Annual Review of Biophysics最新文献

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

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":"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.","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":"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.","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

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":"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.","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

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

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

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":"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":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

引用次数: 0