Biophysical journal最新文献

{"title":"The ATPase asymmetry: Novel computational insight into coupling diverse F_O motors with tripartite F₁.","authors":"Shintaroh Kubo, Yasushi Okada","doi":"10.1016/j.bpj.2024.03.013","DOIUrl":"10.1016/j.bpj.2024.03.013","url":null,"abstract":"<p><p>ATP synthase, a crucial enzyme for cellular bioenergetics, operates via the coordinated coupling of an F_O motor, which presents variable symmetry, and a tripartite F₁ motor. Despite extensive research, the understanding of their coupling dynamics, especially with non-10-fold symmetrical F_O motors, remains incomplete. This study investigates the coupling patterns between eightfold and ninefold F_O motors and the constant threefold F₁ motor using coarse-grained molecular dynamics simulations. We unveil that in the case of a ninefold F_O motor, a 3-3-3 motion is most likely to occur, whereas a 3-3-2 motion predominates with an eightfold F_O motor. Furthermore, our findings propose a revised model for the coupling method, elucidating that the pathways' energy usage is primarily influenced by F₁ rotation and conformational changes hindered by the b-subunits. Our results present a crucial step toward comprehending the energy landscape and mechanisms governing ATP synthase operation.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"891-900"},"PeriodicalIF":3.2,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140064710","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}

{"title":"Empirical methods that provide physical descriptions of dynamic cellular processes.","authors":"Ian Seim, Stephan W Grill","doi":"10.1016/j.bpj.2024.12.003","DOIUrl":"10.1016/j.bpj.2024.12.003","url":null,"abstract":"<p><p>We review empirical methods that can be used to provide physical descriptions of dynamic cellular processes during development and disease. Our focus will be nonspatial descriptions and the inference of underlying interaction networks including cell-state lineages, gene regulatory networks, and molecular interactions in living cells. Our overarching questions are: How much can we learn from just observing? To what degree is it possible to infer causal and/or precise mathematical relationships from observations? We restrict ourselves to data sets arising from only observations, or experiments in which minimal perturbations have taken place to facilitate observation of the systems as they naturally occur. We discuss analysis perspectives in order from those offering the least descriptive power but requiring the least assumptions such as statistical associations. We end with those that are most descriptive, but require stricter assumptions and more previous knowledge of the systems such as causal inference and dynamical systems approaches. We hope to provide and encourage the use of a wide array of options for quantitative cell biologists to learn as much as possible from their observations at all stages of understanding of their system of interest. Finally, we provide our own recipe of how to empirically determine quantitative relationships and growth laws from live-cell microscopy data, the resultant predictions of which can then be verified with perturbation experiments. We also include an extended supplement that describes further inference algorithms and theory for the interested reader.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"861-875"},"PeriodicalIF":3.2,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142784043","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}

{"title":"Developmental biophysics.","authors":"Thorsten Wohland, Timothy E Saunders, Chii Jou Chan","doi":"10.1016/j.bpj.2025.02.009","DOIUrl":"10.1016/j.bpj.2025.02.009","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"E1-E2"},"PeriodicalIF":3.2,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143522523","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}

{"title":"Fine-tuning of Fgf8 morphogen gradient by heparan sulfate proteoglycans in the extracellular matrix.","authors":"Mansi Gupta, Thomas Kurth, Fabian Heinemann, Petra Schwille, Sebastian Keil, Franziska Knopf, Michael Brand","doi":"10.1016/j.bpj.2024.12.009","DOIUrl":"10.1016/j.bpj.2024.12.009","url":null,"abstract":"<p><p>Embryonic development is orchestrated by the action of morphogens, which spread out from a local source and activate, in a field of target cells, different cellular programs based on their concentration gradient. Fibroblast growth factor 8 (Fgf8) is a morphogen with important functions in embryonic organizing centers. It forms a gradient in the extracellular space by free diffusion, interaction with the extracellular matrix (ECM), and receptor-mediated endocytosis. However, morphogen gradient regulation by ECM is still poorly understood. Here, we show that specific heparan sulfate proteoglycans (HSPGs) bind Fgf8 with different affinities directly in the ECM of living zebrafish embryos, thus affecting its diffusion and signaling. Using single-molecule fluorescence correlation spectroscopy, we quantify this binding in vivo, and find two different modes of interaction. First, reducing or increasing the concentration of specific HSPGs in the extracellular space alters Fgf8 diffusion and, thus, its gradient shape. Second, ternary complex formation of Fgf8 ligand with Fgf receptors and HSPGs at the cell surface requires HSPG attachment to the cell membrane. Together, our results show that graded Fgf8 morphogen distribution is achieved by constraining free Fgf8 diffusion through successive interactions with HSPGs at the cell surface and in ECM space.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"996-1010"},"PeriodicalIF":3.2,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142817036","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}

{"title":"Locally fast, globally slow.","authors":"Pierre Recouvreux","doi":"10.1016/j.bpj.2024.07.022","DOIUrl":"10.1016/j.bpj.2024.07.022","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"859-860"},"PeriodicalIF":3.2,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141733492","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}

{"title":"Measurement force, speed and post-mortem time affect the ratio of CNS grey to white matter elasticity.","authors":"Julia Monika Becker, Alexander Kevin Winkel, Eva Kreysing, Kristian Franze","doi":"10.1016/j.bpj.2025.03.009","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.009","url":null,"abstract":"<p><p>For several decades, many attempts have been made to characterise the mechanical properties of grey and white matter, which constitute the two main compartments of the central nervous system (CNS), with various methods and contradictory results. In particular, the ratio of grey-to-white-matter elasticity is sometimes larger than 1 and sometimes smaller; the reason for this apparent discrepancy is currently unknown. Here, we exploited atomic force microscopy (AFM)-based indentation measurements to systematically investigate how the measurement force, measurement speed, post-mortem interval and temperature affect the measured elasticity of spinal cord tissue, and in particular the ratio of grey-to-white-matter elasticity (K_g/K_w). Within the explored parameter space, increasing measurement force and speed increased the measured elasticity of both grey and white matter. However, K_g/K_w declined from values as high as ∼5 at low forces and speeds to ∼1 for high forces and speeds. K_g/K_w also strongly depended on the anatomical plane in which the measurements were conducted and was considerably higher in transverse sections compared to longitudinal sections. Furthermore, the post-mortem interval impacted both the absolute measured tissue elasticity and K_g/K_w. Grey matter elasticity started decreasing ∼3 hours post-mortem until reaching a plateau after ∼6 hours. In contrast, white matter elasticity started declining from the beginning of the measurements until ∼6 hours post-mortem, when it also levelled off. As a result, K_g/K_w increased until ∼6 hours post-mortem before stabilising. Between 20°C and 38°C, both grey and white matter elasticity decreased at a similar rate, without affecting K_g/K_w. We have thus identified differences in the response of grey and white matter to varying strains and strain rates, and the post-mortem interval, and excluded temperature as a factor affecting K_g/K_w. These differential responses likely contribute to the contradictory results obtained with different methods working in different strain regimes.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647047","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}

{"title":"Buckling of red blood cell membrane in narrow capillaries induces excessive wall shear stress.","authors":"Deyun Liu, Kazuyasu Sugiyama, Xiaobo Gong","doi":"10.1016/j.bpj.2025.03.010","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.010","url":null,"abstract":"<p><p>The deformation of red blood cells (RBCs) in Poiseuille flows of capillary vessels is fundamental for hemodynamics in cellular scale for various physiological or pathological scenarios. However, the mechanical criterion for membrane buckling and the impact of the asymmetric deformations of cells on the hemodynamics are currently unclear. In this study, a microfluidic system with narrow tubular channels was set up for experimental observations, and numerical simulations using the Immersed Boundary Method were performed to illustrate the deformation of RBCs and their surrounding flow fields in detail. The dependence of the buckling on the capillary number (a dimensionless parameter measuring the ratio of viscous fluid force with elastic force of membrane) was discovered. Then we derived the criterion of buckling of cell membrane under local circumferential pressure by considering the buckling of an elastic ring with neglecting thickness. Results also show that the extra pressure drop and the wall shear stress associated with the appearance of membrane buckling increase non-linearly. This work provides biomechanical fundamentals for mechanobiological studies of microvascular disease associated with the change of mechanical properties of RBCs.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143647045","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}

{"title":"Aggregation and disaggregation of red blood cells: depletion versus bridging.","authors":"Nicolas Moreno, Kirill Korneev, Alexey Semenov, Alper Topuz, Thomas John, Minne Paul Lettinga, Marco Ellero, Christian Wagner, Dmitry A Fedosov","doi":"10.1016/j.bpj.2025.03.007","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.007","url":null,"abstract":"<p><p>The aggregation of red blood cells (RBCs) is a complex phenomenon that strongly impacts blood flow and tissue perfusion. Despite extensive research for more than 50 years, physical mechanisms that govern RBC aggregation are still under debate. Two proposed mechanisms are based on bridging and depletion interactions between RBCs due to the presence of macromolecules in blood plasma. The bridging hypothesis assumes the formation of bonds between RBCs through adsorbing macromolecules, while the depletion mechanism results from the exclusion of macromolecules from the inter-cellular space, leading to effective attraction. Existing experimental studies generally cannot differentiate between these two aggregation mechanisms, though several recent investigations suggest concurrent involvement of the both mechanisms. We explore dynamic aggregation and disaggregation of two RBCs using three simulation models: a potential-based model mimicking depletion interactions, a bridging model with immobile bonds, and a new bridging model with mobile bonds which can slide along RBC membranes. Simulation results indicate that dynamic aggregation of RBCs primarily arises from depletion interactions, while disaggregation of RBCs involves both mechanisms. The bridging model with mobile bonds reproduces well the corresponding experimental data, offering insights into the interplay between bridging and depletion interactions and providing a framework for studying similar interactions between other biological cells.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633402","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}

{"title":"Structural and Hydrodynamic Characterization of Dimeric Human Oligoadenylate Synthetase 2.","authors":"Amit Koul, Danielle Gemmill, Nikhat Lubna, Markus Meier, Natalie Krahn, Evan P Booy, Jörg Stetefeld, Trushar R Patel, Sean A McKenna","doi":"10.1016/j.bpj.2025.02.025","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.02.025","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143630169","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}

{"title":"Control of cardiac waves in human iPSC-CM syncytia by a Halbach array and magnetic nanoparticles.","authors":"Maria R Pozo, Yuli W Heinson, Christianne J Chua, Emilia Entcheva","doi":"10.1016/j.bpj.2025.03.006","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.006","url":null,"abstract":"<p><p>The Halbach array, originally developed for particle accelerators, is a compact arrangement of permanent magnets that creates well-defined magnetic fields without heating. Here, we demonstrate its use for modulating the speed of electromechanical waves in cardiac syncytia of human stem cell-derived cardiomyocytes. At 40-50 mT magnetic field strength, a cylindrical dipolar Halbach array boosted the conduction velocity, CV, by up to 25% when the magnetic field was co-aligned with the electromechanical wave (but not when perpendicular to it). To observe the effects, a short-term incubation of the cardiac cell constructs with non-targeted magnetic nanoparticles, mNPs, was sufficient. This led to increased CV anisotropy, and effects were most pronounced at slower pacing rates. Instantaneous formation and re-arrangement of elongated mNP clusters upon magnetic field rotation was seen, creating dynamic structural anisotropy that may have contributed to the directional CV effects. This approach may be useful for anti-arrhythmic control of cardiac waves.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143613324","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}