European Biophysics Journal最新文献

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15th EBSA congress, June 30 - July 4, 2025, Rome, Italy - Abstracts. 第15届EBSA大会,2025年6月30日至7月4日,意大利罗马-摘要。
IF 2.2 4区 生物学
European Biophysics Journal Pub Date : 2025-06-01 DOI: 10.1007/s00249-025-01757-9
{"title":"15th EBSA congress, June 30 - July 4, 2025, Rome, Italy - Abstracts.","authors":"","doi":"10.1007/s00249-025-01757-9","DOIUrl":"https://doi.org/10.1007/s00249-025-01757-9","url":null,"abstract":"","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"54 Suppl 1","pages":"1-273"},"PeriodicalIF":2.2,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144197974","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
Bead model hydrodynamics: an in-depth comparison between GRPY and ZENO. 头部模型流体动力学:GRPY和ZENO的深入比较。
IF 2.2 4区 生物学
European Biophysics Journal Pub Date : 2025-05-29 DOI: 10.1007/s00249-025-01758-8
Emre Brookes, Pawel J Żuk, Mattia Rocco
{"title":"Bead model hydrodynamics: an in-depth comparison between GRPY and ZENO.","authors":"Emre Brookes, Pawel J Żuk, Mattia Rocco","doi":"10.1007/s00249-025-01758-8","DOIUrl":"https://doi.org/10.1007/s00249-025-01758-8","url":null,"abstract":"<p><p>Comparing experimental and calculated hydrodynamic properties of (bio)-macromolecules, such as the translational diffusion coefficient <math><msubsup><mi>D</mi> <mrow><mi>t</mi> <mo>(</mo> <mn>20</mn> <mo>,</mo> <mi>w</mi> <mo>)</mo></mrow> <mn>0</mn></msubsup> </math> and the intrinsic viscosity [η], is a useful strategy for the validation of predicted and/or solved atomic-level structures. Bead modeling is a prominent methodology, with several computational tools available. The program GRPY (Generalized Rotne-Prager-Yamakawa) allows the hydrodynamic calculations to be performed at the one-atom one-bead scale, allowing overlaps, but it is computer intensive with CPU requirements depending on the number of beads N as ~ N<sup>3</sup>. The program ZENO, based on the electrostatics-hydrodynamics analogy and using a Monte Carlo numerical path integration, can compute <math><msubsup><mi>D</mi> <mrow><mi>t</mi> <mo>(</mo> <mn>20</mn> <mo>,</mo> <mi>w</mi> <mo>)</mo></mrow> <mn>0</mn></msubsup> </math> and [η] directly on bead models, and it is almost independent of the target size. Since bead models are a very efficient way to include the hydration effect when dealing with bio-macromolecules, we present here an in-depth comparison between GRPY and ZENO, both as implemented in the US-SOMO suite. Relatively low but systematic differences (0.2-2%, increasing with model size) appear when using bead models of proteins at the residue- or atomic-level scales. When comparing the results provided on a restricted set of bead models by two other computationally intensive methods having other drawbacks, the very accurate but not handling overlaps HYDROMULTIPOLE, and the boundary elements BEST requiring extrapolation, GRPY was found to fare better than ZENO. While efforts are in progress to directly improve the ZENO performance, a heuristic correction based on the results for a series of protein bead models is proposed, allowing for a better consistency with GRPY.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144172055","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
Structural and functional characterization of Caenorhabditis elegans cyclic GMP-activated channel TAX-4 via molecular dynamics simulations. 通过分子动力学模拟研究秀丽隐杆线虫环gmp激活通道TAX-4的结构和功能。
IF 2.2 4区 生物学
European Biophysics Journal Pub Date : 2025-05-27 DOI: 10.1007/s00249-025-01756-w
Nicole Luchetti, Marco Lauricella, Velia Minicozzi, Grazia Cottone, Letizia Chiodo
{"title":"Structural and functional characterization of Caenorhabditis elegans cyclic GMP-activated channel TAX-4 via molecular dynamics simulations.","authors":"Nicole Luchetti, Marco Lauricella, Velia Minicozzi, Grazia Cottone, Letizia Chiodo","doi":"10.1007/s00249-025-01756-w","DOIUrl":"https://doi.org/10.1007/s00249-025-01756-w","url":null,"abstract":"<p><p>Cyclic nucleotide-gated (CNG) ion channels are crucial to the intracellular calcium dynamics in neurons and other sensory cells, in several organisms. Mutations in CNG genes are linked to various dysfunctions and diseases. In this work, we propose a theoretical investigation of the structural and functional properties of wild-type TAX-4, a non-selective CNG ion channel, expressed in various sensory neurons of Caenorhabditis elegans, and involved in the permeation of monovalent and multivalent cations. Using a recent cryo-electron microscopy structure of the open state of the channel as the starting conformation, we conduct all-atom molecular dynamics simulations of the full-length channel in a membrane/water/ions system, both in the cGMP-bound and unbound conformations. Several channel structural descriptors are examined and a first-level functional annotation is carried out, on the microsecond time scale. A comparison with the available experimental data on TAX-4 and human homologues allows us to assign the simulated bound and unbound models as the pre-open and closed conformations of TAX-4, respectively. Comparisons between the bound and unbound conformations enable us to suggest key conformational changes underlying the binding-to-gating transition.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144148971","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
Competitive adsorption of a monoclonal antibody and amphiphilic polymers to the air-water interface. 单克隆抗体和两亲性聚合物在空气-水界面上的竞争吸附。
IF 2.2 4区 生物学
European Biophysics Journal Pub Date : 2025-05-22 DOI: 10.1007/s00249-025-01752-0
Elise J Hingst, Michaela Blech, Dariush Hinderberger, Patrick Garidel, Christian Schwieger
{"title":"Competitive adsorption of a monoclonal antibody and amphiphilic polymers to the air-water interface.","authors":"Elise J Hingst, Michaela Blech, Dariush Hinderberger, Patrick Garidel, Christian Schwieger","doi":"10.1007/s00249-025-01752-0","DOIUrl":"https://doi.org/10.1007/s00249-025-01752-0","url":null,"abstract":"<p><p>Understanding the structure and self-organisation of monoclonal antibodies (mAbs) at the air-water interface is crucial for the stability and efficacy of protein drug formulations. This paper investigates the competitive adsorption of mAb and two amphiphilic polymers, poloxamer 188 (P188) and polysorbate 20 (PS20), commonly used to stabilise mAb formulations. Our objective was twofold: to ascertain whether the surfactants in question are capable of preventing mAb adsorption; and to determine whether it is possible to desorb mAb molecules from the air-water interface by surfactant addition. Langmuir film balance measurements and drop shape tensiometry were used to obtain surface pressure and surface tension data. Infrared Reflection-Absorption Spectroscopy (IRRAS) provided information on the surface composition, including the amount of adsorbed molecules. The state adopted by P188 is contingent upon its surface concentration, which determines the self-assembled phases it adopts. We show that the phase state of P188 has a considerable influence on mAb adsorption. The presence of P188 in the brush phase (≥ 0.3 mg/L) consistently inhibits mAb adsorption, but addition of P188 subsequent to the formation of the mAb film does not result in mAb desorption. However, addition of PS20 results in the desorption of freshly-formed interfacial mAb layers of up to two hours' age, whereas an aged mAb layer of 17 h was unable to be desorbed by PS20. Thus there is a time-dependent reorganisation of mAb at the air-water interface, increasing resistance to desorption, which we discuss in the context of potential intermolecular interactions within the interfacial film.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126208","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
Use of cesium chloride density gradient ultracentrifugation for the purification and characterization of recombinant adeno-associated virus. 利用氯化铯密度梯度超离心纯化和鉴定重组腺相关病毒。
IF 2.2 4区 生物学
European Biophysics Journal Pub Date : 2025-05-19 DOI: 10.1007/s00249-025-01751-1
Kiichi Hirohata, Shinichiro Kino, Takuya Yamane, Karin Bandoh, Takeshi Bamba, Shawn M Sternisha, Tetsuo Torisu, Mitsuko Fukuhara, Yuki Yamaguchi, Susumu Uchiyama
{"title":"Use of cesium chloride density gradient ultracentrifugation for the purification and characterization of recombinant adeno-associated virus.","authors":"Kiichi Hirohata, Shinichiro Kino, Takuya Yamane, Karin Bandoh, Takeshi Bamba, Shawn M Sternisha, Tetsuo Torisu, Mitsuko Fukuhara, Yuki Yamaguchi, Susumu Uchiyama","doi":"10.1007/s00249-025-01751-1","DOIUrl":"https://doi.org/10.1007/s00249-025-01751-1","url":null,"abstract":"<p><p>Recombinant adeno-associated virus (rAAV) has been widely used as an effective delivery tool in gene therapy. One of the challenges facing the production of high-quality rAAV is optimization of the production and purification methodologies. Cesium chloride density gradient ultracentrifugation (CsCl-DGUC) has been traditionally utilized for rAAV purification; however, few studies have focused on CsCl-DGUC for rAAV purification despite this technique having a great potential for clinical-grade or large-scale rAAV production. In this study, we aimed to explore the unaddressed challenges associated with rAAV purification using CsCl-DGUC. We clarified that AAV capsids assembled by the different stoichiometries of three viral proteins (VP1, VP2, and VP3) showed heterogeneous population in the CsCl density gradient and encapsidated DNA increased the buoyant density differences of these capsids, resulting in the wider distribution. We implemented CsCl-DGUC using a vertical rotor which improved throughput and enhanced the separation of desired AAV particles from impurities. Furthermore, we examined the effect of CsCl exposure during purification, and the presence of residual CsCl in the purified rAAV. This study provides valuable insights into the application of CsCl-DGUC in the manufacturing of rAAV while ensuring adequate efficacy and safety for gene therapy.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-05-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144092505","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
The influence of the Debye-Hückel factor in estimating the distance between interacting monomers in self-assembling proteins. debye - h<s:1> ckel因子对估计自组装蛋白中相互作用单体之间距离的影响。
IF 2.2 4区 生物学
European Biophysics Journal Pub Date : 2025-05-09 DOI: 10.1007/s00249-025-01754-y
Angel Mozo-Villarías, Enrique Querol, Juan A Cedano
{"title":"The influence of the Debye-Hückel factor in estimating the distance between interacting monomers in self-assembling proteins.","authors":"Angel Mozo-Villarías, Enrique Querol, Juan A Cedano","doi":"10.1007/s00249-025-01754-y","DOIUrl":"https://doi.org/10.1007/s00249-025-01754-y","url":null,"abstract":"<p><p>In the study of protein self-assembly, knowledge of the extent of electrical and hydrophobic interactions is important. In previous work our group deduced an expression for the hydrophobic energy between the monomers of an assembly. This energy decays exponentially with a characteristic distance r<sub>H</sub>. The object of this work is to obtain a more precise physical interpretation of r<sub>H</sub>. In very simple systems, according to our model, r<sub>H</sub> turns out to be the distance between the hydrophobic dipole moment vectors H. As systems become more complex and the action of the electrostatic dipole moment vectors D appear, discrepancies begin to be seen between the values obtained for r<sub>H</sub> and the distances between vectors. It is observed that the simple application of Coulomb's law is not sufficient to explain these discrepancies. We introduce the (D-H) factor into the electrostatic interaction, since proteins interact within an ionic medium. This formulation implies the appearance of an exponential decay factor r<sub>D</sub>, which is the thickness of the ionic atmosphere surrounding protein molecules. The distance adopted by two interacting monomers in a protein assembly is affected by both types of interaction and therefore is a function of both r<sub>H</sub> and r<sub>D</sub>. In a number of cases, the electrostatic interaction between D vectors is repulsive, generating a potential barrier that monomers are able to cross thanks to an overwhelmingly attractive hydrophobic potential well. In other cases both interactions are attractive and the distance between monomers appears as a compromise of both r<sub>H</sub> and r<sub>D</sub>.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143962937","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
Location of oncogene-induced DNA damage sites revealed by quantitative analysis of a DNA counterstain. DNA反染定量分析揭示癌基因诱导的DNA损伤位点的位置。
IF 2.2 4区 生物学
European Biophysics Journal Pub Date : 2025-05-07 DOI: 10.1007/s00249-025-01755-x
Greta Paternò, Silvia Scalisi, Gaetano Ivan Dellino, Mario Faretta, Pier Giuseppe Pelicci, Alberto Diaspro, Luca Lanzanò
{"title":"Location of oncogene-induced DNA damage sites revealed by quantitative analysis of a DNA counterstain.","authors":"Greta Paternò, Silvia Scalisi, Gaetano Ivan Dellino, Mario Faretta, Pier Giuseppe Pelicci, Alberto Diaspro, Luca Lanzanò","doi":"10.1007/s00249-025-01755-x","DOIUrl":"https://doi.org/10.1007/s00249-025-01755-x","url":null,"abstract":"<p><p>Oncogene activation is a key driver of cancer development, inducing aberrant cellular proliferation and DNA replication stress. This in turn, leads to DNA damage-which accumulates in specific genomic regions-contributing to genomic instability in cancer. However, the interplay between oncogene-induced DNA damage and chromatin organization is still poorly understood. In this study, we introduce a QUantitative ANalysis of DNA cOunterstains (QUANDO) to investigate the subnuclear localization of DNA damage in single-cell nuclei of U937-PR9 cells, an in vitro model of acute promyelocytic leukemia (APL). Using advanced imaging techniques, including DNA intensity analysis and colocalization by image cross-correlation spectroscopy (ICCS), we map DNA damage foci and correlate them with chromatin regions of different density. QUANDO is applied to dual-color confocal images of the DNA damage marker γ-H2AX and the DNA counterstain DAPI, allowing single-cell measurements of foci distribution within areas of low or high DNA density. We find that spontaneous DNA damage and DNA damage induced by the activation of PML-RARα oncogene predominantly localize in euchromatic regions. Conversely, when DNA damage is induced by the radiomimetic agent neocarzinostatin (NCS), the foci appear more evenly distributed in euchromatic and heterochromatic regions. These findings underscore the complex interplay between oncogene activation and chromatin organization, revealing how disruptions in DNA damage distribution can contribute to genomic instability and offering new insights for targeting DNA repair mechanisms in cancer therapies.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143960936","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
Facilitating the simulation of sedimentation velocity data: new features of SViMULATE. 便于沉降速度数据的模拟:svsimulation的新特性。
IF 2.2 4区 生物学
European Biophysics Journal Pub Date : 2025-05-05 DOI: 10.1007/s00249-025-01753-z
Chad A Brautigam
{"title":"Facilitating the simulation of sedimentation velocity data: new features of SViMULATE.","authors":"Chad A Brautigam","doi":"10.1007/s00249-025-01753-z","DOIUrl":"https://doi.org/10.1007/s00249-025-01753-z","url":null,"abstract":"<p><p>The simulation of analytical ultracentrifugation data in the sedimentation velocity (SV) mode is extremely useful for experimental planning and hypothesis testing. However, undertaking such simulations can be daunting, especially if one is unpracticed in SV analytic software and the underlying hydrodynamic precepts of the method. Recently, to address this need, the software SViMULATE was introduced. This software featured a simple user interface and facile, on-the-fly conversions of familiar macromolecular properties (e.g., molar mass, shape) to the quantities needed for a successful SV simulation (the sedimentation coefficient, s, and the translational diffusion coefficient, D<sub>T</sub>). The software offered an easy route to simulate an unlimited number of species, and two experimental modes, normal and difference SV, were enabled. In the current work, features added to SViMULATE since its initial release are detailed. These include new experimental modes: two interacting systems, nonideal sedimentation, flotation, and band (or \"analytical zone\") SV. Further, the modeling of polydisperse species as a series of related individual species has been enabled, and more sophisticated radial and time discretizations enhance the numerical stability of the simulation engine. These features significantly expand the scope and utility of the software, and the advances described herein are immediately available in version 1.4.0 of SViMULATE.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143956684","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
Statistical mechanics of bone damage: a constitutive model 骨损伤的统计力学:一个本构模型。
IF 2.2 4区 生物学
European Biophysics Journal Pub Date : 2025-05-03 DOI: 10.1007/s00249-025-01749-9
S. García-Vilana, D. Sánchez-Molina
{"title":"Statistical mechanics of bone damage: a constitutive model","authors":"S. García-Vilana,&nbsp;D. Sánchez-Molina","doi":"10.1007/s00249-025-01749-9","DOIUrl":"10.1007/s00249-025-01749-9","url":null,"abstract":"<div><p>After the elastic regime is surpassed, cortical bone exhibits significant microcracking in its post-elastic mechanical behavior. This work develops a thermodynamically consistent, nonlinear constitutive model based on statistical mechanics, designed to predict the stress–strain relationship and the progression of inter-osteon microcracking. To assess the model’s sufficiency, precise tensile and bending tests were performed in comparison to empirical curves that illustrated theoretical predictions of constitutive relationships. Moreover, entropy increases were quantitatively assessed using model parameters refined through experimental data. A large-size sample was utilized, comprising 51 dog-bone-shaped cortical bone specimens from the 4th ribs of various subjects for uniaxial tensile tests, and 15 complete fourth ribs for bending tests. Displacement and strain fields were meticulously recorded using digital image correlation and video analysis. The model demonstrated robustness, accurately fitting the data from all experimental specimens and revealing correlations between constitutive parameters and anthropometric variables. Entropy calculations provide insights into the behavior of the bone under varying strains: microcracking is minimal at low strains with stress nearly proportional to strain, escalating significantly beyond a critical threshold, thus challenging the linear relationship between stress and strain.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"54 3-4","pages":"185 - 200"},"PeriodicalIF":2.2,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-025-01749-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143954988","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
Analysis of ligand binding mechanism by dimeric receptors using stopped-flow fluorimetry—application to the human decapping scavenger enzyme 用停止流动荧光法分析二聚体受体的配体结合机制——在人脱帽清除酶中的应用。
IF 2.2 4区 生物学
European Biophysics Journal Pub Date : 2025-04-26 DOI: 10.1007/s00249-025-01748-w
Zbigniew M. Darzynkiewicz, Megerditch Kiledjian, Jan M. Antosiewicz
{"title":"Analysis of ligand binding mechanism by dimeric receptors using stopped-flow fluorimetry—application to the human decapping scavenger enzyme","authors":"Zbigniew M. Darzynkiewicz,&nbsp;Megerditch Kiledjian,&nbsp;Jan M. Antosiewicz","doi":"10.1007/s00249-025-01748-w","DOIUrl":"10.1007/s00249-025-01748-w","url":null,"abstract":"<div><p>Association of a ligand with the binding site of a receptor is usually at least a two-step process - formation of an initial encounter complex followed by a conformational transition of the complex. Consequently, the description of binding by dimeric receptors requires a two-dimensional reaction scheme. An interesting example of a dimeric receptor is the decapping scavenger enzyme, DcpS. It is a critical determinant of mRNA metabolism that hydrolyses the 5’-end <span>(hbox {m}^7)</span>GpppN cap following 3’-end mRNA decay. The DcpS family of proteins function as homodimers with one active site in each protomer. We investigate the binding of substrate and product analogues of the mRNA cap, <span>(hbox {m}^7)</span>Gp(<span>(hbox {CH}_2)</span>)ppG and <span>(hbox {m}^7)</span>GMP, respectively, by human DcpS wild-type (<span>(hbox {DcpS}^{mathrm {WT/WT}})</span>) and its one-site compromised mutant (<span>(hbox {DcpS}^{mathrm {WT/BC}})</span>) using stopped-flow fluorimetry. Based on observations for the mutant <span>(hbox {DcpS}^{mathrm {WT/BC}})</span>, binding by each active site and for each ligand proceeds through the formation of an encounter complex followed by conformational transitions. In the case of <span>(hbox {DcpS}^{mathrm {WT/WT}})</span>, we show that only two association rate constants, one for the apo-enzyme with both sites empty and the second for the enzyme with one site already occupied, can be determined with satisfactory accuracy from experimental progress curves, even for experimental data with a high signal-to-noise ratio. An interesting and biologically relevant observation is that binding of substrate analogue by one site prevents binding by the remaining empty site, whereas in the case of the <span>(hbox {m}^7)</span>GMP product both sites bind ligand independently of the binding state of the other site.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"54 3-4","pages":"171 - 184"},"PeriodicalIF":2.2,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143962789","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
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