Biophysical journal最新文献_第2页

Collagen as a stress test and a tool for improvement of Glycine and Proline conformations in biomolecular force fields. 胶原蛋白在生物分子力场中作为压力测试和改善甘氨酸和脯氨酸构象的工具。

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-07-22 DOI: 10.1016/j.bpj.2025.07.018

Kenno Vanommeslaeghe

引用次数: 0

Crumbs2 acts as a dynamic cellular sensor triggering stable podocyte cell-matrix anchorage. crums2作为一个动态的细胞传感器，触发稳定的足细胞-基质锚定。

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-07-22 DOI: 10.1016/j.bpj.2025.07.020

Rohan Bhatia,Annika Möller-Kerutt,Sven Gerlach,Yannick Herfs,Rebecca Rixen,Hermann Pavenstädt,Bernd Hoffmann,Rudolf Merkel,Ulrich Kubitscheck,Thomas Weide,Jan Peter Siebrasse

{"title":"Crumbs2 acts as a dynamic cellular sensor triggering stable podocyte cell-matrix anchorage.","authors":"Rohan Bhatia,Annika Möller-Kerutt,Sven Gerlach,Yannick Herfs,Rebecca Rixen,Hermann Pavenstädt,Bernd Hoffmann,Rudolf Merkel,Ulrich Kubitscheck,Thomas Weide,Jan Peter Siebrasse","doi":"10.1016/j.bpj.2025.07.020","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.07.020","url":null,"abstract":"Mammalian crumbs proteins (CRB) 2 and 3 are expressed in the kidney, with CRB2 mainly found within podocytes. Here, we focused on the function of CRB2 in podocytes. We investigated the CRB2/CRB3A membrane dynamics at the podocyte-podocyte contact interface in a cell culture model. Traction force microscopy was employed to clarify whether the homophilic CRB2 interactions occur in cis or trans. Live-cell imaging revealed the effects of CRB2 and CRB3A expression on cell migration from the single cell level to large cellular networks at long space and time scales. We found that CRB2 interacts in trans, but surprisingly does not form stable interconnections. Instead, CRB2 acts as a dynamic sensor for the cellular environment and triggers a massive reorganisation of focal adhesions and the actin cytoskeleton upon contact of CRB2-positive cells resulting in a strongly increased cell-matrix anchoring. Cytoskeleton reorganization can also be triggered by CRB3A, however, the increased cell-matrix anchorage is CRB2-specific.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"67 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144693435","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 Membrane Properties Determine Protein Function - A New Aspect of Allosteric Modulation. 膜性质决定蛋白质功能——变构调节的新视角。

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-07-22 DOI: 10.1016/j.bpj.2025.07.019

Daniel Huster

引用次数: 0

3D multiscale shape analysis of nuclei and in-vivo elastic stress sensors allows force inference. 核的三维多尺度形状分析和体内弹性应力传感器允许力推断。

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-07-22 DOI: 10.1016/j.bpj.2025.07.015

Alejandro Jurado,Jonas Isensee,Arne Hofemeier,Lea Johanna Krüger,Raphael Wittkowski,Ramin Golestanian,Philip Bittihn,Timo Betz

引用次数: 0

Allometric cell spreading and the geometrical control of focal adhesion collective organization. 异速细胞扩张与黏附集体组织的几何控制。

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-07-21 DOI: 10.1016/j.bpj.2025.07.016

Célian Bimbard,Ali-Alhadi Wahhod,Démosthéne Mitrossilis,Joseph Vermeil,Rémi Bousquet,Alain Richert,David Pereira,Pauline Durand-Smet,Sophie Asnacios,Jocelyn Étienne,Atef Asnacios,Jonathan Fouchard

{"title":"Allometric cell spreading and the geometrical control of focal adhesion collective organization.","authors":"Célian Bimbard,Ali-Alhadi Wahhod,Démosthéne Mitrossilis,Joseph Vermeil,Rémi Bousquet,Alain Richert,David Pereira,Pauline Durand-Smet,Sophie Asnacios,Jocelyn Étienne,Atef Asnacios,Jonathan Fouchard","doi":"10.1016/j.bpj.2025.07.016","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.07.016","url":null,"abstract":"Focal adhesions are protein complexes that transmit actin cytoskeleton forces to the extracellular matrix and serve as signaling hubs that regulate cell physiology. While their growth is achieved through a local force-dependent process, the requirement of sustaining stress at the cell scale suggests a global regulation of the collective organization of focal adhesions. To investigate evidence of such large-scale regulation, we compared changes in cell shape and the organization of focal adhesion-like structures during the early spreading of fibroblasts either on a two-dimensional substrate or confined between two parallel plates, and for cells of different volumes. In this way, we reveal that the areal density of focal adhesions is conserved regardless of cell size or third-dimensional confinement, despite different absolute values of the surface covered by adhesion clusters. In particular, the width of the focal adhesions ring, which fills the flat lamella at the cell front, adapts to cell size and third-dimensional confinement and scales with cell-substrate contact radius. We find that this contact radius also adapts in the parallel-plate geometry so that the cumulated area of cell-substrate contact is conserved at the cell scale. We suggest that this behavior is the result of 3D cell shape changes which govern spreading transitions. Indeed, because of volume conservation constraints, the evolution of cell-body contact angle, adjusts according to cell size and confinement, whereas the rate of early spreading at the cell-substrate contact is not affected by third-dimensional geometry. Overall, our data suggest that a coordination between global and local scales mediates the adaptation of cell-substrate contacts and focal adhesions distribution to large scale geometrical constraints, which allows an invariant cell-substrate adhesive energy.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"47 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144684243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Role of Dynamical Instability in QT Interval Variability and Early Afterdepolarization Propensity. 动态不稳定性在QT间期变异性和早期后去极化倾向中的作用。

IF 3.1 3区生物学

Biophysical journal Pub Date : 2025-07-21 DOI: 10.1016/j.bpj.2025.07.017

Daisuke Sato, Bence Hegyi, Crystal M Ripplinger, Donald M Bers

{"title":"Role of Dynamical Instability in QT Interval Variability and Early Afterdepolarization Propensity.","authors":"Daisuke Sato, Bence Hegyi, Crystal M Ripplinger, Donald M Bers","doi":"10.1016/j.bpj.2025.07.017","DOIUrl":"10.1016/j.bpj.2025.07.017","url":null,"abstract":"Beat-to-beat variability of the QT interval (QTV) is a well-established marker of cardiac health, with increased QTV (> 5 ms) often associated with a higher risk of arrhythmias. However, the underlying mechanisms contributing to this phenomenon remain poorly understood. Recently, we showed that cardiac instability is a major cause of QTV. Early afterdepolarizations (EADs) are abnormal electrical oscillations that occur during the plateau phase of the cardiac action potential (AP), often arising when the membrane potential becomes unstable. In this study, we use a physiologically detailed computational model of rabbit ventricular myocytes with stochastic ion channel gating to investigate the relationship between QTV and EAD propensity. We found that increased AP duration (APD) variability, which serves as a surrogate for QTV on the ECG at the single-cell level, can arise even in the absence of apparent EADs, driven by intrinsic dynamical instability. As the cellular state approaches the threshold for EAD generation, small perturbations in membrane voltage are amplified, leading to increased APD variability. The phase-plane analysis in the voltage-calcium channel inactivation space demonstrates that proximity to the EAD-generating basin of attraction strongly influences repolarization variability, establishing a mechanistic link between QTV and EAD propensity. Furthermore, we observed that QTV increases at longer pacing cycle lengths (PCLs), distinguishing it from alternans-associated APD variability, which increases at shorter PCLs. These findings suggest that increased QTV may serve as an early indicator of arrhythmic risk before the manifestation of EADs, potentially offering a critical window for preventive intervention. Our results provide novel insights into the fundamental mechanisms underlying QTV and its potential role in arrhythmia prediction.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.1,"publicationDate":"2025-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144688790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Comparative Analysis of the Bending Modulus for Phosphatidylcholine, Phosphatidylethanolamine, and Sphingomyelin Membranes Based on Coarse-Grained Molecular Dynamics Simulations. 基于粗粒度分子动力学模拟的磷脂酰胆碱、磷脂酰乙醇胺和鞘磷脂膜弯曲模量的比较分析。

IF 3.4 3区生物学

Biophysical journal Pub Date : 2025-07-16 DOI: 10.1016/j.bpj.2025.07.014

Sam Brown,Jessica Pallarez,Marat R Talipov

{"title":"Comparative Analysis of the Bending Modulus for Phosphatidylcholine, Phosphatidylethanolamine, and Sphingomyelin Membranes Based on Coarse-Grained Molecular Dynamics Simulations.","authors":"Sam Brown,Jessica Pallarez,Marat R Talipov","doi":"10.1016/j.bpj.2025.07.014","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.07.014","url":null,"abstract":"Bilayer membranes are essential biological structures with complex and largely unexplored mechanical properties. Using coarse-grained molecular dynamics simulations, we evaluated the bending modulus across diverse lipid compositions, including phosphatidylcholine (PC), phosphatidylethanolamine (PE), and sphingomyelin (SM). Three computational techniques were employed to calculate the bending modulus from thermal fluctuations of the simulated bilayers: the Fourier transform of the lipid height function (q-4 fitting), Bedeaux-Weeks Density Correlation Functions (BW-DCF) method, and Real Space Fluctuations (RSF). The analysis revealed substantial variations in bending modulus values across methods, underscoring the inherent complexities and discrepancies in computational assessments. These findings advance our understanding of membrane dynamics and provide valuable insights into bilayer structural behavior. The results support the broader application of computational approaches to study biological systems and inspire the development of biomimetic materials with tailored mechanical properties.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"153 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144652905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Thermal adaptation of extremozymes: Temperature-sensitive contact analysis of serine proteases. 极端酶的热适应：丝氨酸蛋白酶的温度敏感接触分析。

IF 3.2 3区生物学

Biophysical journal Pub Date : 2025-07-15 Epub Date: 2025-06-05 DOI: 10.1016/j.bpj.2025.06.001

Dulitha P Kulathunga, Davit A Potoyan

{"title":"Thermal adaptation of extremozymes: Temperature-sensitive contact analysis of serine proteases.","authors":"Dulitha P Kulathunga, Davit A Potoyan","doi":"10.1016/j.bpj.2025.06.001","DOIUrl":"10.1016/j.bpj.2025.06.001","url":null,"abstract":"Enzyme thermal adaptation reflects a delicate interplay between the sequence, structure, and dynamics of proteins which are fined tuned to meet environmental demands of organisms. Understanding these evolutionary relationships can drive advances in bioengineering, including the design of industrial enzymes and the development of novel therapeutics. This work explores sequence-to-dynamics connections in subtilisin-like serine protease homologs using a recently developed computational methodology that employs expanded ensemble simulations and temperature-sensitive contact analysis. We reveal that thermophilic enzymes achieve thermal stability through extensive salt bridges and hydrophobic networks, whereas psychrophilic enzymes rely on the stability of targeted interactions for cold adaptation. An unsupervised cluster analysis of residue conservation, flexibility, and hydrophobic interactions provides a comprehensive view of residue-specific contributions to thermal adaptation. These findings highlight the coordinated roles of conserved and variable regions in enzyme stability, offering a framework for tailoring enzymes to specific thermal properties for biotechnological applications.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"2291-2302"},"PeriodicalIF":3.2,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144246246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

DNA coronas resist nuclease degradation. DNA冠状体抗核酸酶降解。

IF 3.2 3区生物学

Biophysical journal Pub Date : 2025-07-15 Epub Date: 2025-05-29 DOI: 10.1016/j.bpj.2025.05.028

Faisal Anees, Diego A Montoya, David S Pisetsky, Tariq Khan, Abhishek Kalpattu, Christine K Payne

{"title":"DNA coronas resist nuclease degradation.","authors":"Faisal Anees, Diego A Montoya, David S Pisetsky, Tariq Khan, Abhishek Kalpattu, Christine K Payne","doi":"10.1016/j.bpj.2025.05.028","DOIUrl":"10.1016/j.bpj.2025.05.028","url":null,"abstract":"The interaction of cell-free DNA with biological particles has been linked to autoimmune diseases such as systemic lupus erythematosus, but mechanistic details are lacking. Our recent work has shown that DNA adsorbed on the surface of synthetic particles, forming a DNA \"corona,\" leads to an enhanced immunostimulatory response in macrophages, providing a model system to understand how DNA-particle interactions may lead to autoimmune diseases. This current study provides a detailed examination of DNA (500-600 base pairs and ∼10,000 base pairs) interacting with synthetic particles (40 nm to 10 μm) and planar surfaces. Of specific interest is how DNA adsorbed on the surface of particles is resistant to degradation by DNase 1, a common nuclease. DNA-particle complexes are characterized by a colorimetric DNA concentration assay (PicoGreen), spectroscopy (NanoDrop), dynamic light scattering (DLS), confocal fluorescence microscopy, and transmission electron microscopy. These studies show that the protective effect of the particle is size dependent, with smaller (40 and 200 nm) particles providing less protection. Correlated with this lack of protection is significantly increased particle aggregation, suggesting that a DNA corona formed on the larger particles is protective, whereas particle aggregation, which dominates the smaller particles, is not protective. The formation of a single-stranded DNA corona leads to the opposite protective effect, with smaller (200 nm) particles leading to near-complete protection of DNA from nuclease degradation. Overall, this study provides an important biophysical basis for the interaction of DNA with particles with the goal of guiding future in vitro and in vivo studies of cell-free DNA and particles in autoimmune disease.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"2253-2262"},"PeriodicalIF":3.2,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144191433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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

Protein-DNA co-condensation is prewetting to a collapsed polymer. 蛋白质- dna共缩聚是预湿的一个崩溃的聚合物。

IF 3.1 3区生物学

Biophysical journal Pub Date : 2025-07-15 Epub Date: 2025-06-04 DOI: 10.1016/j.bpj.2025.05.031

Mason N Rouches, Benjamin B Machta

{"title":"Protein-DNA co-condensation is prewetting to a collapsed polymer.","authors":"Mason N Rouches, Benjamin B Machta","doi":"10.1016/j.bpj.2025.05.031","DOIUrl":"10.1016/j.bpj.2025.05.031","url":null,"abstract":"The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with particular sequences of DNA. At unphysiological concentrations, many of these nuclear proteins can phase separate in the absence of DNA. In vivo, the thermodynamic forces driving these phases lead the chromosome to co-condense with nuclear proteins. However, it is unclear how DNA, itself a long polymer subject to configurational transitions, interacts with three-dimensional protein phases. Here, we show that a long compressible polymer can be coupled to interacting protein mixtures, leading to a generalized prewetting transition where polymer collapse is coincident with a locally stabilized liquid droplet. We use lattice Monte-Carlo simulations and a mean-field theory to show that these phases can be stable even in regimes where both polymer collapse and coexisting liquid phases are unstable in isolation and that these new transitions can be either abrupt or continuous. For polymers with internal linear structure, we further show that changes in the concentration of bulk components can lead to changes in three-dimensional polymer structure. In the nucleus, there are many distinct proteins that interact with many different regions of chromatin, potentially giving rise to many different prewet phases. The simple systems we consider here highlight chromatin's role as a lower-dimensional surface whose interactions with proteins are required for these novel phases.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"2280-2290"},"PeriodicalIF":3.1,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144233069","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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