Annual Review of Biophysics最新文献

Mechanisms of Inheritance of Chromatin States: From Yeast to Human.

IF 10.4 1区生物学

Annual Review of Biophysics Pub Date : 2024-12-23 DOI: 10.1146/annurev-biophys-070524-091904

Hiten D Madhani

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 : 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":"https://doi.org/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":""},"PeriodicalIF":10.4,"publicationDate":"2024-12-17","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

Protein Modeling with DEER Spectroscopy. 利用 DEER 光谱建立蛋白质模型。

IF 10.4 1区生物学

Annual Review of Biophysics Pub Date : 2024-12-17 DOI: 10.1146/annurev-biophys-030524-013431

Maxx H Tessmer, Stefan Stoll

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 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-030722-020555

McKenze J Moss, Laura M Chamness, Patricia L Clark

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 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-030822-032904

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":10.4,"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

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 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-030822-035656

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":10.4,"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

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

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-030822-034116

Tatsuya Morisaki, O'Neil Wiggan, Timothy J Stasevich

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 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-030722-021359

Michelle S Frei, Sohum Mehta, Jin Zhang

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 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-030722-111729

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":10.4,"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

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 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-030722-125440

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":10.4,"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