Annual Review of Biophysics最新文献_第2页

Emergent Spatiotemporal Organization in Stochastic Intracellular Transport Dynamics. 随机细胞内运输动力学中的新兴时空组织

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-030422-044448

Kunaal Joshi, Harrison M York, Charles S Wright, Rudro R Biswas, Senthil Arumugam, Srividya Iyer-Biswas

{"title":"Emergent Spatiotemporal Organization in Stochastic Intracellular Transport Dynamics.","authors":"Kunaal Joshi, Harrison M York, Charles S Wright, Rudro R Biswas, Senthil Arumugam, Srividya Iyer-Biswas","doi":"10.1146/annurev-biophys-030422-044448","DOIUrl":"10.1146/annurev-biophys-030422-044448","url":null,"abstract":"The interior of a living cell is an active, fluctuating, and crowded environment, yet it maintains a high level of coherent organization. This dichotomy is readily apparent in the intracellular transport system of the cell. Membrane-bound compartments called endosomes play a key role in carrying cargo, in conjunction with myriad components including cargo adaptor proteins, membrane sculptors, motor proteins, and the cytoskeleton. These components coordinate to effectively navigate the crowded cell interior and transport cargo to specific intracellular locations, even though the underlying protein interactions and enzymatic reactions exhibit stochastic behavior. A major challenge is to measure, analyze, and understand how, despite the inherent stochasticity of the constituent processes, the collective outcomes show an emergent spatiotemporal order that is precise and robust. This review focuses on this intriguing dichotomy, providing insights into the known mechanisms of noise suppression and noise utilization in intracellular transport processes, and also identifies opportunities for future inquiry.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"193-220"},"PeriodicalIF":10.4,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139724895","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

Fitness Landscapes and Evolution of Catalytic RNA. 催化 RNA 的适应性景观和进化。

IF 10.4 1区生物学

Annual Review of Biophysics Pub Date : 2024-07-01 DOI: 10.1146/annurev-biophys-030822-025038

Ranajay Saha, Alberto Vázquez-Salazar, Aditya Nandy, Irene A Chen

引用次数: 0

Biomolecular Condensates in Contact with Membranes. 与膜接触的生物分子凝结物。

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-030722-121518

Agustín Mangiarotti, Rumiana Dimova

引用次数: 0

Mitochondrial Dynamics at Different Levels: From Cristae Dynamics to Interorganellar Cross Talk. 不同层次的线粒体动力学：从晶状体动力学到细胞器间的交叉对话

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-030822-020736

Arun Kumar Kondadi, Andreas S Reichert

{"title":"Mitochondrial Dynamics at Different Levels: From Cristae Dynamics to Interorganellar Cross Talk.","authors":"Arun Kumar Kondadi, Andreas S Reichert","doi":"10.1146/annurev-biophys-030822-020736","DOIUrl":"10.1146/annurev-biophys-030822-020736","url":null,"abstract":"Mitochondria are essential organelles performing important cellular functions ranging from bioenergetics and metabolism to apoptotic signaling and immune responses. They are highly dynamic at different structural and functional levels. Mitochondria have been shown to constantly undergo fusion and fission processes and dynamically interact with other organelles such as the endoplasmic reticulum, peroxisomes, and lipid droplets. The field of mitochondrial dynamics has evolved hand in hand with technological achievements including advanced fluorescence super-resolution nanoscopy. Dynamic remodeling of the cristae membrane within individual mitochondria, discovered very recently, opens up a further exciting layer of mitochondrial dynamics. In this review, we discuss mitochondrial dynamics at the following levels: (a) within an individual mitochondrion, (b) among mitochondria, and (c) between mitochondria and other organelles. Although the three tiers of mitochondrial dynamics have in the past been classified in a hierarchical manner, they are functionally connected and must act in a coordinated manner to maintain cellular functions and thus prevent various human diseases.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"147-168"},"PeriodicalIF":10.4,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139081095","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

Structure Function Studies of Photosystem II Using X-Ray Free Electron Lasers. 利用 X 射线自由电子激光对光子系统 II 进行结构功能研究。

IF 10.4 1区生物学

Annual Review of Biophysics Pub Date : 2024-07-01 DOI: 10.1146/annurev-biophys-071723-102519

Junko Yano, Jan Kern, Vittal K Yachandra

引用次数: 0

Single-Molecule Imaging of Integral Membrane Protein Dynamics and Function. 整体膜蛋白动态和功能的单分子成像。

IF 10.4 1区生物学

Annual Review of Biophysics Pub Date : 2024-07-01 DOI: 10.1146/annurev-biophys-070323-024308

Arnab Modak, Zeliha Kilic, Kanokporn Chattrakun, Daniel S Terry, Ravi C Kalathur, Scott C Blanchard

引用次数: 0

From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization. 从核小体到分区：染色质组织的物理化学相互作用。

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-030822-032650

Shuming Liu, Advait Athreya, Zhuohan Lao, Bin Zhang

{"title":"From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization.","authors":"Shuming Liu, Advait Athreya, Zhuohan Lao, Bin Zhang","doi":"10.1146/annurev-biophys-030822-032650","DOIUrl":"10.1146/annurev-biophys-030822-032650","url":null,"abstract":"Chromatin organization plays a critical role in cellular function by regulating access to genetic information. However, understanding chromatin folding is challenging due to its complex, multiscale nature. Significant progress has been made in studying in vitro systems, uncovering the structure of individual nucleosomes and their arrays, and elucidating the role of physicochemical forces in stabilizing these structures. Additionally, remarkable advancements have been achieved in characterizing chromatin organization in vivo, particularly at the whole-chromosome level, revealing important features such as chromatin loops, topologically associating domains, and nuclear compartments. However, bridging the gap between in vitro and in vivo studies remains challenging. The resemblance between in vitro and in vivo chromatin conformations and the relevance of internucleosomal interactions for chromatin folding in vivo are subjects of debate. This article reviews experimental and computational studies conducted at various length scales, highlighting the significance of intrinsic interactions between nucleosomes and their roles in chromatin folding in vivo.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"221-245"},"PeriodicalIF":10.4,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11369498/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139724896","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

NMR and Single-Molecule FRET Insights into Fast Protein Motions and Their Relation to Function. 核磁共振和单分子 FRET 透视快速蛋白质运动及其与功能的关系

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-070323-022428

Paul Schanda, Gilad Haran

{"title":"NMR and Single-Molecule FRET Insights into Fast Protein Motions and Their Relation to Function.","authors":"Paul Schanda, Gilad Haran","doi":"10.1146/annurev-biophys-070323-022428","DOIUrl":"10.1146/annurev-biophys-070323-022428","url":null,"abstract":"Proteins often undergo large-scale conformational transitions, in which secondary and tertiary structure elements (loops, helices, and domains) change their structures or their positions with respect to each other. Simple considerations suggest that such dynamics should be relatively fast, but the functional cycles of many proteins are often relatively slow. Sophisticated experimental methods are starting to tackle this dichotomy and shed light on the contribution of large-scale conformational dynamics to protein function. In this review, we focus on the contribution of single-molecule Förster resonance energy transfer and nuclear magnetic resonance (NMR) spectroscopies to the study of conformational dynamics. We briefly describe the state of the art in each of these techniques and then point out their similarities and differences, as well as the relative strengths and weaknesses of each. Several case studies, in which the connection between fast conformational dynamics and slower function has been demonstrated, are then introduced and discussed. These examples include both enzymes and large protein machines, some of which have been studied by both NMR and fluorescence spectroscopies.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"247-273"},"PeriodicalIF":10.4,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139724898","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

Biophysical Modeling of Synaptic Plasticity 突触可塑性的生物物理建模

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2024-02-21 DOI: 10.1146/annurev-biophys-072123-124954

Christopher T. Lee, Miriam Bell, Mayte Bonilla-Quintana, Padmini Rangamani

{"title":"Biophysical Modeling of Synaptic Plasticity","authors":"Christopher T. Lee, Miriam Bell, Mayte Bonilla-Quintana, Padmini Rangamani","doi":"10.1146/annurev-biophys-072123-124954","DOIUrl":"https://doi.org/10.1146/annurev-biophys-072123-124954","url":null,"abstract":"Dendritic spines are small, bulbous compartments that function as postsynaptic sites and undergo intense biochemical and biophysical activity. The role of the myriad signaling pathways that are implicated in synaptic plasticity is well studied. A recent abundance of quantitative experimental data has made the events associated with synaptic plasticity amenable to quantitative biophysical modeling. Spines are also fascinating biophysical computational units because spine geometry, signal transduction, and mechanics work in a complex feedback loop to tune synaptic plasticity. In this sense, ideas from modeling cell motility can inspire us to develop multiscale approaches for predictive modeling of synaptic plasticity. In this article, we review the key steps in postsynaptic plasticity with a specific focus on the impact of spine geometry on signaling, cytoskeleton rearrangement, and membrane mechanics. We summarize the main experimental observations and highlight how theory and computation can aid our understanding of these complex processes.Expected final online publication date for the Annual Review of Biophysics, Volume 53 is May 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"259 1","pages":""},"PeriodicalIF":12.4,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139923425","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

Bacterial Electrophysiology 细菌电生理学

IF 12.4 1区生物学

Annual Review of Biophysics Pub Date : 2024-02-21 DOI: 10.1146/annurev-biophys-030822-032215

Wei-Chang Lo, Ekaterina Krasnopeeva, Teuta Pilizota

{"title":"Bacterial Electrophysiology","authors":"Wei-Chang Lo, Ekaterina Krasnopeeva, Teuta Pilizota","doi":"10.1146/annurev-biophys-030822-032215","DOIUrl":"https://doi.org/10.1146/annurev-biophys-030822-032215","url":null,"abstract":"Bacterial ion fluxes are involved in the generation of energy, transport, and motility. As such, bacterial electrophysiology is fundamentally important for the bacterial life cycle, but it is often neglected and consequently, by and large, not understood. Arguably, the two main reasons for this are the complexity of measuring relevant variables in small cells with a cell envelope that contains the cell wall and the fact that, in a unicellular organism, relevant variables become intertwined in a nontrivial manner. To help give bacterial electrophysiology studies a firm footing, in this review, we go back to basics. We look first at the biophysics of bacterial membrane potential, and then at the approaches and models developed mostly for the study of neurons and eukaryotic mitochondria. We discuss their applicability to bacterial cells. Finally, we connect bacterial membrane potential with other relevant (electro)physiological variables and summarize methods that can be used to both measure and influence bacterial electrophysiology.Expected final online publication date for the Annual Review of Biophysics, Volume 53 is May 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":"690 1","pages":""},"PeriodicalIF":12.4,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139928014","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