Biophysical journal最新文献

{"title":"FAIR Data for Optical Tweezers Experiments.","authors":"Matthew T J Halma, Sowmiyaa Kumar, Jan van Eck, Sanne Abeln, Alexander Gates, Gijs J L Wuite","doi":"10.1016/j.bpj.2025.03.005","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.005","url":null,"abstract":"<p><p>The single-molecule biophysics community has delivered significant impacts to our understanding of fundamental biological processes, yet the field is also siloed and has fragmented data structures which impede data sharing and limit the ability to conduct comprehensive meta-analyses. To advance the field of optical tweezers in single-molecule biophysics, it is important that the field adopts open and collaborative data sharing that facilitate meta-analyses that combine diverse resources and supports more advanced analyses, akin to those seen in projects like the Protein Data Bank and the 1000 Genomes Project. Here, we assess the state of data findability, accessibility, interoperability, and reusability (the FAIR principles) within the single-molecule optical tweezers field. By combining a qualitative review with quantitative tools from bibliometrics, our analysis suggests that the field has significant room for improvement in terms of FAIR adherence. Finally, we discuss the potential of compulsory data deposition and a minimal set of metadata standards to ensure reproducibility and interoperability between systems. While implementing these measures may not be straightforward, they are key steps that will enhance the integration of optical tweezers biophysics with the broader biomedical literature.</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":"143623369","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":"Electrotaxis disrupts patterns of cell-cell interactions of human corneal epithelial cells in vitro.","authors":"Rebecca M Crossley, Simon F Martina-Perez","doi":"10.1016/j.bpj.2025.03.004","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.004","url":null,"abstract":"<p><p>Electrotaxis, the process by which eukaryotic cells establish a polarity and move directionally along an electric field, is a well-studied mechanism to steer the migration of cells in vitro and in vivo. While the influence of an electric field on single cells in culture is well-documented, the influence of the electric field on cell-cell interactions has not been well studied. In this work, we quantify the length, duration and number of cell-cell interactions during electrotaxis of human corneal epithelial cells and compare the properties of these interactions with those arising in the absence of an electric field. We find that contact inhibition of locomotion and velocity alignment, two key behaviours observed during dynamic physical interactions between cells in vitro, are strongly affected by an electric field. Furthermore, we establish a link between the location of a cell-cell contact on the cell surface and the resulting cell interaction behaviours. By mapping the regions of the cell surface with a characteristic response to contact with another cell, we find that the spatial distribution of possible responses upon cell-cell contact is altered upon induction of an electric field. Altogether, this work shows how the electric field not only influences individual cell motility and directionality, but also affects cell-cell interactions.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143613325","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":"Escherichia coli α-hemolysin induces red blood cell retention in a microfluidic spleen-like device.","authors":"Nicolás Andrés Saffioti, Emilia Belén Sousa, Mickaël Marin, María Florencia Leal Denis, Mariano Aníbal Ostuni, Vanesa Herlax, Pablo Julio Schwarzbaum, Diego Pallarola","doi":"10.1016/j.bpj.2025.03.001","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.001","url":null,"abstract":"<p><p>α-hemolysin (HlyA) is a major exotoxin secreted by uropathogenic Escherichia coli (UPEC), known for its ability to lyse red blood cells (RBCs). While its lytic effects are well characterized, the non-lytic alterations on RBCs, such as increased permeability to Ca²⁺, osmotic imbalance, and morphological alterations, remain less understood and may be critical in UPEC pathogenesis. This study investigates the impact of these non-lytic alterations on the rheology and mechanics of RBCs using two biomimetic microfluidic devices that model key aspects of RBCs' circulation. In the first device, which mimics the mechanical deformation of RBCs in narrow capillaries, HlyA sublytic concentrations were found to significantly impair RBC deformability. These changes were accompanied by an increase in cytosolic Ca²⁺ and volume expansion. In contrast, the non-acylated protoxin, ProHlyA, neither impaired the deformability of RBCs nor triggered changes in cytosolic Ca²⁺ or cell volume. The second device, which simulates the RBCs' filtration by the spleen's red pulp, revealed that HlyA, but not ProHlyA, increased RBCs' retention in small gaps resembling splenic fenestrations. The extent of RBCs' retention was partially mitigated by blocking purinergic signaling, indicating a contribution of the HlyA-induced volume increase in this process. Our results suggest that the increase in cytosolic Ca²⁺ elicited by HlyA impacts RBCs' circulation by decreasing RBCs' deformability and increasing spleen retention. However, this impairment of RBCs' performance can function as a defense mechanism to aid in the retention of HlyA-bound RBCs, removing them from circulation, and potentially preventing vascular hemolysis.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143613326","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":"Pair cross-correlation analysis for assessing protein co-localization.","authors":"Pintu Patra, Cecilia Sanchez, Michael Lanzer, Ulrich S Schwarz","doi":"10.1016/j.bpj.2025.03.002","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.002","url":null,"abstract":"<p><p>Measuring co-localization of different types of molecules is essential to understand molecular organization in biological systems. The pair cross-correlation (PCC) function computed from two-color microscopy images provides a measure of co-localization between differently labeled molecules. Here, we compute a theoretical expression for the PCC function between two molecules using two-dimensional Gaussian distributions as the effective point spread functions for single molecules. Through our analytical calculations, we provide a quantitative description of PCC in the case of multiple signal pairs. By fitting our analytical solutions to simulated images, we can estimate both small and large separation distances. We then apply this method to malaria-infected red blood cells (RBCs) imaged by stimulated emission depletion (STED) microscopy. We cross-correlate the signal for the knob-associated histidine-rich protein (KAHRP), which the parasite uses to remodel the spectrin-actin network of RBCs, with different signals from the RBCs and find that its average separation from the ankyrin junctions increases from 40 nm to 120 nm during the 48 hours of the infectious cycle.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143613327","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":"The brief life-story of irreversibly sickled cells.","authors":"Merav Socolovsky","doi":"10.1016/j.bpj.2025.03.003","DOIUrl":"10.1016/j.bpj.2025.03.003","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603881","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":"Does vitamin E behave like cholesterol? An examination of vitamin E's effects on phospholipid membrane structure and dynamics through sum-frequency vibrational spectroscopy.","authors":"Joshua M Taylor, Kai H Gerton, John C Conboy","doi":"10.1016/j.bpj.2025.02.028","DOIUrl":"10.1016/j.bpj.2025.02.028","url":null,"abstract":"<p><p>Vitamin E (VE) has historically been described as an antioxidant and its roles in radical species scavenging and nutrition are well studied. VE has been proposed to have secondary roles within the membrane but these roles are not as well characterized, with contradictory results emerging throughout the literature. Due to similar structural motifs, comparisons between VE and cholesterol (CHO), another membrane component, have been commonly made. Despite these comparisons showing that phospholipid-CHO and phospholipid-VE interactions may behave similarly, VE's potential influence on phospholipid flip-flop specifically is not as well studied when compared with CHO's influence. Here, we show through the use of sum-frequency vibrational spectroscopy that VE at both biological (0.5-1.5 mol %) and supraphysiological (2.5-5 mol %) concentrations shows similar characteristics to that of CHO in its ability to induce alkyl chain ordering of phospholipids within planar supported lipid bilayers of the saturated lipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine. In addition to chain ordering, the introduction of VE accelerates phospholipid flip-flop by approximately three times (0.5-2.5 mol %) with rates approaching an order-of-magnitude increase (5 mol %) at high VE content. The increase in phospholipid flip-flop rates is attributed to the decrease in the molar compression modulus of the membrane. These results suggest that VE influences the ordering and compressibility of the membrane similar to CHO.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143584480","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":"Enhancing fluorescence correlation spectroscopy with machine learning to infer anomalous molecular motion.","authors":"Nathan Quiblier, Jan-Michael Rye, Pierre Leclerc, Henri Truong, Abdelkrim Hannou, Laurent Heliot, Hugues Berry","doi":"10.1016/j.bpj.2025.01.026","DOIUrl":"10.1016/j.bpj.2025.01.026","url":null,"abstract":"<p><p>The random motion of molecules in living cells has consistently been reported to deviate from standard Brownian motion, a behavior coined as \"anomalous diffusion.\" To study this phenomenon in living cells, fluorescence correlation spectroscopy (FCS) and single-particle tracking (SPT) are the two main methods of reference. In opposition to SPT, FCS, with its classical analysis methodology, cannot consider models of motion for which no analytical expression of the auto-correlation function is known. This excludes, for instance, anomalous continuous-time random walks and random walk on fractal. Moreover, the whole acquisition sequence of the classical FCS methodology takes several tens of minutes. Here, we propose a new analysis approach that frees FCS of these limitations. Our approach associates each individual FCS recording with a vector of features based on an estimator of the auto-correlation function and uses machine learning to infer the underlying model of motion and to estimate the values of the motion parameters. Using simulated recordings, we show that this approach endows FCS with the capacity to distinguish between a range of standard and anomalous random motions, including continuous-time random walk and random walk on fractal. Our approach exhibits performances comparable to the best-in-class state-of-the-art algorithms for SPT and can be used with a range of FCS setup parameters. Since it can be applied on individual recordings of short duration, we show that, with our method, FCS can be used to monitor rapid changes of the motion parameters. Finally, we apply our method on experimental FCS recordings of calibrated fluorescent beads in increasing concentrations of glycerol in water. Our results accurately predict that the beads follow Brownian motion with a diffusion coefficient and anomalous exponent, which agree with classical predictions from Stokes-Einstein law even at large glycerol concentrations. Taken together, our approach significantly augments the analysis power of FCS to capacities that are similar to state-of-the-art SPT approaches.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"844-856"},"PeriodicalIF":3.2,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897545/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143373579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Theory of photosynthetic membrane influence on B800-B850 energy transfer in the LH2 complex.","authors":"Chawntell Kulkarni, Hallmann Óskar Gestsson, Lorenzo Cupellini, Benedetta Mennucci, Alexandra Olaya-Castro","doi":"10.1016/j.bpj.2025.01.011","DOIUrl":"10.1016/j.bpj.2025.01.011","url":null,"abstract":"<p><p>Photosynthetic organisms rely on a network of light-harvesting protein-pigment complexes to efficiently absorb sunlight and transfer excitation energy to reaction center proteins where charge separation occurs. In photosynthetic purple bacteria, these complexes are embedded within the cell membrane, with lipid composition affecting complex clustering, thereby impacting inter-complex energy transfer. However, the impact of the lipid bilayer on intra-complex excitation dynamics is less understood. Recent experiments have addressed this question by comparing photo-excitation dynamics in detergent-isolated light-harvesting complex 2 (LH2) to LH2 complexes embedded in membrane discs mimicking the biological environment, revealing differences in spectra and energy-transfer rates. In this paper, we use available quantum chemical and spectroscopy data to develop a complementary theoretical study on the excitonic structure and intra-complex energy-transfer kinetics of the LH2 of photosynthetic purple bacteria Rhodoblastus (Rbl.) acidophilus (formerly Rhodopseudomonas acidophila) in two different conditions: the LH2 in a membrane environment and detergent-isolated LH2. We find that dark excitonic states, crucial for B800-B850 energy transfer within LH2, are more delocalized in the membrane model. Using nonperturbative and generalized Förster calculations, we show that such increased quantum delocalization results in a 30% faster B800 to B850 transfer rate in the membrane model, in agreement with experimental results. We identify the dominant energy-transfer pathways in each environment and demonstrate how differences in the B800 to B850 transfer rate arise from changes in LH2's electronic properties when embedded in the membrane. Furthermore, by accounting for the quasi-static variations of electronic excitation energies in the LH2, we show that the broadening of the distribution of the B800-B850 transfer rates is affected by the lipid composition. We argue that such variation in broadening could be a signature of a speed-accuracy trade-off, commonly seen in biological process.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"722-739"},"PeriodicalIF":3.2,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897548/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143027791","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Physical effects of crowdant size and concentration on collective microtubule polymerization.","authors":"Jashaswi Basu, Aman Soni, Chaitanya A Athale","doi":"10.1016/j.bpj.2025.01.020","DOIUrl":"10.1016/j.bpj.2025.01.020","url":null,"abstract":"<p><p>The polymerization of cytoskeletal filaments is regulated by both biochemical pathways, as well as physical factors such as crowding. The effect of crowding in vivo emerges from the density of intracellular components. Due to the complexity of the intracellular environment, most studies are based on either in vitro reconstitution or theory. Crowding agent (crowdants) size has been shown to influence polymerization of both actin and microtubules (MTs). Previously, the elongation rates of MT dynamics observed at single filament scale were reported to decrease with increasing concentrations of small but not large crowdants, and this correlated with in vivo viscosity increases. However, the exact nature of the connection between viscosity, crowdant size, nucleation, and MT elongation has remained unclear. Here, we use in vitro reconstitution of bulk MT polymerization kinetics and microscopy to examine the collective effect of crowdant molecular weight, volume occupancy, and viscosity on elongation and spontaneous polymerization. We find MT elongation rates obtained from bulk polymerization decrease in the presence of multiple low-molecular weight (LMW) crowdants, while increasing with high-molecular weight (HMW) crowdants. Lattice Monte Carlo simulations of an effective model of collective polymerization demonstrate reduced polymerization rates arise due to decrease in monomer diffusion due to small-sized crowdants. However, MT polymerization in the absence of nucleators, de novo, shows a crowdant size independence of polymerization rate and critical concentration, depending solely on concentration of the crowdant. In microscopy, we find LMW crowdants result in short but many filaments, while HMW crowdants increase filament density, but have little effect on lengths. The effect of crowdant volume fraction ϕ_C and size in de novo polymerization match simulations, demonstrating crowdants affect elongation independent of nucleation. Thus, the effect of viscosity on collective MT dynamics, i.e., filament numbers and lengths, shows crowdant size dependence for elongation, but independence for de novo polymerization.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"789-806"},"PeriodicalIF":3.2,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897549/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143063188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In silico analyses of molecular force sensors for mechanical characterization of biological systems.","authors":"Diana M Lopez, Carlos E Castro, Marcos Sotomayor","doi":"10.1016/j.bpj.2025.01.025","DOIUrl":"10.1016/j.bpj.2025.01.025","url":null,"abstract":"<p><p>Mechanical forces play key roles in biological processes such as cell migration and sensory perception. In recent years, molecular force sensors have been developed as tools for in situ force measurements. Here, we use all-atom steered molecular dynamics simulations to predict and study the relationship between design parameters and mechanical properties for three types of molecular force sensors commonly used in cellular biological research: two peptide and one DNA based. The peptide-based sensors consist of a pair of fluorescent proteins that can undergo Förster resonance energy transfer, linked by spider silk (GPGGA)_n or synthetic (GGSGGS)_n disordered regions. The DNA-based sensor consists of two fluorophore-labeled strands of DNA that can be unzipped or sheared upon force application with a Förster resonance energy transfer signal as readout of dissociation. We simulated nine sensors, three of each kind. After equilibration, flexible peptide linkers of three different lengths were stretched by applying forces to their N- and C-terminal Cα atoms in opposite directions. Similarly, we equilibrated a DNA-based sensor and pulled on the phosphate atom of the terminal guanine of one strand and a selected phosphate atom on the other strand for pulling in the opposite direction. These simulations were performed at constant velocity (0.01-10 nm/ns) and constant force (10-500 pN) for all versions of the sensors. Our results show how the force response of these sensors depends on their length, sequence, configuration, and loading rate. Mechanistic insights gained from simulations analyses indicate that interpretation of experimental results should consider the influence of transient formation of secondary structure in peptide-based sensors and of overstretching in DNA-based sensors. These predictions can guide optimal fluorophore choice and facilitate the rational design of new sensors for use in protein, DNA, hybrid systems, and molecular devices.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"829-843"},"PeriodicalIF":3.2,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11897771/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143188020","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}