Biophysical reviews最新文献_第3页

Analyzing aptamer structure and interactions: in silico modelling and instrumental methods. 分析适体结构和相互作用：在硅建模和仪器方法。

IF 4.9

Biophysical reviews Pub Date : 2024-11-20 eCollection Date: 2024-12-01 DOI: 10.1007/s12551-024-01252-z

Daria O Malysheva, Maya A Dymova, Vladimir A Richter

{"title":"Analyzing aptamer structure and interactions: in silico modelling and instrumental methods.","authors":"Daria O Malysheva, Maya A Dymova, Vladimir A Richter","doi":"10.1007/s12551-024-01252-z","DOIUrl":"10.1007/s12551-024-01252-z","url":null,"abstract":"Aptamers are short oligonucleotides that bind specifically to various ligands and are characterized by their low immunogenicity, thermostability, and ease of labeling. Many biomedical applications of aptamers as biosensors and drug delivery agents are currently being actively researched. Selective affinity selection with exponential ligand enrichment (SELEX) allows to discover aptamers for a specific target, but it only provides information about the sequence of aptamers; hence other approaches are used for determining aptamer structure, aptamer-ligand interactions and the mechanism of action. The first one is in silico modelling that allows to infer likely secondary and tertiary structures and model their interactions with a ligand. The second approach is to use instrumental methods to study structure and aptamer-ligand interaction. In silico modelling and instrumental methods are complimentary and their combined use allows to eliminate some ambiguity in their respective results. This review examines both the advantages and limitations of in silico modelling and instrumental approaches currently used to study aptamers, which will allow researchers to develop optimal study designs for analyzing aptamer structure and ligand interactions.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 6","pages":"685-700"},"PeriodicalIF":4.9,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11735759/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143000019","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

Survey of the Aβ-peptide structural diversity: molecular dynamics approaches. a - β肽结构多样性的研究：分子动力学方法。

IF 4.9

Biophysical reviews Pub Date : 2024-11-20 eCollection Date: 2024-12-01 DOI: 10.1007/s12551-024-01253-y

Anna P Tolstova, Alexei A Adzhubei, Maria A Strelkova, Alexander A Makarov, Vladimir A Mitkevich

引用次数: 0

Diatoms: harnessing nature's microscopic marvels for biosensing and multifaceted applications. 硅藻：利用自然界的微观奇迹进行生物传感和多方面的应用。

IF 4.9

Biophysical reviews Pub Date : 2024-11-05 eCollection Date: 2025-02-01 DOI: 10.1007/s12551-024-01249-8

Krupa Bhat, Maryam Abdul Ajees, Pawas Kumar, Vibha, Vyasraj G Bhat, Roopa Nayak, Nirmal Mazumder

{"title":"Diatoms: harnessing nature's microscopic marvels for biosensing and multifaceted applications.","authors":"Krupa Bhat, Maryam Abdul Ajees, Pawas Kumar, Vibha, Vyasraj G Bhat, Roopa Nayak, Nirmal Mazumder","doi":"10.1007/s12551-024-01249-8","DOIUrl":"10.1007/s12551-024-01249-8","url":null,"abstract":"This article discusses the use of diatom in biosensing and various applications. A thorough understanding of the biosensing properties of diatoms is essential for the advancement of life sciences technologies. This review elucidates the emerging significance of diatoms in biosensing applications by highlighting the high surface area-to-volume ratio, biocompatibility, and facile functionalization of them. We examined the possible application of diatoms as flexible biosensing systems for the detection of various analytes, such as biological molecules, heavy metals, and poisons, by considering the findings of earlier research. Additionally, to show how diatoms can be used to create precise and sensitive biosensors, by integrating with several transduction modalities, including optical, electrochemical, and piezoelectric methods. We also delve into the potential applications of diatom-based biosensing in the future as well as pertinent topics such as repeatability, stability, and scalability. This provides an in-depth analysis of the quickly evolving field of diatom-based biosensing, which could affect several industries, such as environmental monitoring, food security and medical diagnostics.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"17 1","pages":"103-125"},"PeriodicalIF":4.9,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11885778/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584711","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

The dry lab microscopist or prompt microscopist: do we need them? 干式实验室显微镜师或即时显微镜师：我们需要他们吗？

IF 4.9

Biophysical reviews Pub Date : 2024-10-30 eCollection Date: 2024-12-01 DOI: 10.1007/s12551-024-01250-1

Filip Braet, Weidong Cai

引用次数: 0

Structure, function, and biophysics of bacterial motility and the flagellar motor-IUPAB2024 session commentary. 细菌运动和鞭毛运动的结构，功能和生物物理学- iupab2024会议评论。

IF 4.9

Biophysical reviews Pub Date : 2024-10-28 eCollection Date: 2024-10-01 DOI: 10.1007/s12551-024-01243-0

Matthew A B Baker, Seiji Kojima

引用次数: 0

Friction in soft biological systems and surface self-organization: the role of viscoelasticity. 软生物系统中的摩擦与表面自组织：粘弹性的作用。

IF 4.9

Biophysical reviews Pub Date : 2024-10-28 eCollection Date: 2024-12-01 DOI: 10.1007/s12551-024-01248-9

Ivana Pajic-Lijakovic, Milan Milivojevic, Peter V E McClintock

引用次数: 0

Meet the IUPAB Councillor: A/Prof Matthew AB Baker (UNSW Sydney, Australia). 会见IUPAB委员：A/ Matthew AB Baker教授（澳大利亚悉尼新南威尔士大学）。

IF 4.9

Biophysical reviews Pub Date : 2024-10-28 eCollection Date: 2024-10-01 DOI: 10.1007/s12551-024-01240-3

Matthew A B Baker

引用次数: 0

Mechanobiology of 3D cell confinement and extracellular crowding. 三维细胞禁闭和细胞外拥挤的力学生物学。

IF 4.9

Biophysical reviews Pub Date : 2024-10-23 eCollection Date: 2024-12-01 DOI: 10.1007/s12551-024-01244-z

Gabriela Da Silva André, Céline Labouesse

{"title":"Mechanobiology of 3D cell confinement and extracellular crowding.","authors":"Gabriela Da Silva André, Céline Labouesse","doi":"10.1007/s12551-024-01244-z","DOIUrl":"10.1007/s12551-024-01244-z","url":null,"abstract":"Cells and tissues are often under some level of confinement, imposed by the microenvironment and neighboring cells, meaning that there are limitations to cell size, volume changes, and fluid exchanges. 3D cell culture, increasingly used for both single cells and organoids, inherently impose levels of confinement absent in 2D systems. It is thus key to understand how different levels of confinement influences cell survival, cell function, and cell fate. It is well known that the mechanical properties of the microenvironment, such as stiffness and stress relaxation, are important in activating mechanosensitive pathways, and these are responsive to confinement conditions. In this review, we look at how low, intermediate, and high levels of confinement modulate the activation of known mechanobiology pathways, in single cells, organoids, and tumor spheroids, with a specific focus on 3D confinement in microwells, elastic, or viscoelastic scaffolds. In addition, a confining microenvironment can drastically limit cellular communication in both healthy and diseased tissues, due to extracellular crowding. We discuss potential implications of extracellular crowding on molecular transport, extracellular matrix deposition, and fluid transport. Understanding how cells sense and respond to various levels of confinement should inform the design of 3D engineered matrices that recapitulate the physical properties of tissues.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 6","pages":"833-849"},"PeriodicalIF":4.9,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11735831/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142999969","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

"Meet the IUPAB councilor"-Thomas Gutsmann. “见见IUPAB委员”——托马斯·古斯曼。

IF 4.9

Biophysical reviews Pub Date : 2024-10-21 eCollection Date: 2024-10-01 DOI: 10.1007/s12551-024-01226-1

Thomas Gutsmann

{"title":"\"Meet the IUPAB councilor\"-Thomas Gutsmann.","authors":"Thomas Gutsmann","doi":"10.1007/s12551-024-01226-1","DOIUrl":"https://doi.org/10.1007/s12551-024-01226-1","url":null,"abstract":"As one of the twelve newly elected councillors, it is my pleasure to provide a brief biographical sketch for the readers of Biophys. Rev. and the members of the Biophysical Societies. I have been actively involved in the German Biophysical Society (DGfB) since 2008, initially as the speaker for the \"Membrane Biophysics\" section and, since 2015, as the secretary. Within the IUPAB council I follow Prof. Hans-Joachim Galla, former Secretary and President of the German Biophysical Society, who served as a councillor for two terms from 2018 to 2024. Thus, a direct continuation of the German contribution to the IUPAB is guaranteed. My journey in biophysics began during my studies of physics at the University of Kiel, where I specialized in physiology and biophysics. After earning my doctorate in the lab of Ulrich Seydel at the Research Center Borstel, I spent two years at the University of California, Santa Barbara, working in Paul Hansma's lab on the development and application of atomic force microscopy. During my time at UCSB, I also collaborated with Jacob Israelachvili's lab on membrane properties. Since 2008, I have been leading the Biophysics Research Group at the Research Center Borstel, Leibniz Lung Center. In 2010, I was appointed as a professor at the University of Lübeck. Additionally, since 2023, I have been serving as an associate member at the Centre for Structural Systems Biology (CSSB) in Hamburg.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 5","pages":"515-517"},"PeriodicalIF":4.9,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11604882/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142766096","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

Structural changes in troponin during activation of skeletal and heart muscle determined in situ by polarised fluorescence. 在骨骼肌和心肌激活过程中肌钙蛋白的结构变化通过极化荧光原位测定。

IF 4.9

Biophysical reviews Pub Date : 2024-10-19 eCollection Date: 2024-12-01 DOI: 10.1007/s12551-024-01245-y

Ivanka R Sevrieva, Thomas Kampourakis, Malcolm Irving

{"title":"Structural changes in troponin during activation of skeletal and heart muscle determined in situ by polarised fluorescence.","authors":"Ivanka R Sevrieva, Thomas Kampourakis, Malcolm Irving","doi":"10.1007/s12551-024-01245-y","DOIUrl":"10.1007/s12551-024-01245-y","url":null,"abstract":"Calcium binding to troponin triggers the contraction of skeletal and heart muscle through structural changes in the thin filaments that allow myosin motors from the thick filaments to bind to actin and drive filament sliding. Here, we review studies in which those changes were determined in demembranated fibres of skeletal and heart muscle using fluorescence for in situ structure (FISS), which determines domain orientations using polarised fluorescence from bifunctional rhodamine attached to cysteine pairs in the target domain. We describe the changes in the orientations of the N-terminal lobe of troponin C (TnCN) and the troponin IT arm in skeletal and cardiac muscle cells associated with contraction and compare the orientations with those determined in isolated cardiac thin filaments by cryo-electron microscopy. We show that the orientations of the IT arm determined by the two approaches are essentially the same and that this region acts as an almost rigid scaffold for regulatory changes in the more mobile regions of troponin. However, the TnCN orientations determined by the two methods are clearly distinct in both low- and high-calcium conditions. We discuss the implications of these results for the role of TnCN in mediating the multiple signalling pathways acting through troponin in heart muscle cells and the general advantages and limitations of FISS and cryo-EM for determining protein domain orientations in cells and multiprotein complexes.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":"16 6","pages":"753-772"},"PeriodicalIF":4.9,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11735716/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142999958","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