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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 10.4 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
{"title":"Mechanisms of Inheritance of Chromatin States: From Yeast to Human.","authors":"Hiten D Madhani","doi":"10.1146/annurev-biophys-070524-091904","DOIUrl":"10.1146/annurev-biophys-070524-091904","url":null,"abstract":"<p><p>In this article I review mechanisms that underpin epigenetic inheritance of CpG methylation and histone H3 lysine 9 methylation (H3K9me) in chromatin in fungi and mammals. CpG methylation can be faithfully inherited epigenetically at some sites for a lifetime in vertebrates and, remarkably, can be propagated for millions of years in some fungal lineages. Transmission of methylation patterns requires maintenance-type DNA methyltransferases (DNMTs) that recognize hemimethylated CpG DNA produced by replication. DNMT1 is the maintenance enzyme in vertebrates; we recently identified DNMT5 as an ATP-dependent CpG maintenance enzyme found in fungi and protists. In vivo, CpG methylation is coupled to H3K9me. H3K9me is itself reestablished after replication via local histone H3-H4 tetramer recycling involving mobile and nonmobile chaperones, de novo nucleosome assembly, and read-write mechanisms that modify naive nucleosomes. Additional proteins recognize hemimethylated CpG or fully methylated CpG-containing motifs and enhance restoration of methylation by recruiting and/or activating the maintenance methylase.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"59-79"},"PeriodicalIF":10.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142883280","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
Protein Modeling with DEER Spectroscopy. 利用 DEER 光谱建立蛋白质模型。
IF 10.4 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
{"title":"Protein Modeling with DEER Spectroscopy.","authors":"Maxx H Tessmer, Stefan Stoll","doi":"10.1146/annurev-biophys-030524-013431","DOIUrl":"10.1146/annurev-biophys-030524-013431","url":null,"abstract":"<p><p>Double electron-electron resonance (DEER) combined with site-directed spin labeling can provide distance distributions between selected protein residues to investigate protein structure and conformational heterogeneity. The utilization of the full quantitative information contained in DEER data requires effective protein and spin label modeling methods. Here, we review the application of DEER data to protein modeling. First, we discuss the significance of spin label modeling for accurate extraction of protein structural information and review the most popular label modeling methods. Next, we review several important aspects of protein modeling with DEER, including site selection, how DEER restraints are applied, common artifacts, and the unique potential of DEER data for modeling structural ensembles and conformational landscapes. Finally, we discuss common applications of protein modeling with DEER data and provide an outlook.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"35-57"},"PeriodicalIF":10.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142848345","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 : 2025-05-01 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":"<p><p>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.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"163-184"},"PeriodicalIF":10.4,"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 10.4 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":"https://doi.org/10.1146/annurev-biophys-070524-100658","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"54 1","pages":"141-162"},"PeriodicalIF":10.4,"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 10.4 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":"<p><p>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.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"121-139"},"PeriodicalIF":10.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","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 10.4 1区 生物学
Annual Review of Biophysics Pub Date : 2025-05-01 DOI: 10.1146/annurev-biophys-071624-095107
Deborah F Kelly
{"title":"Liquid-Electron Microscopy and the Real-Time Revolution.","authors":"Deborah F Kelly","doi":"10.1146/annurev-biophys-071624-095107","DOIUrl":"https://doi.org/10.1146/annurev-biophys-071624-095107","url":null,"abstract":"<p><p>Advances in imaging technology enable striking views of life's most minute details. A missing piece of the puzzle, however, is the direct atomic observation of biomolecules in action. Liquid-phase transmission electron microscopy (liquid-EM) is the room-temperature correlate to cryo-electron microscopy, which is leading the resolution revolution in biophysics. This article reviews current challenges and opportunities in the liquid-EM field while discussing technical considerations for specimen enclosures, devices and systems, and scientific data management. Since liquid-EM is gaining traction in the life sciences community, cross talk among the disciplines of materials and life sciences is needed to disseminate knowledge of best practices along with high-level user engagement. How liquid-EM technology is inspiring the real-time revolution in molecular microscopy is also discussed. Looking ahead, the new movement can be better supported through open resource sharing and partnerships among academic, industry, and federal organizations, which may benefit from the scientific equity foundational to the technique.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"54 1","pages":"1-15"},"PeriodicalIF":10.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143990417","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
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 : 2025-05-01 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":"<p><p>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.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"249-274"},"PeriodicalIF":10.4,"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
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 : 2025-05-01 Epub 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":"10.1146/annurev-biophys-061824-104900","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"227-247"},"PeriodicalIF":10.4,"publicationDate":"2025-05-01","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
Mass Photometry. 大规模测光。
IF 10.4 1区 生物学
Annual Review of Biophysics Pub Date : 2025-05-01 DOI: 10.1146/annurev-biophys-061824-111652
Roi Asor, Dan Loewenthal, Raman van Wee, Justin L P Benesch, Philipp Kukura
{"title":"Mass Photometry.","authors":"Roi Asor, Dan Loewenthal, Raman van Wee, Justin L P Benesch, Philipp Kukura","doi":"10.1146/annurev-biophys-061824-111652","DOIUrl":"https://doi.org/10.1146/annurev-biophys-061824-111652","url":null,"abstract":"<p><p>Mass photometry (MP) is a technology for the mass measurement of biological macromolecules in solution. Its mass accuracy and resolution have transformed label-free optical detection into a quantitative measurement, enabling the identification of distinct species in a mixture and the characterization of their relative abundances. Its applicability to a variety of biomolecules, including polypeptides, nucleic acids, lipids, and sugars, coupled with the ability to quantify heterogeneity, interaction energies, and kinetics, has driven the rapid and widespread adoption of MP across the life sciences community. These applications have been largely orthogonal to those traditionally associated with microscopy, such as detection, imaging, and tracking, instead focusing on the constituents of biomolecular complexes and their change with time. Here, we present an overview of the origins of MP, its current applications, and future improvements that will further expand its scope.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"54 1","pages":"379-399"},"PeriodicalIF":10.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144004363","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
The Effects of Codon Usage on Protein Structure and Folding. 密码子使用对蛋白质结构和折叠的影响
IF 10.4 1区 生物学
Annual Review of Biophysics Pub Date : 2024-07-01 Epub Date: 2024-06-28 DOI: 10.1146/annurev-biophys-030722-020555
McKenze J Moss, Laura M Chamness, Patricia L Clark
{"title":"The Effects of Codon Usage on Protein Structure and Folding.","authors":"McKenze J Moss, Laura M Chamness, Patricia L Clark","doi":"10.1146/annurev-biophys-030722-020555","DOIUrl":"10.1146/annurev-biophys-030722-020555","url":null,"abstract":"<p><p>The rate of protein synthesis is slower than many folding reactions and varies depending on the synonymous codons encoding the protein sequence. Synonymous codon substitutions thus have the potential to regulate cotranslational protein folding mechanisms, and a growing number of proteins have been identified with folding mechanisms sensitive to codon usage. Typically, these proteins have complex folding pathways and kinetically stable native structures. Kinetically stable proteins may fold only once over their lifetime, and thus, codon-mediated regulation of the pioneer round of protein folding can have a lasting impact. Supporting an important role for codon usage in folding, conserved patterns of codon usage appear in homologous gene families, hinting at selection. Despite these exciting developments, there remains few experimental methods capable of quantifying translation elongation rates and cotranslational folding mechanisms in the cell, which challenges the development of a predictive understanding of how biology uses codons to regulate protein folding.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"87-108"},"PeriodicalIF":10.4,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11227313/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138886545","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
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