Biophysical reviews最新文献

Biophysical Reviews: welcoming a new year in biophysics.

IF 4.9

Biophysical reviews Pub Date : 2025-02-27 eCollection Date: 2025-02-01 DOI: 10.1007/s12551-025-01291-0

Wilma K Olson

引用次数: 0

Wiener filter unifies Hilbert and Zernike phase plates in electron microscopy.

IF 4.9

Biophysical reviews Pub Date : 2025-02-13 eCollection Date: 2025-02-01 DOI: 10.1007/s12551-025-01272-3

Kuniaki Nagayama

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Differential scanning fluorimetry followed by microscale thermophoresis and/or isothermal titration calorimetry as an efficient tool for ligand screening.

IF 4.9

Biophysical reviews Pub Date : 2025-02-13 eCollection Date: 2025-02-01 DOI: 10.1007/s12551-025-01280-3

Maria Winiewska-Szajewska, Jarosław Poznański

{"title":"Differential scanning fluorimetry followed by microscale thermophoresis and/or isothermal titration calorimetry as an efficient tool for ligand screening.","authors":"Maria Winiewska-Szajewska, Jarosław Poznański","doi":"10.1007/s12551-025-01280-3","DOIUrl":"10.1007/s12551-025-01280-3","url":null,"abstract":"Various biophysical and biochemical techniques have been developed to measure the affinity of interacting molecules. This review analyzes the combination of three methods: differential scanning fluorimetry as the initial high-throughput screening technique and microscale thermophoresis and isothermal titration calorimetry as complementary methods to quantify binding affinity. The presented work is the first to detailed compare the strengths and flaws of these three specific methods, as well as their application possibilities and complementarity. The fundamentals of these methods will be covered, including the most often-used models for characterizing observable phenomena and an emphasis on methods for analyzing data. A comprehensive review of numerous approaches to data analysis found in the literature is additionally provided, with the benefits and drawbacks of each, as well as the pitfalls and related concerns. Finally, examples of different systems will be presented, and methods used and some discrepancies in results will be described and discussed.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 1","pages":"199-223"},"PeriodicalIF":4.9,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11885780/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Single-molecule magnetic tweezers to unravel protein folding dynamics under force.

IF 4.9

Biophysical reviews Pub Date : 2025-02-08 eCollection Date: 2025-02-01 DOI: 10.1007/s12551-025-01274-1

Rafael Tapia-Rojo

{"title":"Single-molecule magnetic tweezers to unravel protein folding dynamics under force.","authors":"Rafael Tapia-Rojo","doi":"10.1007/s12551-025-01274-1","DOIUrl":"10.1007/s12551-025-01274-1","url":null,"abstract":"Single-molecule magnetic tweezers have recently emerged as a powerful technique for measuring the equilibrium dynamics of individual proteins under force. In magnetic tweezers, a single protein is tethered between a glass coverslip and a superparamagnetic bead, and by applying and controlling a magnetic field, the protein is mechanically stretched while force-induced conformational changes are measured by tracking the vertical position of the bead. The soft trap created by the magnetic field provides intrinsic force-clamp conditions, which makes magnetic tweezers particularly well-suited to measure protein conformational dynamics. Traditionally employed to study DNA due to their initially low spatial and temporal resolutions, magnetic tweezers instrumentation has experienced significant progress in recent years. The development of high-speed cameras, stronger illumination sources, advanced image analysis algorithms, and dedicated chemical functionalization strategies, now allow for high-resolution and ultra-stable experiments. Together with their ability to apply and control low forces, magnetic tweezers can capture long-term equilibrium protein folding dynamics, not possible with any other technique. These capabilities have proven particularly valuable in the study of force-sensing protein systems, which often exhibit low mechanical stabilities that are challenging to measure with other techniques. In this review, we will discuss the current status of magnetic tweezers instrumentation for studying protein folding dynamics, focusing on both the instrumental aspects and methodologies to interpret nanomechanical experiments.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 1","pages":"25-44"},"PeriodicalIF":4.9,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11885773/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584721","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Phase Space Invaders' podcast episode with Tamar Schlick: a trajectory from mathematics to biology.

IF 4.9

Biophysical reviews Pub Date : 2025-01-28 eCollection Date: 2025-02-01 DOI: 10.1007/s12551-025-01271-4

Miłosz Wieczór, Tamar Schlick

引用次数: 0

An open call for contributions to a Special Issue of Biophysical Reviews highlighting current advances in modern biophysical methods discussed on the Russian Autumn School on Biophysics in Kazan 2024.

IF 4.9

Biophysical reviews Pub Date : 2025-01-28 eCollection Date: 2025-02-01 DOI: 10.1007/s12551-025-01273-2

Anastasia A Anashkina, Yuriy F Zuev, Konstantin S Usachev, Vladimir I Polshakov, Bogdan S Melnik, Yuriy L Orlov, Andrey B Rubin

引用次数: 0

The flexible chain: regulation of structure and activity of ETC complexes defines rate of ATP synthesis and sites of superoxide generation.

IF 4.9

Biophysical reviews Pub Date : 2025-01-25 eCollection Date: 2025-02-01 DOI: 10.1007/s12551-025-01270-5

Zhanna V Bochkova, Adil A Baizhumanov, Alexander I Yusipovich, Kseniia I Morozova, Evelina I Nikelshparg, Anna A Fedotova, Alisa B Tiaglik, Yu Xu, Alexey R Brazhe, Georgy V Maksimov, Dmitry S Bilan, Yuliya V Khramova, Evgeniya Yu Parshina, Nadezda A Brazhe

{"title":"The flexible chain: regulation of structure and activity of ETC complexes defines rate of ATP synthesis and sites of superoxide generation.","authors":"Zhanna V Bochkova, Adil A Baizhumanov, Alexander I Yusipovich, Kseniia I Morozova, Evelina I Nikelshparg, Anna A Fedotova, Alisa B Tiaglik, Yu Xu, Alexey R Brazhe, Georgy V Maksimov, Dmitry S Bilan, Yuliya V Khramova, Evgeniya Yu Parshina, Nadezda A Brazhe","doi":"10.1007/s12551-025-01270-5","DOIUrl":"10.1007/s12551-025-01270-5","url":null,"abstract":"This review highlights current insights into the regulation of the mitochondrial respiratory chain (electron transport chain, ETC) activity. The regulation of ETC properties optimizes ATP synthesis and controls the generation of the superoxide anion radical (O2 •-) which can be converted into other reactive oxygen species (ROS) playing a dual role by initiating signaling cascades or contributing to oxidative stress. We examine how ETC activity is influenced by the structure and conformation of its complexes, their allosteric or post-translational modifications, and their interactions with membrane lipids. The formation and function of supercomplexes, as well as their cell-type-specific characteristics, are also discussed, alongside with the role of intracellular Ca2+ concentration in the modulation of ETC activity. Furthermore, we discuss mechanisms and sites of O2 •- generation within ETC complexes, O2 •- fate in the mitochondrial matrix, and the impact of cytochrome c (Cyt c) conformation and allosteric modifications on ETC function. Finally, we discuss various abnormalities in ETC complexes, emphasizing their relevance to mitochondrial dysfunction and disease.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 1","pages":"55-88"},"PeriodicalIF":4.9,"publicationDate":"2025-01-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11885220/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584724","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Half a century of biophysics: a comparison of participant statistics from the 6th and 21st IUPAB congresses.

IF 4.9

Biophysical reviews Pub Date : 2025-01-24 eCollection Date: 2025-02-01 DOI: 10.1007/s12551-025-01268-z

Kuniaki Nagayama, Mikio Kataoka

引用次数: 0

On the distance to the transition state of protein folding in optical tweezers experiments.

IF 4.9

Biophysical reviews Pub Date : 2025-01-09 eCollection Date: 2025-02-01 DOI: 10.1007/s12551-024-01264-9

Camila G Corrêa, Christian A M Wilson

{"title":"On the distance to the transition state of protein folding in optical tweezers experiments.","authors":"Camila G Corrêa, Christian A M Wilson","doi":"10.1007/s12551-024-01264-9","DOIUrl":"10.1007/s12551-024-01264-9","url":null,"abstract":"The distance to the transition state ( <math> <msup><mrow><mi>x</mi></mrow> <mo>‡</mo></msup> </math> ) is an important parameter for understanding the energy landscape of chemical reactions. In protein folding, <math> <msup><mrow><mi>x</mi></mrow> <mo>‡</mo></msup> </math> represents the distance to the high energy structure between folded and unfolded states. This correlates with the deformation of the protein as it crosses the energy barrier defining its rigidity. This parameter can be determined by unfolding the protein, analyzing the kinetics of unfolding and refolding, and fitting the data to various models. An approach to determine the <math> <msup><mrow><mi>x</mi></mrow> <mo>‡</mo></msup> </math> is using force as a way to tilt the energy landscape. Force spectroscopy studies, particularly at the single-molecule level, offer a powerful approach for this purpose. One of these techniques is optical tweezers, which allow the application of force by pulling on a bead attached to the protein via spacers, thereby unfolding it. This method provides measurements of force and distance between the folded and unfolded states of the protein. By analyzing force histograms, we can apply different models as the phenomenological Bell-Evans or Kramers theory-based models. Additionally, an alternative direct approach involves summing the distances to the transition state to fit the data of the distance of total protein unfolding. Using this approach, we can plot force versus distance and obtain the <math> <msup><mrow><mi>x</mi></mrow> <mo>‡</mo></msup> </math> and the energy to the transition state from folded to unfolding and vice versa. Furthermore, these results can be correlated with elastic models, such as the worm-like chain model. By integrating these approaches, we can gain deeper insights into protein folding mechanisms.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 1","pages":"45-54"},"PeriodicalIF":4.9,"publicationDate":"2025-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11885770/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","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 Reviews: the IUPAB journal promoting biophysics on an international stage. 《生物物理评论》：IUPAB在国际舞台上推广生物物理学的期刊。

IF 4.9

Biophysical reviews Pub Date : 2025-01-03 eCollection Date: 2024-12-01 DOI: 10.1007/s12551-024-01266-7

Wilma K Olson

引用次数: 0