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Annual Review of Biophysics最新文献

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Fold-Switching Proteins. Fold-Switching蛋白质。
IF 12.9 1区 生物学
Annual Review of Biophysics Pub Date : 2026-05-01 Epub Date: 2025-11-18 DOI: 10.1146/annurev-biophys-022924-012038
Devlina Chakravarty, Lauren L Porter
{"title":"Fold-Switching Proteins.","authors":"Devlina Chakravarty, Lauren L Porter","doi":"10.1146/annurev-biophys-022924-012038","DOIUrl":"10.1146/annurev-biophys-022924-012038","url":null,"abstract":"<p><p>Globular proteins are expected to assume folds with fixed secondary structures, α-helices and β-sheets. Fold-switching proteins challenge this expectation by remodeling their secondary and/or tertiary structures in response to cellular stimuli. Though these shape-shifting proteins were once thought to be haphazard evolutionary by-products with little intrinsic biological relevance, recent work has shown that evolution has selected for their dual-folding behavior, which plays critical roles in biological processes across all kingdoms of life. The widening scope of fold switching draws attention to the ways it challenges conventional wisdom, raising fundamental unanswered questions about protein structure, biophysics, and evolution. Here we discuss the progress being made to answer these questions and suggest future directions for the field.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"17-37"},"PeriodicalIF":12.9,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12629603/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145551737","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
Tethered Signaling Proteins. 系留信号蛋白。
IF 13.7 1区 生物学
Annual Review of Biophysics Pub Date : 2026-05-01 Epub Date: 2026-01-16 DOI: 10.1146/annurev-biophys-021424-125547
Jun Allard, Omer Dushek
{"title":"Tethered Signaling Proteins.","authors":"Jun Allard, Omer Dushek","doi":"10.1146/annurev-biophys-021424-125547","DOIUrl":"10.1146/annurev-biophys-021424-125547","url":null,"abstract":"<p><p>Cells process signals by using large and complex networks of molecules that interact with and modify one another. Some of these interactions occur among molecules connected by long flexible tethers, often made of intrinsically disordered protein regions. In this review, we present recent research showing that tethered reactions (<i>a</i>) are ubiquitous in cells, (<i>b</i>) are exploited by cell signaling networks, (<i>c</i>) can be qualitatively and quantitatively understood using simple polymer physics, (<i>d</i>) give rise to categorically different features compared with molecular interactions driven by free diffusion, and (<i>e</i>) provide novel avenues for therapeutics and bioengineering. Recent studies have begun to shed light on cases in which the tethers must reach between different molecular assemblies that are not connected by protein scaffolding. We provide an in-depth case study of immune receptors, where such tethered signaling plays a vital role in signal integration and immune cell decisions.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"177-198"},"PeriodicalIF":13.7,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145991686","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
Pattern Formation Beyond Turing: Physical Principles of Mass-Conserving Reaction-Diffusion Systems. 图灵之外的模式形成：质量守恒反应扩散系统的物理原理。
IF 12.9 1区 生物学
Annual Review of Biophysics Pub Date : 2026-05-01 Epub Date: 2026-02-10 DOI: 10.1146/annurev-biophys-030822-031638
Erwin Frey, Henrik Weyer
{"title":"Pattern Formation Beyond Turing: Physical Principles of Mass-Conserving Reaction-Diffusion Systems.","authors":"Erwin Frey, Henrik Weyer","doi":"10.1146/annurev-biophys-030822-031638","DOIUrl":"10.1146/annurev-biophys-030822-031638","url":null,"abstract":"<p><p>Intracellular protein patterns govern essential cellular functions by dynamically redistributing proteins between membrane-bound and cytosolic states, conserving their total numbers. This review presents a theoretical framework for understanding such patterns based on mass-conserving reaction-diffusion systems. The emergence, selection, and evolution of patterns are analyzed in terms of mass redistribution and interface motion, resulting in mesoscale laws of coarsening and wavelength selection. A geometric phase-space perspective provides a conceptual tool to link local reactive equilibria with global pattern dynamics through conserved mass fluxes. The Min protein system of <i>Escherichia coli</i> provides a paradigmatic example, enabling direct comparison between theory and experiment. Successive model refinements capture both the robustness of pattern formation and the diversity of dynamic regimes observed in vivo and in vitro. The Min system thus illustrates how to extract predictive, multiscale theory from biochemical detail, providing a foundation for understanding pattern formation in more complex and synthetic systems.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"493-514"},"PeriodicalIF":12.9,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146159220","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
Hopfield Networks as Models of Emergent Function in Biology. Hopfield网络作为生物学中涌现功能的模型。
IF 12.9 1区 生物学
Annual Review of Biophysics Pub Date : 2026-05-01 Epub Date: 2026-02-04 DOI: 10.1146/annurev-biophys-101425-023356
Maria Yampolskaya, Pankaj Mehta
{"title":"Hopfield Networks as Models of Emergent Function in Biology.","authors":"Maria Yampolskaya, Pankaj Mehta","doi":"10.1146/annurev-biophys-101425-023356","DOIUrl":"10.1146/annurev-biophys-101425-023356","url":null,"abstract":"<p><p>Hopfield models, originally developed to study memory retrieval in neural networks, have become versatile tools for modeling diverse biological systems in which function emerges from collective dynamics. In this review, we provide a pedagogical introduction to both classic and modern Hopfield networks from a biophysical perspective. After presenting the underlying mathematics, we build physical intuition through three complementary interpretations of Hopfield dynamics: as noise discrimination, as a geometric construction defining a natural coordinate system in pattern space, and as gradient-like descent on an energy landscape. We then survey applications of Hopfield networks in a variety of biological settings, including cellular differentiation and epigenetic memory, molecular self-assembly, and spatial neural representations.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"323-342"},"PeriodicalIF":12.9,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146121105","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
Seeking Biology's Physics Stories: Simplify, Simplify. 寻找生物学的物理故事：简化，简化。
IF 12.9 1区 生物学
Annual Review of Biophysics Pub Date : 2026-05-01 DOI: 10.1146/annurev-biophys-022224-110227
Ken A Dill
{"title":"Seeking Biology's Physics Stories: Simplify, Simplify.","authors":"Ken A Dill","doi":"10.1146/annurev-biophys-022224-110227","DOIUrl":"10.1146/annurev-biophys-022224-110227","url":null,"abstract":"<p><p>The American poet Muriel Rukeyser said, \"The universe is made of stories, not of atoms.\" I've sought stories in biophysics, mostly through theoretical modeling, often through simplified models. My colleagues and I brought polymer statistical physics to help solve the physical protein folding problem. In related questions of water physics, principles of nonequilibria, cell fitnesses, and the chemical origins of life, our work has been about entropies, driving forces, and nature's funneling of disorder to order. This is a story of my personal journey.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"55 1","pages":"1-15"},"PeriodicalIF":12.9,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147845671","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 Evolution of Lipids from Solvents to Substrates. 脂类从溶剂到底物的演化。
IF 12.9 1区 生物学
Annual Review of Biophysics Pub Date : 2026-05-01 Epub Date: 2025-11-21 DOI: 10.1146/annurev-biophys-021424-012603
Aninda Dutta, Charlotte Hannis, Nathan Feinberg, Linda Columbus
{"title":"The Evolution of Lipids from Solvents to Substrates.","authors":"Aninda Dutta, Charlotte Hannis, Nathan Feinberg, Linda Columbus","doi":"10.1146/annurev-biophys-021424-012603","DOIUrl":"10.1146/annurev-biophys-021424-012603","url":null,"abstract":"<p><p>While the role of water in soluble protein structure and function is well-established, the analogous role of lipids as a solvent for membrane proteins is less understood. Bacterial membranes exhibit extraordinary lipid diversity, with <i>Escherichia coli</i> synthesizing over 1,800 distinct glycerophospholipids. This lipid diversity gives rise to bulk membrane properties and specific lipid-lipid and lipid-protein interactions that directly affect α-IMP folding, assembly, and function. In this review, we use the same thermodynamic framework for understanding the solvation of soluble proteins to examine bacterial α-helical integral membrane protein (α-IMP) interactions with chemically diverse lipid environments. We propose that preferential solvent interactions were essential evolutionary drivers that enabled lipids to evolve as protein cofactors and substrates, with lipid chemical diversity creating unique evolutionary pressures distinct from those of aqueous systems.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"57-74"},"PeriodicalIF":12.9,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12951313/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145574859","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
The Mitochondrial Permeability Transition Pore: Past, Present, and Future. 线粒体通透性过渡孔：过去，现在和未来。
IF 13.7 1区 生物学
Annual Review of Biophysics Pub Date : 2026-05-01 Epub Date: 2025-12-12 DOI: 10.1146/annurev-biophys-030722-020832
Michela Carraro, Christoph Gerle, Paolo Bernardi
{"title":"The Mitochondrial Permeability Transition Pore: Past, Present, and Future.","authors":"Michela Carraro, Christoph Gerle, Paolo Bernardi","doi":"10.1146/annurev-biophys-030722-020832","DOIUrl":"10.1146/annurev-biophys-030722-020832","url":null,"abstract":"<p><p>The mitochondrial permeability transition (PT) is a Ca2+-dependent permeability increase of the inner mitochondrial membrane mediated by opening of a high-conductance channel, the PT pore. Its molecular nature has been the subject of intense research and the source of controversies, but a considerable consensus has been reached that the PT originates from specific conformations of the F<sub>O</sub>F<sub>1</sub>-ATP synthase and of the adenine nucleotide translocator. The ATP synthase forms high-conductance channels in mammals and yeast but not in the anoxia- and salt-tolerant brine shrimp <i>Artemia franciscana</i>, which is refractory to the PT; it forms low-conductance and Ca2+-selective channels in <i>Drosophila melanogaster</i>, which undergoes a process of Ca2+-induced Ca2+ release but not a PT. The structural definition of ATP synthases from several species may allow for some inferences to be made about the mechanism of channel formation, or lack thereof, and provides a testable framework for future research.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"93-112"},"PeriodicalIF":13.7,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145745455","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
A Tubules-First Model for the Origin of Eukaryotic Membrane Traffic. 真核生物膜交通起源的小管优先模型。
IF 12.9 1区 生物学
Annual Review of Biophysics Pub Date : 2026-05-01 DOI: 10.1146/annurev-biophys-021424-013933
Mukund Thattai
{"title":"A Tubules-First Model for the Origin of Eukaryotic Membrane Traffic.","authors":"Mukund Thattai","doi":"10.1146/annurev-biophys-021424-013933","DOIUrl":"10.1146/annurev-biophys-021424-013933","url":null,"abstract":"<p><p>The discovery of membrane trafficking proteins in Asgard archaea-the closest archaeal relatives of eukaryotes-reveals the deep evolutionary roots of the eukaryotic endomembrane system. This review synthesizes genomic, structural, and functional studies of archaea and eukaryotes to explore how these ancient proteins contributed to the emergence of intracellular membranes. While Asgard archaea appear to lack the canonical machinery for coated vesicle formation, they encode a full complement of proteins involved in membrane tubulation, scission, tethering, and fusion. This molecular repertoire suggests that the archaeal ancestor of eukaryotes was capable of membrane remodeling, potentially via transient tubules. In early eukaryotes-following mitochondrial acquisition and internalization of the endoplasmic reticulum-tubules may have served as the principal carriers of membrane traffic. Coated vesicles-spherical vesicles that use scaffold proteins and sterol-rich membranes to stabilize high-curvature buds-may represent a later innovation prior to the last eukaryotic common ancestor. Archaea-derived tubular trafficking pathways play essential roles in modern eukaryotic cells.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"55 1","pages":"301-322"},"PeriodicalIF":12.9,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147845659","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
Learning the Principles of T Cell Antigen Discernment. 学习T细胞抗原识别原理。
IF 12.9 1区 生物学
Annual Review of Biophysics Pub Date : 2026-05-01 Epub Date: 2026-02-05 DOI: 10.1146/annurev-biophys-021424-013707
François X P Bourassa, Sooraj Achar, Grégoire Altan-Bonnet, Paul François
{"title":"Learning the Principles of T Cell Antigen Discernment.","authors":"François X P Bourassa, Sooraj Achar, Grégoire Altan-Bonnet, Paul François","doi":"10.1146/annurev-biophys-021424-013707","DOIUrl":"10.1146/annurev-biophys-021424-013707","url":null,"abstract":"<p><p>T cells are central to the adaptive immune response, capable of detecting pathogenic antigens while ignoring healthy tissues with remarkable specificity and sensitivity. Quantitatively understanding how T cell receptors discern among antigens requires biophysical models and theoretical analyses of signaling networks. Here, we review current theoretical frameworks of antigen recognition in the context of modern experimental and computational advances. Antigen potency spans a continuum and exhibits nonlinear effects within complex mixtures, challenging discrete classification and simple threshold-based models. This complexity motivates the development of models, such as adaptive kinetic proofreading, that integrate both activating and inhibitory signals. Advances in high-throughput technologies now generate large-scale, quantitative data sets, enabling the refinement of such models through statistical and machine learning approaches. This convergence of theory, data, and computation promises deeper insights into immune decision-making and opens new avenues for rational immunotherapy design.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"365-390"},"PeriodicalIF":12.9,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146127468","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 Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms. 扩展的组蛋白宇宙：非真核生物中基于组蛋白的DNA组织。
IF 12.9 1区 生物学
Annual Review of Biophysics Pub Date : 2026-05-01 Epub Date: 2025-12-02 DOI: 10.1146/annurev-biophys-091125-045046
Alejandro Villalta, Sashi R Weerawarana, Michael L Nosella, Nathaniel L Hamel, Karolin Luger
{"title":"The Expanding Histone Universe: Histone-Based DNA Organization in Noneukaryotic Organisms.","authors":"Alejandro Villalta, Sashi R Weerawarana, Michael L Nosella, Nathaniel L Hamel, Karolin Luger","doi":"10.1146/annurev-biophys-091125-045046","DOIUrl":"10.1146/annurev-biophys-091125-045046","url":null,"abstract":"<p><p>Histones are small basic proteins that form the proteinaceous core of the nucleosome, the repeating building block of chromatin in all eukaryotes. Long thought to be exclusive to eukaryotes, histones are now increasingly appreciated for their roles in organizing genomes across all domains of life, namely in archaea, bacteria, and even viruses. We survey recent advances in our understanding of the imaginative uses of histones in disparate biological entities, ranging from nucleosome-like metastable particles in giant viruses to slinky-like hypernucleosomes in archaea to bacterial histones that bind DNA in decidedly unorthodox ways. Across these different contexts, we examine how DNA compaction and conformation emanate from evolutionarily conserved aspects of histone structure, including how the oligomeric states of histones dictate their capacity to contort DNA in different conformations. It appears that relatively small tweaks to the amino acid sequences of histones can result in structural and functional variations in DNA binding. As such, nucleosomes in eukaryotes sample only a narrow range of possible structures.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"75-91"},"PeriodicalIF":12.9,"publicationDate":"2026-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145662616","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
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