Annual Review of Biophysics最新文献_第5页

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 12.9 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":"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.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"227-247"},"PeriodicalIF":12.9,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13411409/pdf/","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":"OA","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 13.7 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

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 13.7 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

引用次数: 0

Translation Dynamics of Single mRNAs in Live Cells. 活细胞中单 mRNA 的翻译动态。

IF 13.7 1区生物学

Annual Review of Biophysics Pub Date : 2024-07-01 Epub Date: 2024-06-28 DOI: 10.1146/annurev-biophys-030822-034116

Tatsuya Morisaki, O'Neil Wiggan, Timothy J Stasevich

引用次数: 0

Unveiling the Intricate Connection: Cell Volume as a Key Regulator of Mechanotransduction. 揭开错综复杂的联系：细胞体积是机械传导的关键调节器。

IF 13.7 1区生物学

Annual Review of Biophysics Pub Date : 2024-07-01 Epub Date: 2024-06-28 DOI: 10.1146/annurev-biophys-030822-035656

Jing Xie, Wilhelm T S Huck, Min Bao

{"title":"Unveiling the Intricate Connection: Cell Volume as a Key Regulator of Mechanotransduction.","authors":"Jing Xie, Wilhelm T S Huck, Min Bao","doi":"10.1146/annurev-biophys-030822-035656","DOIUrl":"10.1146/annurev-biophys-030822-035656","url":null,"abstract":"The volumes of living cells undergo dynamic changes to maintain the cells' structural and functional integrity in many physiological processes. Minor fluctuations in cell volume can serve as intrinsic signals that play a crucial role in cell fate determination during mechanotransduction. In this review, we discuss the variability of cell volume and its role in vivo, along with an overview of the mechanisms governing cell volume regulation. Additionally, we provide insights into the current approaches used to control cell volume in vitro. Furthermore, we summarize the biological implications of cell volume regulation and discuss recent advances in understanding the fundamental relationship between cell volume and mechanotransduction. Finally, we delve into the potential underlying mechanisms, including intracellular macromolecular crowding and cellular mechanics, that govern the global regulation of cell fate in response to changes in cell volume. By exploring the intricate interplay between cell volume and mechanotransduction, we underscore the importance of considering cell volume as a fundamental signaling cue to unravel the basic principles of mechanotransduction. Additionally, we propose future research directions that can extend our current understanding of cell volume in mechanotransduction. Overall, this review highlights the significance of considering cell volume as a fundamental signal in understanding the basic principles in mechanotransduction and points out the possibility of controlling cell volume to control cell fate, mitigate disease-related damage, and facilitate the healing of damaged tissues.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"299-317"},"PeriodicalIF":13.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139998196","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

When Force Met Fluorescence: Single-Molecule Manipulation and Visualization of Protein-DNA Interactions. 当力遇到荧光：蛋白质-DNA 相互作用的单分子操作和可视化。

IF 13.7 1区生物学

Annual Review of Biophysics Pub Date : 2024-07-01 Epub Date: 2024-06-28 DOI: 10.1146/annurev-biophys-030822-032904

Gabriella N L Chua, Shixin Liu

{"title":"When Force Met Fluorescence: Single-Molecule Manipulation and Visualization of Protein-DNA Interactions.","authors":"Gabriella N L Chua, Shixin Liu","doi":"10.1146/annurev-biophys-030822-032904","DOIUrl":"10.1146/annurev-biophys-030822-032904","url":null,"abstract":"Myriad DNA-binding proteins undergo dynamic assembly, translocation, and conformational changes while on DNA or alter the physical configuration of the DNA substrate to control its metabolism. It is now possible to directly observe these activities-often central to the protein function-thanks to the advent of single-molecule fluorescence- and force-based techniques. In particular, the integration of fluorescence detection and force manipulation has unlocked multidimensional measurements of protein-DNA interactions and yielded unprecedented mechanistic insights into the biomolecular processes that orchestrate cellular life. In this review, we first introduce the different experimental geometries developed for single-molecule correlative force and fluorescence microscopy, with a focus on optical tweezers as the manipulation technique. We then describe the utility of these integrative platforms for imaging protein dynamics on DNA and chromatin, as well as their unique capabilities in generating complex DNA configurations and uncovering force-dependent protein behaviors. Finally, we give a perspective on the future directions of this emerging research field.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"169-191"},"PeriodicalIF":13.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139492494","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

Next-Generation Genetically Encoded Fluorescent Biosensors Illuminate Cell Signaling and Metabolism. 下一代基因编码荧光生物传感器照亮细胞信号传导和新陈代谢。

IF 13.7 1区生物学

Annual Review of Biophysics Pub Date : 2024-07-01 Epub Date: 2024-06-28 DOI: 10.1146/annurev-biophys-030722-021359

Michelle S Frei, Sohum Mehta, Jin Zhang

引用次数: 0

Ancestral Reconstruction and the Evolution of Protein Energy Landscapes. 蛋白质能量景观的祖先重建与进化

IF 13.7 1区生物学

Annual Review of Biophysics Pub Date : 2024-07-01 Epub Date: 2024-06-28 DOI: 10.1146/annurev-biophys-030722-125440

Lauren O Chisholm, Kona N Orlandi, Sophia R Phillips, Michael J Shavlik, Michael J Harms

{"title":"Ancestral Reconstruction and the Evolution of Protein Energy Landscapes.","authors":"Lauren O Chisholm, Kona N Orlandi, Sophia R Phillips, Michael J Shavlik, Michael J Harms","doi":"10.1146/annurev-biophys-030722-125440","DOIUrl":"10.1146/annurev-biophys-030722-125440","url":null,"abstract":"A protein's sequence determines its conformational energy landscape. This, in turn, determines the protein's function. Understanding the evolution of new protein functions therefore requires understanding how mutations alter the protein energy landscape. Ancestral sequence reconstruction (ASR) has proven a valuable tool for tackling this problem. In ASR, one phylogenetically infers the sequences of ancient proteins, allowing characterization of their properties. When coupled to biophysical, biochemical, and functional characterization, ASR can reveal how historical mutations altered the energy landscape of ancient proteins, allowing the evolution of enzyme activity, altered conformations, binding specificity, oligomerization, and many other protein features. In this article, we review how ASR studies have been used to dissect the evolution of energy landscapes. We also discuss ASR studies that reveal how energy landscapes have shaped protein evolution. Finally, we propose that thinking about evolution from the perspective of an energy landscape can improve how we approach and interpret ASR studies.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"127-146"},"PeriodicalIF":13.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11192866/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138886544","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

Biophysical Principles Emerging from Experiments on Protein-Protein Association and Aggregation. 蛋白质-蛋白质结合和聚集实验中出现的生物物理原理。

IF 13.7 1区生物学

Annual Review of Biophysics Pub Date : 2024-07-01 Epub Date: 2024-06-28 DOI: 10.1146/annurev-biophys-030722-111729

Barbara Hribar-Lee, Miha Lukšič

{"title":"Biophysical Principles Emerging from Experiments on Protein-Protein Association and Aggregation.","authors":"Barbara Hribar-Lee, Miha Lukšič","doi":"10.1146/annurev-biophys-030722-111729","DOIUrl":"10.1146/annurev-biophys-030722-111729","url":null,"abstract":"Protein-protein association and aggregation are fundamental processes that play critical roles in various biological phenomena, from cellular signaling to disease progression. Understanding the underlying biophysical principles governing these processes is crucial for elucidating their mechanisms and developing strategies for therapeutic intervention. In this review, we provide an overview of recent experimental studies focused on protein-protein association and aggregation. We explore the key biophysical factors that influence these processes, including protein structure, conformational dynamics, and intermolecular interactions. We discuss the effects of environmental conditions such as temperature, pH and related buffer-specific effects, and ionic strength and related ion-specific effects on protein aggregation. The effects of polymer crowders and sugars are also addressed. We list the techniques used to study aggregation. We analyze emerging trends and challenges in the field, including the development of computational models and the integration of multidisciplinary approaches for a comprehensive understanding of protein-protein association and aggregation.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":"1-18"},"PeriodicalIF":13.7,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71428740","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

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 13.7 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":13.7,"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