Biophysical reviews最新文献_第9页

Fifty years of biophysics in Argentina. 阿根廷生物物理学五十年。

IF 4.9

Biophysical reviews Pub Date : 2023-08-25 eCollection Date: 2023-08-01 DOI: 10.1007/s12551-023-01114-0

Silvia Del V Alonso, F Luis González Flecha

引用次数: 0

The Latin American Federation of Biophysical Societies (LAFeBS). 拉丁美洲生物物理协会联合会（LAFeBS）。

IF 4.9

Biophysical reviews Pub Date : 2023-08-22 eCollection Date: 2023-08-01 DOI: 10.1007/s12551-023-01119-9

Silvia Del Valle Alonso, Rosangela Itri, Leandro R S Barbosa, R Daniel Peluffo, F Luis González Flecha

引用次数: 0

Luciola mingrelica firefly luciferase as a marker in bioluminescent immunoassays. 萤火虫萤光素酶作为生物发光免疫测定的标记

IF 4.9

Biophysical reviews Pub Date : 2023-08-18 eCollection Date: 2023-10-01 DOI: 10.1007/s12551-023-01115-z

Galina Yu Lomakina, Natalia N Ugarova

{"title":"Luciola mingrelica firefly luciferase as a marker in bioluminescent immunoassays.","authors":"Galina Yu Lomakina, Natalia N Ugarova","doi":"10.1007/s12551-023-01115-z","DOIUrl":"10.1007/s12551-023-01115-z","url":null,"abstract":"Chemical modification of the enzymes with biospecific macromolecules is used in various fields of biotechnology to impart new functions or improve their properties and is a fast and convenient way to get the final products. The preparation of highly active, stable, and functionally active conjugates of the thermostable luciferase through the NH2-groups or free SH-groups of the enzyme with target molecules of different molecular weight (albumin, avidin from chicken eggs, antibodies, and progesterone) is described. The obtained conjugates were successfully tested as a reporter in bioluminescent immunoassay for the detection of the molecules and pathogens. Thus, the luc-albumin (Luc-Alb) and luc-insulin (Luc-Ins) conjugates were used in competitive ELISA for the detection of an analyte (albumin or insulin) in the samples. Luc-progesterone (Luc-Pg) was used in the rapid homogeneous immunoassay of progesterone by the BRET technique with the detection limit of 0.5 ng/ml. Luciferase conjugates with avidin (Luc-Avi) and secondary and primary antibodies (Luc-RAM and Luc-Sal) were used for enzyme immunoassay detection of Salmonella paratyphi A cells with the cell detection limit of 5 × 104 CFU/ml. To reduce the detection limit of Salmonella cells, we developed a pseudo-homogeneous bioluminescent enzyme immunoassay of cells using a new matrix for the analyte capture-polystyrene microparticles coated with Pluronic F108, covalently labeled with Sal antibodies. This allowed to achieve efficient trapping of cells from solution, significantly reduced nonspecific sorption and decreased the cell detection limit to 2.7 × 103 CFU/ml without prior concentration of the sample. The methodology that was developed in this study can be applied for the development of novel bioanalytical systems based on firefly luciferases.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2023-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10643422/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46908979","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

Approaches to vascular network, blood flow, and metabolite distribution modeling in brain tissue. 脑组织中血管网络、血流和代谢产物分布建模的方法

IF 4.9

Biophysical reviews Pub Date : 2023-08-18 eCollection Date: 2023-10-01 DOI: 10.1007/s12551-023-01106-0

Veronika Kopylova, Stanislav Boronovskiy, Yaroslav Nartsissov

{"title":"Approaches to vascular network, blood flow, and metabolite distribution modeling in brain tissue.","authors":"Veronika Kopylova, Stanislav Boronovskiy, Yaroslav Nartsissov","doi":"10.1007/s12551-023-01106-0","DOIUrl":"10.1007/s12551-023-01106-0","url":null,"abstract":"The cardiovascular system plays a key role in the transport of nutrients, ensuring a continuous supply of all cells of the body with the metabolites necessary for life. The blood supply to the brain is carried out by the large arteries located on its surface, which branch into smaller arterioles that penetrate the cerebral cortex and feed the capillary bed, thereby forming an extensive branching network. The formation of blood vessels is carried out via vasculogenesis and angiogenesis, which play an important role in both embryo and adult life. The review presents approaches to modeling various aspects of both the formation of vascular networks and the construction of the formed arterial tree. In addition, a brief description of models that allows one to study the blood flow in various parts of the circulatory system and the spatiotemporal metabolite distribution in brain tissues is given. Experimental study of these issues is not always possible due to both the complexity of the cardiovascular system and the mechanisms through which the perfusion of all body cells is carried out. In this regard, mathematical models are a good tool for studying hemodynamics and can be used in clinical practice to diagnose vascular diseases and assess the need for treatment.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2023-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10643724/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43220443","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

Role of hydrogen-bond networks on the donor side of photosynthetic reaction centers from purple bacteria. 氢键网络在紫色细菌光合反应中心供体侧的作用

IF 4.9

Biophysical reviews Pub Date : 2023-08-18 eCollection Date: 2023-10-01 DOI: 10.1007/s12551-023-01109-x

T Yu Fufina, L G Vasilieva

{"title":"Role of hydrogen-bond networks on the donor side of photosynthetic reaction centers from purple bacteria.","authors":"T Yu Fufina, L G Vasilieva","doi":"10.1007/s12551-023-01109-x","DOIUrl":"10.1007/s12551-023-01109-x","url":null,"abstract":"For the last decades, significant progress has been made in studying the biological functions of H-bond networks in membrane proteins, proton transporters, receptors, and photosynthetic reaction centers. Increasing availability of the X-ray crystal and cryo-electron microscopy structures of photosynthetic complexes resolved with high atomic resolution provides a platform for their comparative analysis. It allows identifying structural factors that are ensuring the high quantum yield of the photochemical reactions and are responsible for the stability of the membrane complexes. The H-bond networks are known to be responsible for proton transport associated with electron transfer from the primary to the secondary quinone as well as in the processes of water oxidation in photosystem II. Participation of such networks in reactions proceeding on the periplasmic side of bacterial photosynthetic reaction centers is less studied. This review summarizes the current understanding of the role of H-bond networks on the donor side of photosynthetic reaction centers from purple bacteria. It is discussed that the networks may be involved in providing close association with mobile electron carriers, in light-induced proton transport, in regulation of the redox properties of bacteriochlorophyll cofactors, and in stabilization of the membrane protein structure at the interface of membrane and soluble phases.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2023-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10643783/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48017341","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

Thermodynamic and mechanistic analysis of the functional properties of dengue virus NS3 helicase. 登革热病毒 NS3 螺旋酶功能特性的热力学和机理分析。

IF 4.9

Biophysical reviews Pub Date : 2023-08-17 eCollection Date: 2023-08-01 DOI: 10.1007/s12551-023-01101-5

J Jeremías Incicco, Leila A Cababie, Carolina Sarto, Natalia S Adler, Fernando Amrein, Evelyn Mikkelsen, Mehrnoosh Arrar, Sergio B Kaufman

引用次数: 0

Protein translational diffusion as a way to detect intermolecular interactions. 蛋白质翻译扩散作为一种检测分子间相互作用的方法

IF 4.9

Biophysical reviews Pub Date : 2023-08-16 eCollection Date: 2023-10-01 DOI: 10.1007/s12551-023-01108-y

Yuriy F Zuev, Aleksandra M Kusova, Aleksandr E Sitnitsky

{"title":"Protein translational diffusion as a way to detect intermolecular interactions.","authors":"Yuriy F Zuev, Aleksandra M Kusova, Aleksandr E Sitnitsky","doi":"10.1007/s12551-023-01108-y","DOIUrl":"10.1007/s12551-023-01108-y","url":null,"abstract":"In this work, we analyze the information on the protein intermolecular interactions obtained from macromolecular diffusion. We have shown that the most hopeful results are given by our approach based on analysis of protein translational self-diffusion and collective diffusion obtained by dynamic light scattering and pulsed-field gradient NMR (PFG NMR) spectroscopy with the help of Vink's approach to analyze diffusion motion of particles by frictional formalism of non-equilibrium thermodynamics and the usage of the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory of colloid particles interactions in electrolyte solutions. Early we have shown that integration of Vink's theory with DLVO provides a reliable basis for uniform interpreting of PFG NMR and DLS experiments on concentration dependence of diffusion coefficients. Basic details of theoretical and mathematical procedures and a broad analysis of experimental attestation of proposed conception on proteins of various structural form, size, and shape are presented. In the present review, the main capabilities of our approach obtain the details of intermolecular interactions of proteins with different shapes, internal structures, and mass. The universality of Vink's approach is experimentally shown, which gives the appropriate description of experimental results for proteins of complicated structure and shape.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2023-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10643801/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46868742","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

Mathematical models describing oxygen binding by hemoglobin. 描述血红蛋白结合氧的数学模型

IF 4.9

Biophysical reviews Pub Date : 2023-08-16 eCollection Date: 2023-10-01 DOI: 10.1007/s12551-023-01110-4

Igor A Lavrinenko, Gennady A Vashanov, José L Hernández Cáceres, Yury D Nechipurenko

{"title":"Mathematical models describing oxygen binding by hemoglobin.","authors":"Igor A Lavrinenko, Gennady A Vashanov, José L Hernández Cáceres, Yury D Nechipurenko","doi":"10.1007/s12551-023-01110-4","DOIUrl":"10.1007/s12551-023-01110-4","url":null,"abstract":"Despite the fact that the investigation of the structural and functional properties of hemoglobin dates back more than 150 years, the topic has not lost its relevance today. The most important component of these studies is the development of mathematical models that formalize and generalize the mechanisms determining the cooperative binding of ligands based on data on the structural and functional state of the protein. In this work, we review the mathematical relationships describing oxygen binding by hemoglobin, ranging from the classical Hüfner, Hill, and Adair equations to the Szabo-Karplus and tertiary two-state mathematical models based on the Monod-Wyman-Changeux and Koshland-Némethy-Filmer concepts. The generality of the considered equations as mathematical functions, bearing in their basis a power dependence, is demonstrated. The problems and possible solutions related to approximation of experimental data by the oxygenation equations with correlated fitting parameters are noted. Attention is paid to empirical equations, extended versions of the Hill equation, where the coefficient of cooperation is modulated by Gauss and Lorentz distributions as functions of partial oxygen pressure.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2023-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10643423/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44593516","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 nanocondensates: the next frontier. 蛋白质纳米凝结物：下一个前沿领域。

IF 4.9

Biophysical reviews Pub Date : 2023-08-09 eCollection Date: 2023-08-01 DOI: 10.1007/s12551-023-01105-1

Pamela L Toledo, Alejo R Gianotti, Diego S Vazquez, Mario R Ermácora

{"title":"Protein nanocondensates: the next frontier.","authors":"Pamela L Toledo, Alejo R Gianotti, Diego S Vazquez, Mario R Ermácora","doi":"10.1007/s12551-023-01105-1","DOIUrl":"10.1007/s12551-023-01105-1","url":null,"abstract":"Over the past decade, myriads of studies have highlighted the central role of protein condensation in subcellular compartmentalization and spatiotemporal organization of biological processes. Conceptually, protein condensation stands at the highest level in protein structure hierarchy, accounting for the assembly of bodies ranging from thousands to billions of molecules and for densities ranging from dense liquids to solid materials. In size, protein condensates range from nanocondensates of hundreds of nanometers (mesoscopic clusters) to phase-separated micron-sized condensates. In this review, we focus on protein nanocondensation, a process that can occur in subsaturated solutions and can nucleate dense liquid phases, crystals, amorphous aggregates, and fibers. We discuss the nanocondensation of proteins in the light of general physical principles and examine the biophysical properties of several outstanding examples of nanocondensation. We conclude that protein nanocondensation cannot be fully explained by the conceptual framework of micron-scale biomolecular condensation. The evolution of nanocondensates through changes in density and order is currently under intense investigation, and this should lead to the development of a general theoretical framework, capable of encompassing the full range of sizes and densities found in protein condensates.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2023-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10480383/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10180614","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 role of water in reactions catalysed by hydrolases under conditions of molecular crowding. 分子拥挤条件下水在水解酶催化反应中的作用。

IF 4.9

Biophysical reviews Pub Date : 2023-08-09 eCollection Date: 2023-08-01 DOI: 10.1007/s12551-023-01104-2

Maria A Perillo, Inés Burgos, Eduardo M Clop, Julieta M Sanchez, Verónica Nolan

{"title":"The role of water in reactions catalysed by hydrolases under conditions of molecular crowding.","authors":"Maria A Perillo, Inés Burgos, Eduardo M Clop, Julieta M Sanchez, Verónica Nolan","doi":"10.1007/s12551-023-01104-2","DOIUrl":"10.1007/s12551-023-01104-2","url":null,"abstract":"Under macromolecular crowding (MC) conditions such as cellular, extracellular, food and other environments of biotechnological interest, the thermodynamic activity of the different macromolecules present in the system is several orders of magnitude higher than in dilute solutions. In this state, the diffusion rates are affected by the volume exclusion induced by the crowders. Immiscible liquid phases, which may arise in MC by liquid-liquid phase separation, may induce a dynamic confinement of reactants, products and/or enzymes, tuning reaction rates. In cellular environments and other crowding conditions, membranes and macromolecules provide, on the whole, large surfaces that can perturb the solvent, causing its immobilisation by adsorption in the short range and also affecting the solvent viscosity in the long range. The latter phenomenon can affect the conformation of a protein and/or the degree of association of its protomers and, consequently, its activity. Changes in the water structure can also alter the enzyme-substrate interaction, and, in the case of hydrolytic enzymes, where water is one of the substrates, it also affects the reaction mechanism. Here, we review the evidence for how macromolecular crowding affects the catalysis induced by hydrolytic enzymes, focusing on the structure and dynamics of water.","PeriodicalId":9094,"journal":{"name":"Biophysical reviews","volume":null,"pages":null},"PeriodicalIF":4.9,"publicationDate":"2023-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10480385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10189650","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