用次数: 0

Toward Principles of Brain Network Organization and Function. 脑网络组织与功能原理探讨。

IF 10.4 1区生物学

Annual Review of Biophysics Pub Date : 2025-02-14 DOI: 10.1146/annurev-biophys-030722-110624

Suman Kulkarni, Dani S Bassett

{"title":"Toward Principles of Brain Network Organization and Function.","authors":"Suman Kulkarni, Dani S Bassett","doi":"10.1146/annurev-biophys-030722-110624","DOIUrl":"https://doi.org/10.1146/annurev-biophys-030722-110624","url":null,"abstract":"The brain is immensely complex, with diverse components and dynamic interactions building upon one another to orchestrate a wide range of behaviors. Understanding the patterns of these complex interactions and how they are coordinated to support collective neural function is critical for parsing human and animal behavior, treating mental illness, and developing artificial intelligence. Rapid experimental advances in imaging, recording, and perturbing neural systems across various species now provide opportunities to distill underlying principles of brain organization and function. Here, we take stock of recent progress and review methods used in the statistical analysis of brain networks, drawing from fields of statistical physics, network theory, and information theory. Our discussion is organized by scale, starting with models of individual neurons and extending to large-scale networks mapped across brain regions. We then examine organizing principles and constraints that shape the biological structure and function of neural circuits. We conclude with an overview of several critical frontiers, including expanding current models, fostering tighter feedback between theory and experiment, and leveraging perturbative approaches to understand neural systems. Alongside these efforts, we highlight the importance of contextualizing their contributions by linking them to formal accounts of explanation and causation.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":""},"PeriodicalIF":10.4,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143426589","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 Level Super-Resolution Fluorescence Imaging. 分子级超分辨率荧光成像。

IF 10.4 1区生物学

Annual Review of Biophysics Pub Date : 2025-02-14 DOI: 10.1146/annurev-biophys-071524-105321

Niels Radmacher, Alexey I Chizhik, Oleksii Nevskyi, José Ignacio Gallea, Ingo Gregor, Jörg Enderlein

{"title":"Molecular Level Super-Resolution Fluorescence Imaging.","authors":"Niels Radmacher, Alexey I Chizhik, Oleksii Nevskyi, José Ignacio Gallea, Ingo Gregor, Jörg Enderlein","doi":"10.1146/annurev-biophys-071524-105321","DOIUrl":"https://doi.org/10.1146/annurev-biophys-071524-105321","url":null,"abstract":"Over the last 30 years, fluorescence microscopy, renowned for its sensitivity and specificity, has undergone a revolution in resolving ever-smaller details. This advancement began with stimulated emission depletion (STED) microscopy and progressed with techniques such as photoactivatable localization microscopy and stochastic optical reconstruction microscopy (STORM). Single-molecule localization microscopy (SMLM), which encompasses methods like direct STORM, has significantly enhanced image resolution. Even though its speed is slower than that of STED, SMLM achieves higher resolution by overcoming photobleaching limitations, particularly through DNA point accumulation for imaging in nanoscale topography (DNA-PAINT), which continuously renews fluorescent labels. Additionally, cryo-fluorescence microscopy and advanced techniques like minimal photon fluxes imaging (MINFLUX) have pushed the boundaries toward molecular resolution SMLM. This review discusses the latest developments in SMLM, highlighting methods like resolution enhancement by sequential imaging (RESI) and PAINT-MINFLUX and exploring axial localization techniques such as supercritical angle fluorescence and metal-induced energy transfer. These advancements promise to revolutionize fluorescence microscopy, providing resolution comparable to that of electron microscopy.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":""},"PeriodicalIF":10.4,"publicationDate":"2025-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143426588","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

Kinetics of Amyloid Oligomer Formation. 淀粉样蛋白低聚物形成动力学。

IF 10.4 1区生物学

Annual Review of Biophysics Pub Date : 2025-02-10 DOI: 10.1146/annurev-biophys-080124-122953

Jiapeng Wei, Georg Meisl, Alexander J Dear, Thomas C T Michaels, Tuomas P J Knowles

{"title":"Kinetics of Amyloid Oligomer Formation.","authors":"Jiapeng Wei, Georg Meisl, Alexander J Dear, Thomas C T Michaels, Tuomas P J Knowles","doi":"10.1146/annurev-biophys-080124-122953","DOIUrl":"https://doi.org/10.1146/annurev-biophys-080124-122953","url":null,"abstract":"Low-molecular-weight oligomers formed from amyloidogenic peptides and proteins have been identified as key cytotoxins across a range of neurodegenerative disorders, including Alzheimer's disease and Parkinson's disease. Developing therapeutic strategies that target oligomers is therefore emerging as a promising approach for combating protein misfolding diseases. As such, there is a great need to understand the fundamental properties, dynamics, and mechanisms associated with oligomer formation. In this review, we discuss how chemical kinetics provides a powerful tool for studying these systems. We review the chemical kinetics approach to determining the underlying molecular pathways of protein aggregation and discuss its applications to oligomer formation and dynamics. We discuss how this approach can reveal detailed mechanisms of primary and secondary oligomer formation, including the role of interfaces in these processes. We further use this framework to describe the processes of oligomer conversion and dissociation, and highlight the distinction between on-pathway and off-pathway oligomers. Furthermore, we showcase on the basis of experimental data the diversity of pathways leading to oligomer formation in various in vitro and in silico systems. Finally, using the lens of the chemical kinetics framework, we look at the current oligomer inhibitor strategies both in vitro and in vivo.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":""},"PeriodicalIF":10.4,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143392063","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

Mechanics of Single Cytoskeletal Filaments. 单细胞骨架细丝的力学。

IF 10.4 1区生物学

Annual Review of Biophysics Pub Date : 2025-02-10 DOI: 10.1146/annurev-biophys-030722-120914

Guillaume Romet-Lemonne, Cécile Leduc, Antoine Jégou, Hugo Wioland

引用次数: 0

Information Processing in Biochemical Networks. 生化网络中的信息处理。

IF 10.4 1区生物学

Annual Review of Biophysics Pub Date : 2025-02-10 DOI: 10.1146/annurev-biophys-060524-102720

Gašper Tkačik, Pieter Rein Ten Wolde

{"title":"Information Processing in Biochemical Networks.","authors":"Gašper Tkačik, Pieter Rein Ten Wolde","doi":"10.1146/annurev-biophys-060524-102720","DOIUrl":"https://doi.org/10.1146/annurev-biophys-060524-102720","url":null,"abstract":"Living systems are characterized by controlled flows of matter, energy, and information. While the biophysics community has productively engaged with the first two, addressing information flows has been more challenging, with some scattered success in evolutionary theory and a more coherent track record in neuroscience. Nevertheless, interdisciplinary work of the past two decades at the interface of biophysics, quantitative biology, and engineering has led to an emerging mathematical language for describing information flows at the molecular scale. This is where the central processes of life unfold: from detection and transduction of environmental signals to the readout or copying of genetic information and the triggering of adaptive cellular responses. Such processes are coordinated by complex biochemical reaction networks that operate at room temperature, are out of equilibrium, and use low copy numbers of diverse molecular species with limited interaction specificity. Here we review how flows of information through biochemical networks can be formalized using information-theoretic quantities, quantified from data, and computed within various modeling frameworks. Optimization of information flows is presented as a candidate design principle that navigates the relevant time, energy, crosstalk, and metabolic constraints to predict reliable cellular signaling and gene regulation architectures built of individually noisy components.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":""},"PeriodicalIF":10.4,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143391992","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

Statistical Thermodynamics of the Protein Ensemble: Mediating Function and Evolution. 蛋白质集合的统计热力学：中介功能和进化。

IF 10.4 1区生物学

Annual Review of Biophysics Pub Date : 2025-02-10 DOI: 10.1146/annurev-biophys-061824-104900

Vincent J Hilser, James O Wrabl, Charles E F Millard, Anna Schmitz, Sarah J Brantley, Marie Pearce, Joe Rehfus, Miranda M Russo, Keila Voortman-Sheetz

{"title":"Statistical Thermodynamics of the Protein Ensemble: Mediating Function and Evolution.","authors":"Vincent J Hilser, James O Wrabl, Charles E F Millard, Anna Schmitz, Sarah J Brantley, Marie Pearce, Joe Rehfus, Miranda M Russo, Keila Voortman-Sheetz","doi":"10.1146/annurev-biophys-061824-104900","DOIUrl":"https://doi.org/10.1146/annurev-biophys-061824-104900","url":null,"abstract":"The growing appreciation of native state conformational fluctuations mediating protein function calls for critical reevaluation of protein evolution and adaptation. If proteins are ensembles, does nature select solely for ground state structure, or are conformational equilibria between functional states also conserved? If so, what is the mechanism and how can it be measured? Addressing these fundamental questions, we review our investigation into the role of local unfolding fluctuations in the native state ensembles of proteins. We describe the functional importance of these ubiquitous fluctuations, as revealed through studies of adenylate kinase. We then summarize elucidation of thermodynamic organizing principles, which culminate in a quantitative probe for evolutionary conservation of protein energetics. Finally, we show that these principles are predictive of sequence compatibility for multiple folds, providing a unique thermodynamic perspective on metamorphic proteins. These research areas demonstrate that the locally unfolded ensemble is an emerging, important mechanism of protein evolution.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":""},"PeriodicalIF":10.4,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143392259","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

Mechanisms for DNA Interplay in Eukaryotic Transcription Factors. 真核生物转录因子中DNA相互作用的机制。

IF 10.4 1区生物学

Annual Review of Biophysics Pub Date : 2025-01-29 DOI: 10.1146/annurev-biophys-071524-111008

Victor Muñoz, Rama Reddy Goluguri, Catherine Ghosh, Benjamin Tanielian, Mourad Sadqi

引用次数: 0

Metabolic Engineering of Yeast. 酵母代谢工程。

IF 10.4 1区生物学

Annual Review of Biophysics Pub Date : 2025-01-21 DOI: 10.1146/annurev-biophys-070924-103134

Shuobo Shi, Yu Chen, Jens Nielsen

引用次数: 0