European Biophysics Journal最新文献_第3页

Extreme enthalpy‒entropy compensation in the dimerization of small solutes in aqueous solution 水溶液中小溶质二聚化过程中的极端焓熵补偿。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-10-15 DOI: 10.1007/s00249-024-01722-y

David J. Scott, Donald J. Winzor

{"title":"Extreme enthalpy‒entropy compensation in the dimerization of small solutes in aqueous solution","authors":"David J. Scott, Donald J. Winzor","doi":"10.1007/s00249-024-01722-y","DOIUrl":"10.1007/s00249-024-01722-y","url":null,"abstract":"<div><p>This communication summarizes findings from the earliest encounters with extreme enthalpy‒entropy compensation, a phenomenon first detected in the 1950s by a reappraisal of isopiestic and calorimetric measurements on aqueous urea solutions in terms of solute self-association. Because concurrent studies of carboxylic acid association were confined to measurement of the equilibrium constant by conductance, IR spectrophotometry or potentiometric titration measurements, temperature-independence of the dimerization constant was mistakenly taken to signify a value of zero for Δ<span>(H^o)</span> instead of (Δ<span>(H^o)</span> ‒ TΔ<span>(S^o)</span>). In those studies of small-solute self-association the extreme enthalpy‒entropy compensation was reflecting the action of water as a reactant whose hydroxyl groups were competing for the solute carbonyl involved in self-association. Such action gives rise to a positive temperature dependence of Δ<span>(H^o)</span> that could well be operating in concert with that responsible for the commonly observed negative dependence for protein‒ligand interactions exhibiting extreme enthalpy‒entropy compensation, where the solvent contribution to the energetics reflects changes in the extent of ordered water structure in hydrophobic environments.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 7-8","pages":"373 - 384"},"PeriodicalIF":2.2,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-024-01722-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142455352","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

Application of artificial neural network for the mechano-bactericidal effect of bioinspired nanopatterned surfaces 应用人工神经网络研究生物启发纳米图案表面的机械杀菌效果。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-10-07 DOI: 10.1007/s00249-024-01723-x

Ecren Uzun Yaylacı

引用次数: 0

Structural investigation, computational analysis, and theoretical cryoprotectant approach of antifreeze protein type IV mutants 抗冻蛋白 IV 型突变体的结构研究、计算分析和理论低温保护方法。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-09-27 DOI: 10.1007/s00249-024-01719-7

Azadeh Eskandari, Thean Chor Leow, Mohd Basyaruddin Abdul Rahman, Siti Nurbaya Oslan

{"title":"Structural investigation, computational analysis, and theoretical cryoprotectant approach of antifreeze protein type IV mutants","authors":"Azadeh Eskandari, Thean Chor Leow, Mohd Basyaruddin Abdul Rahman, Siti Nurbaya Oslan","doi":"10.1007/s00249-024-01719-7","DOIUrl":"10.1007/s00249-024-01719-7","url":null,"abstract":"<div><p>Antifreeze proteins (AFPs) have unique features to sustain life in sub-zero environments due to ice recrystallization inhibition (IRI) and thermal hysteresis (TH). AFPs are in demand as agents in cryopreservation, but some antifreeze proteins have low levels of activity. This research aims to improve the cryopreservation activity of an AFPIV. In this in silico study, the helical peptide afp1m from an Antarctic yeast AFP was modeled into a sculpin AFPIV, to replace each of its four <i>α</i>-helices in turn, using various computational tools. Additionally, a new linker between the first two helices of AFPIV was designed, based on a flounder AFPI, to boost the ice interaction activity of the mutants. Bioinformatics tools such as ExPASy Prot-Param, Pep-Wheel, SOPMA, GOR IV, Swiss-Model, Phyre2, MODFOLD, MolPropity, and ProQ were used to validate and analyze the structural and functional properties of the model proteins. Furthermore, to evaluate the AFP/ice interaction, molecular dynamics (MD) simulations were executed for 20, 100, and 500 ns at various temperatures using GROMACS software. The primary, secondary, and 3D modeling analysis showed the best model for a redesigned antifreeze protein (AFP1mb, with afp1m in place of the fourth AFPIV helix) with a QMEAN (Swiss-Model) Z score value of 0.36, a confidence of 99.5%, a coverage score of 22%, and a p value of 0.01. The results of the MD simulations illustrated that AFP1mb had more rigidity and better ice interactions as a potential cryoprotectant than the other models; it also displayed enhanced activity in limiting ice growth at different temperatures.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 7-8","pages":"385 - 403"},"PeriodicalIF":2.2,"publicationDate":"2024-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142338881","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

Computational study on the impact of linkage sequence on the structure and dynamics of lignin 连接序列对木质素结构和动力学影响的计算研究

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-09-19 DOI: 10.1007/s00249-024-01720-0

Derya Vural

{"title":"Computational study on the impact of linkage sequence on the structure and dynamics of lignin","authors":"Derya Vural","doi":"10.1007/s00249-024-01720-0","DOIUrl":"10.1007/s00249-024-01720-0","url":null,"abstract":"<div><p>Lignin, one of the most abundant biopolymers on Earth, is of great research interest due to its industrial applications including biofuel production and materials science. The structural composition of lignin plays an important role in shaping its properties and functionalities. Notably, lignin exhibits substantial compositional diversity, which varies not only between different plant species but even within the same plant. Currently, it is unclear to what extent this compositional diversity plays on the overall structure and dynamics of lignin. To address this question, this paper reports on the development of two models of lignin containing all guaiacyl (G) subunits with varied linkage sequences and makes use of all-atom molecular dynamics simulations to examine the impact of linkage sequence alone on the lignin’s structure and dynamics. This work demonstrates that the structure of the lignin polymer depends on its linkage sequence at temperatures above and below the glass transition temperature (<span>(T_textrm{g})</span>), but the polymers exhibit similar structural properties as it is approaching the viscous flow state (480 K). At low temperatures, both of lignin models have a local dynamics confined in a cage, but the size of cages varies depending on structural differences. Interestingly, at temperatures higher than <span>(T_textrm{g})</span>, the different linkage sequence leads to the subtle dynamical difference which diminishes at 480 K.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 7-8","pages":"405 - 414"},"PeriodicalIF":2.2,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142263850","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

Physical aspects of epithelial cell–cell interactions: hidden system complexities 上皮细胞-细胞相互作用的物理方面：隐藏的系统复杂性

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-09-10 DOI: 10.1007/s00249-024-01721-z

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

{"title":"Physical aspects of epithelial cell–cell interactions: hidden system complexities","authors":"Ivana Pajic-Lijakovic, Milan Milivojevic, Peter V. E. McClintock","doi":"10.1007/s00249-024-01721-z","DOIUrl":"10.1007/s00249-024-01721-z","url":null,"abstract":"<div><p>The maintenance of homeostasis and the retention of ordered epithelial cell self-organization are essential for morphogenesis, wound healing, and the spread of cancer across the epithelium. However, cell–cell interactions in an overcrowded environment introduce a diversity of complications. Such interactions arise from an interplay between the cell compressive and shear stress components that accompany increased cell packing density. They can lead to various kinds of cell rearrangement such as: the epithelial-to-mesenchymal cell state transition; live cell extrusion; and cell jamming. All of these scenarios of cell rearrangement under mechanical stress relate to changes in the strengths of the cell–cell and cell–matrix adhesion contacts. The objective of this review study is twofold: first, to provide a comprehensive summary of the biological and physical factors influencing the effects of cell mechanical stress on cell–cell interactions, and the consequences of these interactions for the status of cell–cell and cell–matrix adhesion contacts; and secondly, to offer a bio-physical/mathematical analysis of the aforementioned biological aspects. By presenting these two approaches in conjunction, we seek to highlight the intricate nature of biological systems, which manifests in the form of complex bio-physical/mathematical equations. Furthermore, the juxtaposition of these apparently disparate approaches underscores the importance of conducting experiments to determine the multitude of parameters that contribute to the development of these intricate bio-physical/mathematical models.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 7-8","pages":"355 - 372"},"PeriodicalIF":2.2,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00249-024-01721-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142178239","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

Modeling study of kinesin-13 MCAK microtubule depolymerase 驱动蛋白-13 MCAK 微管解聚酶的模型研究。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-08-02 DOI: 10.1007/s00249-024-01718-8

Ping Xie

引用次数: 0

Reciprocal effect on lateral diffusion of receptor for advanced glycation endproducts and toll-like receptor 4 in the HEK293 cell membrane 高级糖化终产物受体和收费样受体 4 对 HEK293 细胞膜横向扩散的相互影响

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-07-27 DOI: 10.1007/s00249-024-01717-9

Mohammad K. I. Walid, Sharifur Rahman, Emily A. Smith

{"title":"Reciprocal effect on lateral diffusion of receptor for advanced glycation endproducts and toll-like receptor 4 in the HEK293 cell membrane","authors":"Mohammad K. I. Walid, Sharifur Rahman, Emily A. Smith","doi":"10.1007/s00249-024-01717-9","DOIUrl":"10.1007/s00249-024-01717-9","url":null,"abstract":"<div><p>Receptor for advanced glycation endproducts (RAGE) and toll-like receptor 4 (TLR4) are pattern-recognition receptors that bind to molecular patterns associated with pathogens, stress, and cellular damage. Diffusion plays an important role in receptor functionality in the cell membrane. However, there has been no prior investigation of the reciprocal effect of RAGE and TLR4 diffusion properties in the presence and absence of each receptor. This study reports how RAGE and TLR4 affect the mobility of each other in the human embryonic kidney (HEK) 293 cell membrane. Diffusion properties were measured using single-particle tracking (SPT) with quantum dots (QDs) that are selectively attached to RAGE or TLR4. The Brownian diffusion coefficients of RAGE and TLR4 are affected by the presence of the other receptor, leading to similar diffusion coefficients when both receptors coexist in the cell. When TLR4 is present, the average Brownian diffusion coefficient of RAGE increases by 40%, while the presence of RAGE decreases the average Brownian diffusion coefficient of TLR4 by 32%. Diffusion in confined membrane domains is not altered by the presence of the other receptor. The mobility of the cell membrane lipid remains constant whether one or both receptors are present. Overall, this work shows that the presence of each receptor can affect a subset of diffusion properties of the other receptor without affecting the mobility of the membrane.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 5-6","pages":"327 - 338"},"PeriodicalIF":2.2,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141774914","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

Mechanisms of stationary voltage fluctuation in the neuromuscular junction endplate and corresponding denoising paradigms 神经肌肉接头终板的静态电压波动机制及相应的去噪范例。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-07-15 DOI: 10.1007/s00249-024-01715-x

Jia-Zeng Wang, Pengkun Hu, Shu Ma

引用次数: 0

The Structure of the LysR-type Transcriptional Regulator, CysB, Bound to the Inducer, N-acetylserine 与诱导剂 N-乙酰丝氨酸结合的 LysR 型转录调节器 CysB 的结构。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-07-08 DOI: 10.1007/s00249-024-01716-w

Koen H. G. Verschueren, Eleanor J. Dodson, Anthony J. Wilkinson

{"title":"The Structure of the LysR-type Transcriptional Regulator, CysB, Bound to the Inducer, N-acetylserine","authors":"Koen H. G. Verschueren, Eleanor J. Dodson, Anthony J. Wilkinson","doi":"10.1007/s00249-024-01716-w","DOIUrl":"10.1007/s00249-024-01716-w","url":null,"abstract":"<div><p>In <i>Escherichia coli</i> and <i>Salmonella typhimurium</i>, cysteine biosynthesis requires the products of 20 or more <i>cys</i> genes co-ordinately regulated by CysB. Under conditions of sulphur limitation and in the presence of the inducer, <i>N</i>-acetylserine, CysB binds to <i>cys</i> promoters and activates the transcription of the downstream coding sequences. CysB is a homotetramer, comprising an N-terminal DNA binding domain (DBD) and a C-terminal effector binding domain (EBD). The crystal structure of a dimeric EBD fragment of CysB from <i>Klebsiella aerogenes</i> revealed a protein fold similar to that seen in Lac repressor but with a different symmetry in the dimer so that the mode of DNA binding was not apparent. To elucidate the subunit arrangement in the tetramer, we determined the crystal structure of intact CysB in complex with <i>N</i>-acetylserine. The tetramer has two subunit types that differ in the juxtaposition of their winged helix-turn-helix DNA binding domains with respect to the effector binding domain. In the assembly, the four EBDs form a core with the DNA binding domains arranged in pairs on the surface. <i>N</i>-acetylserine makes extensive polar interactions in an enclosed binding site, and its binding is accompanied by substantial conformational rearrangements of surrounding residues that are propagated to the protein surface where they appear to alter the arrangement of the DNA binding domains. The results are (i) discussed in relation to the extensive mutational data available for CysB and (ii) used to propose a structural mechanism of <i>N</i>-acetylserine induced CysB activation.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 5-6","pages":"311 - 326"},"PeriodicalIF":2.2,"publicationDate":"2024-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11329422/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141553968","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 proteins in the light of mutations 根据突变分析蛋白质。

IF 2.2 4区生物学

European Biophysics Journal Pub Date : 2024-07-02 DOI: 10.1007/s00249-024-01714-y

Jorge A. Vila

{"title":"Analysis of proteins in the light of mutations","authors":"Jorge A. Vila","doi":"10.1007/s00249-024-01714-y","DOIUrl":"10.1007/s00249-024-01714-y","url":null,"abstract":"<div><p>Proteins have evolved through mutations—amino acid substitutions—since life appeared on Earth, some 10<sup>9</sup> years ago. The study of these phenomena has been of particular significance because of their impact on protein stability, function, and structure. This study offers a new viewpoint on how the most recent findings in these areas can be used to explore the impact of mutations on protein sequence, stability, and evolvability. Preliminary results indicate that: (1) mutations can be viewed as sensitive probes to identify ‘typos’ in the amino-acid sequence, and also to assess the resistance of naturally occurring proteins to unwanted sequence alterations; (2) the presence of ‘typos’ in the amino acid sequence, rather than being an evolutionary obstacle, could promote faster evolvability and, in turn, increase the likelihood of higher protein stability; (3) the mutation site is far more important than the substituted amino acid in terms of the marginal stability changes of the protein, and (4) the unpredictability of protein evolution at the molecular level—by mutations—exists even in the absence of epistasis effects. Finally, the Darwinian concept of evolution “descent with modification” and experimental evidence endorse one of the results of this study, which suggests that some regions of any protein sequence are susceptible to mutations while others are not. This work contributes to our general understanding of protein responses to mutations and may spur significant progress in our efforts to develop methods to accurately forecast changes in protein stability, their propensity for metamorphism, and their ability to evolve.</p></div>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":"53 5-6","pages":"255 - 265"},"PeriodicalIF":2.2,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141490428","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