European Biophysics Journal最新文献_第9页

Experimental support for reclassification of the light scattering second virial coefficient from macromolecular solutions as a hydrodynamic parameter 大分子溶液光散射二次维里系数作为水动力参数重新分类的实验支持

IF 2 4区生物学

European Biophysics Journal Pub Date : 2023-07-18 DOI: 10.1007/s00249-023-01665-w

Donald J. Winzor, Vlad Dinu, David J. Scott, Stephen E. Harding

{"title":"Experimental support for reclassification of the light scattering second virial coefficient from macromolecular solutions as a hydrodynamic parameter","authors":"Donald J. Winzor, Vlad Dinu, David J. Scott, Stephen E. Harding","doi":"10.1007/s00249-023-01665-w","DOIUrl":"10.1007/s00249-023-01665-w","url":null,"abstract":"<div><p>This investigation examines the source of the disparity between experimental values of the light scattering second virial coefficient <span>({A}_{2})</span> (mL.mol/g<sup>2</sup>) for proteins and those predicted on the statistical mechanical basis of excluded volume. A much better theoretical description of published results for lysozyme is obtained by considering the experimental parameters to monitor the difference between the thermodynamic excluded volume term and its hydrodynamic counterpart. This involves a combination of parameters quantifying concentration dependence of the translational diffusion coefficient obtained from dynamic light scattering measurements. That finding is shown to account for observations of a strong correlation between <span>({A}_{2}{M}_{2})</span> (mL/g), where <i>M</i><sub>2</sub> is the molar mass (molecular weight) of the macromolecule and the diffusion concentration parameter <span>({k}_{D})</span> (mL/g). On the grounds that <span>({k}_{D})</span> is regarded as a hydrodynamic parameter, the same status should be accorded the light scattering second virial coefficient rather than its current incorrect thermodynamic designation as <span>({B}_{2})</span> (mL.mol/g<sup>2</sup>), or just <i>B</i>, the osmotic second virial coefficient for protein self-interaction.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"52 4-5","pages":"343 - 352"},"PeriodicalIF":2.0,"publicationDate":"2023-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-023-01665-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4723022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

14th EBSA congress, July 31 – August 4, 2023, Stockholm, Sweden – Abstracts 第14届EBSA大会，2023年7月31日- 8月4日，瑞典斯德哥尔摩-摘要

IF 2 4区生物学

European Biophysics Journal Pub Date : 2023-07-12 DOI: 10.1007/s00249-023-01668-7

引用次数: 0

Retrospective rationalization of disparities between the concentration dependence of diffusion coefficients obtained by boundary spreading and dynamic light scattering 由边界扩散和动态光散射得到的扩散系数的浓度依赖性差异的回顾性合理化

IF 2 4区生物学

European Biophysics Journal Pub Date : 2023-07-07 DOI: 10.1007/s00249-023-01664-x

Donald J. Winzor, Vlad Dinu, David J. Scott, Stephen E. Harding

{"title":"Retrospective rationalization of disparities between the concentration dependence of diffusion coefficients obtained by boundary spreading and dynamic light scattering","authors":"Donald J. Winzor, Vlad Dinu, David J. Scott, Stephen E. Harding","doi":"10.1007/s00249-023-01664-x","DOIUrl":"10.1007/s00249-023-01664-x","url":null,"abstract":"<div><p>This study establishes the existence of substantial agreement between published results from traditional boundary spreading measurements (including synthetic boundary measurements in the analytical ultracenrifuge) on two globular proteins (bovine serum albumin, ovalbumin) and the concentration dependence of diffusion coefficient predicted for experiments conducted under the operative thermodynamic constraints of constant temperature and solvent chemical potential. Although slight negative concentration dependence of the translational diffusion coefficient is the experimentally observed as well as theoretically predicted, the extent of the concentration dependence is within the limits of experimental uncertainty inherent in diffusion coefficient measurement. Attention is then directed toward the ionic strength dependence of the concentration dependence coefficient (<span>({k}_{D})</span>) describing diffusion coefficients obtained by dynamic light scattering, where, in principle, the operative thermodynamic constraints of constant temperature and pressure preclude consideration of results in terms of single-solute theory. Nevertheless, good agreement between predicted and published experimental ionic strength dependencies of <span>({k}_{D})</span> for lysozyme and an immunoglobulin is observed by a minor adaptation of the theoretical treatment to accommodate the fact that thermodynamic activity is monitored on the molal concentration scale because of the constraint of constant pressure that pertains in dynamic light scattering experiments.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"52 4-5","pages":"333 - 342"},"PeriodicalIF":2.0,"publicationDate":"2023-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-023-01664-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4306114","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Energy spectrum of the ideal DNA knot on a torus 圆环上理想DNA结的能谱。

IF 2 4区生物学

European Biophysics Journal Pub Date : 2023-07-01 DOI: 10.1007/s00249-023-01670-z

Xuguang Shi

引用次数: 1

The cross-correlation-based analysis to digest the conformational dynamics of the mitoBK channels in terms of their modulation by flavonoids 基于互相关的分析，以消化mitoBK通道在黄酮类化合物调节方面的构象动力学。

IF 2 4区生物学

European Biophysics Journal Pub Date : 2023-06-30 DOI: 10.1007/s00249-023-01666-9

Agata Wawrzkiewicz-Jałowiecka, Paulina Trybek, Beata Dworakowska, Piotr Bednarczyk, Przemysław Borys

{"title":"The cross-correlation-based analysis to digest the conformational dynamics of the mitoBK channels in terms of their modulation by flavonoids","authors":"Agata Wawrzkiewicz-Jałowiecka, Paulina Trybek, Beata Dworakowska, Piotr Bednarczyk, Przemysław Borys","doi":"10.1007/s00249-023-01666-9","DOIUrl":"10.1007/s00249-023-01666-9","url":null,"abstract":"<div><p>The activity of mitochondrial large-conductance voltage- and <span>(Ca^{2+})</span>-activated <span>(K^+)</span> channels (mitoBK) is regulated by a number of biochemical factors, including flavonoids. In particular, naringenin (Nar) and quercetin (Que) reached reasonable scientific attention due to their well-pronounced channel-activating effects. The open-reinforcing outcomes of Nar and Que on the mitoBK channel gating have been already reported. Nevertheless, the molecular picture of the corresponding channel–ligand interactions remains still to be revealed. In this work, we investigate the effects of the Nar and Que on the conformational dynamics of the mitoBK channel. In this aim, the cross-correlation-based analysis of the single-channel signals recorded by the patch-clamp method is performed. The obtained results in the form of phase space diagrams enable us to visually monitor the effects exerted by the considered flavonoids at the level of temporal characteristics of repetitive sequences of channel conformations. It turns out that the mitoBK channel activation by naringenin and quercetin does not lead to the change in the number of clusters within the phase space diagrams, which can be related to the constant number of available channel macroconformations regardless of the flavonoid administration. The localization and occupancy of the clusters of cross-correlated sequences suggest that mitoBK channel stimulation by flavonoids affects the relative stability of channel conformations and the kinetics of switching between them. For most clusters, greater net effects are observed in terms of quercetin administration in comparison with naringenin. It indicates stronger channel interaction with Que than Nar.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"52 6-7","pages":"569 - 582"},"PeriodicalIF":2.0,"publicationDate":"2023-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9696920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Choosing the right density for a concentrated protein system like gluten in a coarse-grained model 为粗粒模型中的面筋等浓缩蛋白质系统选择合适的密度。

IF 2 4区生物学

European Biophysics Journal Pub Date : 2023-06-28 DOI: 10.1007/s00249-023-01667-8

Łukasz Mioduszewski

引用次数: 0

Twist-stretch relations in nucleic acids 核酸中的扭转-拉伸关系。

IF 2 4区生物学

European Biophysics Journal Pub Date : 2023-06-25 DOI: 10.1007/s00249-023-01669-6

Marco Zoli

引用次数: 0

A model for ribosome translocation based on the alternated displacement of its subunits 基于核糖体亚基交替位移的核糖体易位模型

IF 2 4区生物学

European Biophysics Journal Pub Date : 2023-06-09 DOI: 10.1007/s00249-023-01662-z

José S. González-García

{"title":"A model for ribosome translocation based on the alternated displacement of its subunits","authors":"José S. González-García","doi":"10.1007/s00249-023-01662-z","DOIUrl":"10.1007/s00249-023-01662-z","url":null,"abstract":"<div><p>A meaningful dilemma in ribosome translocation arising from experimental facts is that, although the ribosome–mRNA interaction force always has a significant magnitude, the ribosome still moves to the next codon on the mRNA. How does the ribosome move to the next codon in the sequence while holding the mRNA tightly? The hypothesis proposed here is that ribosome subunits alternate the grip of the ribosome on the mRNA, freeing the other subunit of such interaction for a while, thus allowing its motion to the following codon. Based on this assumption, a single-loop cycle of ribosome configurations involving the relative position of its subunits is elaborated. When its dynamic is modeled as a Markov network, it gives expressions for the average ribosome translocation speed and stall force as functions of the equilibrium constants among the proposed ribosome configurations. The calculations have a reasonable agreement with experimental results, and the succession of molecular events considered here is consistent with current biomolecular concepts of the ribosome translocation process. Thus, the alternative displacements hypothesis developed in the present work suggests a feasible explanation of ribosome translocation.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"52 3","pages":"175 - 187"},"PeriodicalIF":2.0,"publicationDate":"2023-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-023-01662-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"4389740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Determination of mRNA copy number in degradable lipid nanoparticles via density contrast analytical ultracentrifugation 密度对比分析超离心法测定可降解脂质纳米颗粒mRNA拷贝数

IF 2 4区生物学

European Biophysics Journal Pub Date : 2023-06-08 DOI: 10.1007/s00249-023-01663-y

Alexander Bepperling, Gesa Richter

引用次数: 1

Pulling short DNA with mismatch base pairs 提取碱基对不匹配的短DNA

IF 2 4区生物学

European Biophysics Journal Pub Date : 2023-05-30 DOI: 10.1007/s00249-023-01659-8

Navin Singh, Nehal Mathur

引用次数: 0