European Biophysics Journal最新文献_第3页

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":"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.","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":"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.","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":"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 rH. The object of this work is to obtain a more precise physical interpretation of rH. In very simple systems, according to our model, rH 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 rH 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 rD, 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 rH and rD. 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 rH and rD.","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":"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.","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":"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, DT). 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.","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, D. Sánchez-Molina","doi":"10.1007/s00249-025-01749-9","DOIUrl":"10.1007/s00249-025-01749-9","url":null,"abstract":"<div>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.</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, Megerditch Kiledjian, Jan M. Antosiewicz","doi":"10.1007/s00249-025-01748-w","DOIUrl":"10.1007/s00249-025-01748-w","url":null,"abstract":"<div>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 (hbox {m}^7)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, (hbox {m}^7)Gp((hbox {CH}_2))ppG and (hbox {m}^7)GMP, respectively, by human DcpS wild-type ((hbox {DcpS}^{mathrm {WT/WT}})) and its one-site compromised mutant ((hbox {DcpS}^{mathrm {WT/BC}})) using stopped-flow fluorimetry. Based on observations for the mutant (hbox {DcpS}^{mathrm {WT/BC}}), 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 (hbox {DcpS}^{mathrm {WT/WT}}), 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 (hbox {m}^7)GMP product both sites bind ligand independently of the binding state of the other site.</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

Analytical ultracentrifugation as a tool for exploring COSAN assemblies. 分析性超离心作为探索COSAN组件的工具。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2025-04-23 DOI: 10.1007/s00249-025-01746-y

Hussein Fakhouri, Caroline Mas, Aline Le Roy, Estelle Marchal, Coralie Pasquier, Olivier Diat, Pierre Bauduin, Christine Ebel

{"title":"Analytical ultracentrifugation as a tool for exploring COSAN assemblies.","authors":"Hussein Fakhouri, Caroline Mas, Aline Le Roy, Estelle Marchal, Coralie Pasquier, Olivier Diat, Pierre Bauduin, Christine Ebel","doi":"10.1007/s00249-025-01746-y","DOIUrl":"https://doi.org/10.1007/s00249-025-01746-y","url":null,"abstract":"The self-assembly of the cobaltabis(dicarbollide) (COSAN) anionic boron clusters into micelles above a critical micelle concentration (cmc) of 10-20 mM and its behavior as \"sticky nano-ions\" facilitating controlled protein aggregation have been previously investigated using scattering techniques. These techniques effectively provide average structural parameters but, when applied to colloidal systems, often rely on models assuming polydispersity or anisotropic shapes. Here, we employed sedimentation velocity analytical ultracentrifugation (SV-AUC), which offers the ability to resolve discrete species. We revisited two key questions: (1) the aggregation behavior of COSAN into micelles, a topic still under debate, and (2) the nature of the protein assemblies induced by COSAN, specifically their size/shape distribution and aggregation number. SV-AUC confirms the cmc of COSAN of 16 mM and reveals that COSAN micelles exhibit low aggregation numbers (8 in water and 14 in dilute salt), consistent with recent hypotheses. It shows that COSAN promotes myoglobin aggregation into discrete oligomeric species with well-defined aggregation numbers, such as dimers, tetramers, and higher-order assemblies, depending on the COSAN-to-protein ratio. COSAN binding could be quantified at the lower COSAN/myoglobin ratios. For example, at ratio 5, myoglobin monomer (25%) binds about two COSANs, dimer (45%) about 14 COSANs, and there are ≈ 30% very large aggregates. These results provide clarity on the discrete nature of COSAN micelle aggregation and protein assembly. This study highlights the complementary role of SV-AUC in understanding supramolecular assemblies, offering useful insights into the behavior of COSAN nano-ions and their interactions with biomacromolecules.","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.2,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143959631","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

Molecular transport through nano-sized multipores of lipid vesicles: a COMSOL simulation study 分子运输通过纳米尺度的多孔脂质囊泡：COMSOL模拟研究。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2025-04-17 DOI: 10.1007/s00249-025-01745-z

Md. Asaduzzaman, Shahariar Emon, Md. Saif Ishtiaque, Md. Imran Hossain, Mahammad Abu Sayem Karal, Md. Masum Billah, Hiromitsu Takaba, Md. Khorshed Alam

{"title":"Molecular transport through nano-sized multipores of lipid vesicles: a COMSOL simulation study","authors":"Md. Asaduzzaman, Shahariar Emon, Md. Saif Ishtiaque, Md. Imran Hossain, Mahammad Abu Sayem Karal, Md. Masum Billah, Hiromitsu Takaba, Md. Khorshed Alam","doi":"10.1007/s00249-025-01745-z","DOIUrl":"10.1007/s00249-025-01745-z","url":null,"abstract":"<div>Biomembranes regulate molecular transport essential to cellular function and numerous biomedical applications, such as drug delivery and gene therapy. This study simulates molecular transport through nano-sized multipores in Giant Unilamellar Vesicles (GUVs) using COMSOL Multiphysics. We analyzed the diffusion dynamics of fluorescent probes—including Calcein, Texas-red dextran 3000 (TRD- 3k), TRD- 10k, and Alexa Fluor-labeled soybean trypsin inhibitor (AF-SBTI)—across different pore sizes, and derived rate constants using curve fitting that closely align with experimental data. Additionally, an analytical model based on Fick’s law of diffusion provides further insight into transport efficiency. This approach offers a novel perspective by examining simultaneous transport through multiple nanopores, which better mimics realistic biological environments compared to traditional single-pore studies. We used COMSOL for efficiently simulating large-scale, multi-nanopore systems, particularly in biomedical applications where modeling of complex transport phenomena is essential. This work provides new insights into multipore-mediated transport, critical for optimizing nanopore-based drug delivery and advancing the understanding of cellular transport mechanisms.</div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"54 3-4","pages":"159 - 169"},"PeriodicalIF":2.2,"publicationDate":"2025-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143951753","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

Exploring the influence of water micro assemblies on protein folding, enzyme catalysis and membrane dynamics 探讨水微组装体对蛋白质折叠、酶催化和膜动力学的影响。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2025-04-14 DOI: 10.1007/s00249-025-01747-x

Arturo Tozzi

{"title":"Exploring the influence of water micro assemblies on protein folding, enzyme catalysis and membrane dynamics","authors":"Arturo Tozzi","doi":"10.1007/s00249-025-01747-x","DOIUrl":"10.1007/s00249-025-01747-x","url":null,"abstract":"<div>Water is central to biological processes not only as a solvent, but also as an agent shaping macromolecular behavior. Insights into water micro assemblies (WMA), defined by transient regions of low-density water (LDW) and high-density water (HDW), have highlighted their potential impact on biological phenomena. LDW, with its structured hydrogen bonding networks and reduced density, stabilizes hydrophobic interfaces and promotes ordered molecular configurations. Conversely, HDW, with its dynamic and flexible nature, facilitates transitions, solute mobility and molecular flexibility. By correlating experimental observations with simulations, we explore the influence of WMA on three key biological processes. In protein folding, LDW may stabilize hydrophobic cores and secondary structures by forming structured exclusion zones, while HDW may introduce dynamic flexibility, promoting the resolution of folding intermediates and leading to dynamic rearrangements. In enzyme catalysis, LDW may form structured hydration shells around active sites stabilizing active sites over longer timescales, while HDW may support substrate access and catalytic flexibility within active sites. In membrane dynamics, LDW may stabilize lipid headgroups, forming structured hydration layers that enhance membrane rigidity and stability, while HDW may ensure the nanosecond-scale flexibility required for vesicle formation and fusion. Across these tree processes, the WMA’s energy contributions, timescales and spatial scales align with the forces and dynamics involved, highlighting the role of LDW and HDW in modulating cellular interactions. This perspective holds implications for the design of lab-on-chip devices, advancements in sensor technologies, development of biomimetic membranes for drug delivery, creation of novel therapeutics and deeper understanding of protein misfolding diseases.</div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"54 3-4","pages":"97 - 108"},"PeriodicalIF":2.2,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143958185","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