Annual Review of Biophysics最新文献

IF 10.4 1区生物学

Annual Review of Biophysics Pub 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":"https://doi.org/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":""},"PeriodicalIF":10.4,"publicationDate":"2025-02-10","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.

IF 10.4 1区生物学

Annual Review of Biophysics Pub 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

Information Processing in Biochemical Networks. 生化网络中的信息处理。

IF 10.4 1区生物学

Annual Review of Biophysics Pub Date : 2025-02-10 DOI: 10.1146/annurev-biophys-060524-102720

Gašper Tkačik, Pieter Rein Ten Wolde

{"title":"Information Processing in Biochemical Networks.","authors":"Gašper Tkačik, Pieter Rein Ten Wolde","doi":"10.1146/annurev-biophys-060524-102720","DOIUrl":"https://doi.org/10.1146/annurev-biophys-060524-102720","url":null,"abstract":"Living systems are characterized by controlled flows of matter, energy, and information. While the biophysics community has productively engaged with the first two, addressing information flows has been more challenging, with some scattered success in evolutionary theory and a more coherent track record in neuroscience. Nevertheless, interdisciplinary work of the past two decades at the interface of biophysics, quantitative biology, and engineering has led to an emerging mathematical language for describing information flows at the molecular scale. This is where the central processes of life unfold: from detection and transduction of environmental signals to the readout or copying of genetic information and the triggering of adaptive cellular responses. Such processes are coordinated by complex biochemical reaction networks that operate at room temperature, are out of equilibrium, and use low copy numbers of diverse molecular species with limited interaction specificity. Here we review how flows of information through biochemical networks can be formalized using information-theoretic quantities, quantified from data, and computed within various modeling frameworks. Optimization of information flows is presented as a candidate design principle that navigates the relevant time, energy, crosstalk, and metabolic constraints to predict reliable cellular signaling and gene regulation architectures built of individually noisy components.","PeriodicalId":50756,"journal":{"name":"Annual Review of Biophysics","volume":" ","pages":""},"PeriodicalIF":10.4,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143391992","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

Statistical Thermodynamics of the Protein Ensemble: Mediating Function and Evolution.

IF 10.4 1区生物学

Annual Review of Biophysics Pub 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":"https://doi.org/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":""},"PeriodicalIF":10.4,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mechanisms for DNA Interplay in Eukaryotic Transcription Factors.

IF 10.4 1区生物学

Annual Review of Biophysics Pub Date : 2025-01-29 DOI: 10.1146/annurev-biophys-071524-111008

Victor Muñoz, Rama Reddy Goluguri, Catherine Ghosh, Benjamin Tanielian, Mourad Sadqi

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 : 2025-01-21 DOI: 10.1146/annurev-biophys-070924-103134

Shuobo Shi, Yu Chen, Jens Nielsen

引用次数: 0

Mechanisms of Inheritance of Chromatin States: From Yeast to Human. 染色质状态的遗传机制：从酵母到人类。

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