Biophysical reviews最新文献_第4页

Wiener filter unifies Hilbert and Zernike phase plates in electron microscopy. 维纳滤波器统一了电子显微镜中的希尔伯特相板和泽尼克相板。

IF 4.9

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

Kuniaki Nagayama

引用次数: 0

Differential scanning fluorimetry followed by microscale thermophoresis and/or isothermal titration calorimetry as an efficient tool for ligand screening. 差示扫描荧光法，然后是微尺度热泳和/或等温滴定量热法，作为配体筛选的有效工具。

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

Building a digital library on research into mineralizing vesicles: a systematic review-based approach. 构建矿化囊泡研究的数字图书馆：基于系统综述的方法。

IF 4.9

Biophysical reviews Pub Date : 2025-02-13 eCollection Date: 2025-04-01 DOI: 10.1007/s12551-025-01282-1

Gildacio Pereira Chaves Filho, Pedro de Andrade Tavares, Ananda Fernanda de Jesus, Pietro Ciancaglini, José Eduardo Santarem Segundo, Ana Paula Ramos

{"title":"Building a digital library on research into mineralizing vesicles: a systematic review-based approach.","authors":"Gildacio Pereira Chaves Filho, Pedro de Andrade Tavares, Ananda Fernanda de Jesus, Pietro Ciancaglini, José Eduardo Santarem Segundo, Ana Paula Ramos","doi":"10.1007/s12551-025-01282-1","DOIUrl":"https://doi.org/10.1007/s12551-025-01282-1","url":null,"abstract":"This systematic review consolidates current research on mineralizing extracellular vesicles, or matrix vesicles (MVs), including their isolation, characterization, and role in physiological and pathological calcification. We searched PubMed/Medline, Scopus, and Web of Knowledge by employing the keywords \"matrix vesicles\" or \"collagenase-released matrix vesicles\" or \"mineralizing vesicles\" and publishing years from 2000 to 2023. Seventy-one studies met the inclusion criteria. The studies described different experimental protocols, especially with respect to methods for isolating MVs, wherein digestion with collagenase combined with centrifugation was the most used. The studies employed characterization techniques, including the determination of alkaline phosphatase (ALP) and transmission electron microscopy (TEM), to assess the functionality, size, and morphology of MVs. MVs contain key proteins such as ALP, annexins, and osteocalcin, along with calcium and phosphate ions, which are all critical for precipitating apatite. In the studies, evaluation of ALP activity revealed that MVs are more effective for mineralization than their parent cells and, hence, a valuable tool to regenerate bone and to engineer tissues. On the other hand, MVs play an essential role in pathologies, and the studies showed how they contribute to vascular calcification. Despite the therapeutic potential of MVs, isolation methods and characterization protocols vary across the studies, so standardized methods are needed. We have consolidated the data resulting from this systematic review in an open digital library on MVs with free access to all researchers. The users of the digital library can apply filters and taxonomy to find and interconnect the data resulting from the review.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 2","pages":"627-651"},"PeriodicalIF":4.9,"publicationDate":"2025-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075729/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075874","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

Non-hyperbolic enzyme kinetics: the case of P-type ATPases. 非双曲型酶动力学：p型atp酶的情况。

IF 4.9

Biophysical reviews Pub Date : 2025-02-11 eCollection Date: 2025-04-01 DOI: 10.1007/s12551-025-01277-y

S E Faraj, M R Montes, R D Peluffo, R M González-Lebrero, R C Rossi

引用次数: 0

Mechanistic aspects of the binding of acid-base ligands to ferric heme proteins. 酸碱配体与铁血红素蛋白结合的机理。

IF 4.9

Biophysical reviews Pub Date : 2025-02-11 eCollection Date: 2025-04-01 DOI: 10.1007/s12551-025-01279-w

Andresa Messias, Melisa Carllinni Colombo, Juan Cruz Palermo, Jonathan A Córdova, Giovanna De Simone, Paolo Ascenzi, Darío A Estrin, Luciana Capece, Sara E Bari

{"title":"Mechanistic aspects of the binding of acid-base ligands to ferric heme proteins.","authors":"Andresa Messias, Melisa Carllinni Colombo, Juan Cruz Palermo, Jonathan A Córdova, Giovanna De Simone, Paolo Ascenzi, Darío A Estrin, Luciana Capece, Sara E Bari","doi":"10.1007/s12551-025-01279-w","DOIUrl":"https://doi.org/10.1007/s12551-025-01279-w","url":null,"abstract":"The kinetics of ligand binding to ferric heme proteins is relevant in a variety of biochemical processes. With a few exceptions, ferric heme proteins at physiological pH typically show the sixth (distal) coordination position of the heme iron occupied by a water molecule. This contrasts with ferrous heme proteins, where this position is usually vacant in the absence of external ligands. In this review, we shed light on mechanistic aspects of this process, by discussing our recent results of binding of hydrogen sulfide and hydrosulfide (H2S/HS-) and disulfane and hydrodisulfide (HSSH/HSS-) to ferric microperoxidase 11 (MP11FeIII) and metmyoglobin (MbFeIII), as well as binding of peroxynitrous acid/peroxynitrite (ONOOH/ONOO-) to ferric M. tuberculosis nitrobindin (NbFeIII). Stopped flow experimental results of ligand binding rates as a function of pH can be analyzed with a mechanistic proposal consisting of ligand migration and ligand binding steps. Ligand migration to the active site was studied by using steered classical molecular dynamics simulations. The process of ligand binding substitution of the coordinated water molecule has been studied using hybrid quantum-classical (QM-MM) tools. Our results suggest that water molecule release is the critical event of the process in most of the cases, consistently with previous proposals. However, the scenario is complex, since water release depends subtly on the heme environment and may be also assisted by the acid-base behavior of the incoming ligands. Ligand migration may also play a key role in cases in which the active site entrance is hindered.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 2","pages":"293-300"},"PeriodicalIF":4.9,"publicationDate":"2025-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075716/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075657","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

Protein folding: basic statistical physics models and computational multipopulation genetic algorithms. 蛋白质折叠：基本统计物理模型和计算多种群遗传算法。

IF 4.9

Biophysical reviews Pub Date : 2025-02-10 eCollection Date: 2025-04-01 DOI: 10.1007/s12551-025-01281-2

Luis Olivares-Quiroz, Marcos Angel Gonzalez Olvera

引用次数: 0

Single-molecule magnetic tweezers to unravel protein folding dynamics under force. 单分子磁性镊子揭开蛋白质在外力作用下的折叠动力学。

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. 与Tamar Schlick一起收听《太空入侵者》播客：从数学到生物学的轨迹。

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. 《生物物理评论》特刊公开征稿，重点介绍现代生物物理方法的最新进展，并于2024年在喀山举行的俄罗斯秋季生物物理学校上进行了讨论。

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

Impact of ecological UV radiation on the photochemistry of nuclear DNA. 生态紫外线辐射对核DNA光化学的影响。

IF 4.9

Biophysical reviews Pub Date : 2025-01-28 eCollection Date: 2025-04-01 DOI: 10.1007/s12551-025-01275-0

Ana G Sánchez, Adriana Gabrielli, Deborah J Keszenman

{"title":"Impact of ecological UV radiation on the photochemistry of nuclear DNA.","authors":"Ana G Sánchez, Adriana Gabrielli, Deborah J Keszenman","doi":"10.1007/s12551-025-01275-0","DOIUrl":"https://doi.org/10.1007/s12551-025-01275-0","url":null,"abstract":"Solar radiation is predominantly Earth's natural ultraviolet (UV) radiation source. The biological effects of UV radiation have been the subject of scientific interest for decades. The most frequent and abundant types of DNA damage comprise the formation of cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone (6-4PP) photoproducts. Upon UVA excitation, the 6-4PPs may undergo an intramolecular 4π electrocyclization of the pyrimidone ring, arising photolesions known as Dewar isomers. The photochemistry pathways of UVA/UVB-induced DNA damage are discussed. Photosensitization-mediated reactions have traditionally been categorized as either oxygen-independent or oxygen-dependent. In oxygen-independent processes, the underlying mechanism involves triplet-triplet energy transfer. Among the reactive oxygen species (ROS) generated by UV radiation (1O2, O2 •-, •OH, H₂O₂), singlet oxygen (1O₂) is highly reactive and a primary contributor to oxidative DNA damage in cells and human skin following UVA exposure, as observed in the production of 8-oxoguanine (8-OxoG). The exposure of melanocytes to UV radiation upregulates nitric oxide synthase (NOS) and NADPH oxidase (NOX), producing nitric oxide and superoxide, which recombine to produce peroxynitrite. This highly oxidizing species is responsible for melanin chemiexcitation, producing carbonyl products that transfer energy to the DNA molecule to produce CPDs in the dark several hours after UV exposure ends. The peroxynitrite generated could also lead to other types of DNA damage, such as the formation of 8-nitroguanine (8-NitroG), which requires further study.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 2","pages":"537-545"},"PeriodicalIF":4.9,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12075728/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144075952","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