Annual Review of Biophysics最新文献

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Bioenergetics and the Evolution of Cellular Traits. 生物能量学与细胞特性的进化。
IF 10.4 1区 生物学
Annual Review of Biophysics Pub Date : 2025-05-01 DOI: 10.1146/annurev-biophys-070524-090334
Paul E Schavemaker, Michael Lynch
{"title":"Bioenergetics and the Evolution of Cellular Traits.","authors":"Paul E Schavemaker, Michael Lynch","doi":"10.1146/annurev-biophys-070524-090334","DOIUrl":"https://doi.org/10.1146/annurev-biophys-070524-090334","url":null,"abstract":"<p><p>Evolutionary processes have transformed simple cellular life into a great diversity of forms, ranging from the ubiquitous eukaryotic cell design to the more specific cellular forms of spirochetes, cyanobacteria, ciliates, heliozoans, amoeba, and many others. The cellular traits that constitute these forms require an evolutionary explanation. Ultimately, the persistence of a cellular trait depends on its net contribution to fitness, a quantitative measure. Independent of any positive effects, a cellular trait exhibits a baseline energetic cost that needs to be accounted for when quantitatively examining its net fitness effect. Here, we explore how the energetic burden introduced by a cellular trait quantitatively affects cellular fitness, describe methods for determining cell energy budgets, summarize the costs of cellular traits across the tree of life, and examine how the fitness impacts of these energetic costs compare to other evolutionary forces and trait benefits.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"54 1","pages":"81-99"},"PeriodicalIF":10.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144062438","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
Collapse and Protein Folding: Should We Be Surprised That Biothermodynamics Works So Well? 崩溃与蛋白质折叠:我们是否应该对生物热力学如此有效感到惊讶?
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-080124-123012
Tobin R Sosnick, Michael C Baxa
{"title":"Collapse and Protein Folding: Should We Be Surprised That Biothermodynamics Works So Well?","authors":"Tobin R Sosnick, Michael C Baxa","doi":"10.1146/annurev-biophys-080124-123012","DOIUrl":"10.1146/annurev-biophys-080124-123012","url":null,"abstract":"<p><p>A complete understanding of protein function and dynamics requires the characterization of the multiple thermodynamic states, including the denatured state ensemble (DSE). Whereas residual structure in the DSE (as well as in partially folded states) is pertinent in many biological contexts, here we are interested in how such structure affects protein thermodynamics. We examine issues related to chain collapse in light of new developments, focusing on potential complications arising from differences in the DSE's properties under various conditions. Despite some variability in the degree of collapse and structure in the DSE, stability measurements are remarkably consistent between two standard methods, calorimetry and chemical denaturation, as well as with hydrogen-deuterium exchange. This robustness is due in part to the DSEs obtained with different perturbations being thermodynamically equivalent and hence able to serve as a common reference state. An examination of the properties of the DSE points to it as being a highly expanded ensemble with minimal amounts of stable hydrogen bonded structure. These two features are likely to be critical in the broad and successful application of thermodynamics to protein folding. Our review concludes with a discussion of the impact of these findings on folding mechanisms and pathways.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"17-34"},"PeriodicalIF":10.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142848343","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 Physics of Sensing and Decision-Making by Animal Groups. 动物群体感知和决策的物理学。
IF 10.4 1区 生物学
Annual Review of Biophysics Pub Date : 2025-05-01 DOI: 10.1146/annurev-biophys-061824-110733
Danielle L Chase, Orit Peleg
{"title":"The Physics of Sensing and Decision-Making by Animal Groups.","authors":"Danielle L Chase, Orit Peleg","doi":"10.1146/annurev-biophys-061824-110733","DOIUrl":"https://doi.org/10.1146/annurev-biophys-061824-110733","url":null,"abstract":"<p><p>To ensure survival and reproduction, individual animals navigating the world must regularly sense their surroundings and use this information for important decision-making. The same is true for animals living in groups, where the roles of sensing, information propagation, and decision-making are distributed on the basis of individual knowledge, spatial position within the group, and more. This review highlights key examples of temporal and spatiotemporal dynamics in animal group decision-making, emphasizing strong connections between mathematical models and experimental observations. We start with models of temporal dynamics, such as reaching consensus and the time dynamics of excitation-inhibition networks. For spatiotemporal dynamics in sparse groups, we explore the propagation of information and synchronization of movement in animal groups with models of self-propelled particles, where interactions are typically parameterized by length and timescales. In dense groups, we examine crowding effects using a soft condensed matter approach, where interactions are parameterized by physical potentials and forces. While focusing on invertebrates, we also demonstrate the applicability of these results to a wide range of organisms, aiming to provide an overview of group behavior dynamics and identify new areas for exploration.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"54 1","pages":"329-351"},"PeriodicalIF":10.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144006653","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
Cryo-EM of Mitochondrial Complex I and ATP Synthase. 线粒体复合体I和ATP合酶的低温电镜分析。
IF 10.4 1区 生物学
Annual Review of Biophysics Pub Date : 2025-05-01 DOI: 10.1146/annurev-biophys-060724-110838
Werner Kühlbrandt, Luis A M Carreira, Özkan Yildiz
{"title":"Cryo-EM of Mitochondrial Complex I and ATP Synthase.","authors":"Werner Kühlbrandt, Luis A M Carreira, Özkan Yildiz","doi":"10.1146/annurev-biophys-060724-110838","DOIUrl":"https://doi.org/10.1146/annurev-biophys-060724-110838","url":null,"abstract":"<p><p>Cryo-electron microscopy (cryo-EM) is the method of choice for investigating the structures of membrane protein complexes at high resolution under near-native conditions. This review focuses on recent cryo-EM work on mitochondrial complex I and ATP synthase. Single-particle cryo-EM structures of complex I from mammals, plants, and fungi extending to a resolution of 2 Å show different functional states, indicating consistent conformational changes of loops near the Q binding site, clusters of internal water molecules in the membrane arm, and an α-π transition in a membrane-spanning helix that opens and closes the proton transfer path. Cryo-EM structures of ATP synthase dimers from mammalian, yeast, and <i>Polytomella</i> mitochondria show several rotary states at a resolution of 2.7 to 3.5 Å. The new structures of complex I and ATP synthase are important steps along the way toward understanding the detailed molecular mechanisms of both complexes. Cryo-electron tomography and subtomogram averaging have the potential to resolve their high-resolution structures in situ.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"54 1","pages":"209-226"},"PeriodicalIF":10.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144027402","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
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 : 2025-05-01 Epub 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":"10.1146/annurev-biophys-030722-110624","url":null,"abstract":"<p><p>The brain is immensely complex, with diverse components and dynamic interactions building upon one another to orchestrate a wide range of behaviors. Understanding 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.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"353-378"},"PeriodicalIF":10.4,"publicationDate":"2025-05-01","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
Metabolic Engineering of Yeast. 酵母代谢工程。
IF 10.4 1区 生物学
Annual Review of Biophysics Pub Date : 2025-05-01 Epub Date: 2025-01-21 DOI: 10.1146/annurev-biophys-070924-103134
Shuobo Shi, Yu Chen, Jens Nielsen
{"title":"Metabolic Engineering of Yeast.","authors":"Shuobo Shi, Yu Chen, Jens Nielsen","doi":"10.1146/annurev-biophys-070924-103134","DOIUrl":"10.1146/annurev-biophys-070924-103134","url":null,"abstract":"<p><p>Microbial cell factories have been developed to produce various compounds in a sustainable and economically viable manner. The yeast <i>Saccharomyces cerevisiae</i> has been used as a platform cell factory in industrial biotechnology with numerous advantages, including ease of operation, rapid growth, and tolerance for various industrial stressors. Advances in synthetic biology and metabolic models have accelerated the design-build-test-learn cycle in metabolic engineering, significantly facilitating the development of yeast strains with complex phenotypes, including the redirection of metabolic fluxes to desired products, the expansion of the spectrum of usable substrates, and the improvement of the physiological properties of strain. Strains with enhanced titer, rate, and yield are now competing with traditional petroleum-based industrial approaches. This review highlights recent advances and perspectives in the metabolic engineering of yeasts for the production of a variety of compounds, including fuels, chemicals, proteins, and peptides, as well as advancements in synthetic biology tools and mathematical modeling.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"101-120"},"PeriodicalIF":10.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143015694","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
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 : 2025-05-01 Epub Date: 2025-02-14 DOI: 10.1146/annurev-biophys-070124-092816
Matthew MacAinsh, Fidha Nazreen Kunnath Muhammedkutty, Ramesh Prasad, Huan-Xiang Zhou
{"title":"Membrane Association of Intrinsically Disordered Proteins.","authors":"Matthew MacAinsh, Fidha Nazreen Kunnath Muhammedkutty, Ramesh Prasad, Huan-Xiang Zhou","doi":"10.1146/annurev-biophys-070124-092816","DOIUrl":"10.1146/annurev-biophys-070124-092816","url":null,"abstract":"<p><p>It is now clear that membrane association of intrinsically disordered proteins or intrinsically disordered regions regulates many cellular processes, such as membrane targeting of Src family kinases and ion channel gating. Residue-specific characterization by nuclear magnetic resonance spectroscopy, molecular dynamics simulations, and other techniques has shown that polybasic motifs and amphipathic helices are the main drivers of membrane association; sequence-based prediction of residue-specific membrane association propensity has become possible. Membrane association facilitates protein-protein interactions and protein aggregation-these effects are due to reduced dimensionality but are similar to those afforded by condensate formation via liquid-liquid phase separation (LLPS). LLPS at the membrane surface provides a powerful means for recruiting and clustering proteins, as well as for membrane remodeling.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"275-302"},"PeriodicalIF":10.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12055482/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143426575","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
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 : 2025-05-01 Epub Date: 2025-02-19 DOI: 10.1146/annurev-biophys-081624-030543
Christopher Joel Russo, Kabir Husain, Arvind Murugan
{"title":"Soft Modes as a Predictive Framework for Low-Dimensional Biological Systems Across Scales.","authors":"Christopher Joel Russo, Kabir Husain, Arvind Murugan","doi":"10.1146/annurev-biophys-081624-030543","DOIUrl":"10.1146/annurev-biophys-081624-030543","url":null,"abstract":"<p><p>All biological systems are subject to perturbations arising from thermal fluctuations, external environments, or mutations. Yet, while biological systems consist of thousands of interacting components, recent high-throughput experiments have shown that their response to perturbations is surprisingly low dimensional: confined to only a few stereotyped changes out of the many possible. In this review, we explore a unifying dynamical systems framework-soft modes-to explain and analyze low dimensionality in biology, from molecules to ecosystems. We argue that this soft mode framework makes nontrivial predictions that generalize classic ideas from developmental biology to disparate systems, namely phenocopying, dual buffering, and global epistasis. While some of these predictions have been borne out in experiments, we discuss how soft modes allow for a surprisingly far-reaching and unifying framework in which to analyze data from protein biophysics to microbial ecology.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"401-426"},"PeriodicalIF":10.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12079786/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143460470","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
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 : 2025-05-01 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":"<p><p>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.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"185-207"},"PeriodicalIF":10.4,"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
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 : 2025-05-01 Epub Date: 2025-02-10 DOI: 10.1146/annurev-biophys-030722-120914
Guillaume Romet-Lemonne, Cécile Leduc, Antoine Jégou, Hugo Wioland
{"title":"Mechanics of Single Cytoskeletal Filaments.","authors":"Guillaume Romet-Lemonne, Cécile Leduc, Antoine Jégou, Hugo Wioland","doi":"10.1146/annurev-biophys-030722-120914","DOIUrl":"10.1146/annurev-biophys-030722-120914","url":null,"abstract":"<p><p>The cytoskeleton comprises networks of different biopolymers, which serve various cellular functions. To accomplish these tasks, their mechanical properties are of particular importance. Understanding them requires detailed knowledge of the mechanical properties of the individual filaments that make up these networks, in particular, microtubules, actin filaments, and intermediate filaments. Far from being homogeneous beams, cytoskeletal filaments have complex mechanical properties, which are directly related to the specific structural arrangement of their subunits. They are also versatile, as the filaments' mechanics and biochemistry are tightly coupled, and their properties can vary with the cellular context. In this review, we summarize decades of research on cytoskeletal filament mechanics, highlighting their most salient features and discussing recent insights from this active field of research.</p>","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"303-327"},"PeriodicalIF":10.4,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143392065","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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