Annual Review of Biophysics最新文献_第4页

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

IF 13.7 1区生物学

Annual Review of Biophysics Pub Date : 2025-05-01 Epub 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

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

IF 13.7 1区生物学

Annual Review of Biophysics Pub Date : 2025-05-01 Epub 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":"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":"185-207"},"PeriodicalIF":13.7,"publicationDate":"2025-05-01","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

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 12.9 1区生物学

Annual Review of Biophysics Pub Date : 2025-05-01 Epub Date: 2025-02-19 DOI: 10.1146/annurev-biophys-081624-030543

Christopher Joel Russo, Kabir Husain, Arvind Murugan

引用次数: 0

Mechanisms of Inheritance of Chromatin States: From Yeast to Human. 染色质状态的遗传机制：从酵母到人类。

IF 13.7 1区生物学

Annual Review of Biophysics Pub Date : 2025-05-01 Epub Date: 2024-12-23 DOI: 10.1146/annurev-biophys-070524-091904

Hiten D Madhani

引用次数: 0

Protein Modeling with DEER Spectroscopy. 利用 DEER 光谱建立蛋白质模型。

IF 13.7 1区生物学

Annual Review of Biophysics Pub Date : 2025-05-01 Epub Date: 2024-12-17 DOI: 10.1146/annurev-biophys-030524-013431

Maxx H Tessmer, Stefan Stoll

引用次数: 0

Molecular Level Super-Resolution Fluorescence Imaging. 分子级超分辨率荧光成像。

IF 13.7 1区生物学

Annual Review of Biophysics Pub Date : 2025-05-01 Epub 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":"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":"163-184"},"PeriodicalIF":13.7,"publicationDate":"2025-05-01","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

Emerging Patterns in Membrane Protein Folding Pathways. 膜蛋白折叠途径的新模式。

IF 13.7 1区生物学

Annual Review of Biophysics Pub Date : 2025-05-01 DOI: 10.1146/annurev-biophys-070524-100658

Sang Ah Kim, Hyun Gyu Kim, W C Bhashini Wijesinghe, Duyoung Min, Tae-Young Yoon

{"title":"Emerging Patterns in Membrane Protein Folding Pathways.","authors":"Sang Ah Kim, Hyun Gyu Kim, W C Bhashini Wijesinghe, Duyoung Min, Tae-Young Yoon","doi":"10.1146/annurev-biophys-070524-100658","DOIUrl":"10.1146/annurev-biophys-070524-100658","url":null,"abstract":"Studies of membrane protein folding have progressed from simple systems such as bacteriorhodopsin to complex structures such as ATP-binding cassette transporters and voltage-gated ion channels. Advances in techniques such as single-molecule force spectroscopy and in vivo force profiling now allow for the detailed examination of membrane protein folding pathways at amino acid resolutions. These proteins navigate rugged energy landscapes partly shaped by the absence of hydrophobic collapse and the viscous nature of the lipid bilayer, imposing biophysical limitations on folding speeds. Furthermore, many transmembrane (TM) helices display reduced hydrophobicity to support functional requirements, simultaneously increasing the energy barriers for membrane insertion, a manifestation of the evolutionary trade-off between functionality and foldability. These less hydrophobic TM helices typically insert and fold as helical hairpins, following the protein synthesis direction from the N terminus to the C terminus, with assistance from endoplasmic reticulum (ER) chaperones like the Sec61 translocon and the ER membrane protein complex. The folding pathways of multidomain membrane proteins are defined by allosteric networks that extend across various domains, where mutations and folding correctors affect seemingly distant domains. A common evolutionary strategy is likely to be domain specialization, where N-terminal domains enhance foldability and C-terminal domains enhance functionality. Thus, despite inherent biophysical constraints, evolution has finely tuned membrane protein sequences to optimize foldability, stability, and functionality.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"54 1","pages":"141-162"},"PeriodicalIF":13.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144013707","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 13.7 1区生物学

Annual Review of Biophysics Pub Date : 2025-05-01 Epub Date: 2025-01-29 DOI: 10.1146/annurev-biophys-071524-111008

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

{"title":"Mechanisms for DNA Interplay in Eukaryotic Transcription Factors.","authors":"Victor Muñoz, Rama Reddy Goluguri, Catherine Ghosh, Benjamin Tanielian, Mourad Sadqi","doi":"10.1146/annurev-biophys-071524-111008","DOIUrl":"10.1146/annurev-biophys-071524-111008","url":null,"abstract":"Like their prokaryotic counterparts, eukaryotic transcription factors must recognize specific DNA sites, search for them efficiently, and bind to them to help recruit or block the transcription machinery. For eukaryotic factors, however, the genetic signals are extremely complex and scattered over vast, multichromosome genomes, while the DNA interplay occurs in a varying landscape defined by chromatin remodeling events and epigenetic modifications. Eukaryotic factors are rich in intrinsically disordered regions and are also distinct in their recognition of short DNA motifs and utilization of open DNA interaction interfaces as ways to gain access to DNA on nucleosomes. Recent findings are revealing the profound, unforeseen implications of such characteristics for the mechanisms of DNA interplay. In this review we discuss these implications and how they are shaping the eukaryotic transcription control paradigm into one of promiscuous signal recognition, highly dynamic interactions, heterogeneous DNA scanning, and multiprong conformational control.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"121-139"},"PeriodicalIF":13.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12815392/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143069306","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

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

IF 13.7 1区生物学

Annual Review of Biophysics Pub Date : 2025-05-01 Epub 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":"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":"249-274"},"PeriodicalIF":13.7,"publicationDate":"2025-05-01","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

Liquid-Electron Microscopy and the Real-Time Revolution. 液体电子显微镜和实时革命。

IF 13.7 1区生物学

Annual Review of Biophysics Pub Date : 2025-05-01 DOI: 10.1146/annurev-biophys-071624-095107

Deborah F Kelly

引用次数: 0