Biophysical journal最新文献

{"title":"Distinct roles of protrusions and collagen deformation in collective invasion of cancer cell types.","authors":"Ye Lim Lee, Gregory D Longmore, Amit Pathak","doi":"10.1016/j.bpj.2025.03.032","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.032","url":null,"abstract":"<p><p>The breast tumor microenvironment is composed of heterogeneous cell populations, including normal epithelial cells, cancer-associated fibroblasts, and tumor cells that lead collective cell invasion. Both leader tumor cells and CAFs are known to play important roles in tumor invasion across the collagen-rich stromal boundary. However, their individual abilities to utilize their cell-intrinsic protrusions and perform force-based collagen remodeling to collectively invade remain unclear. To compare collective invasion phenotypes of leader-like tumor cells and CAFs, we embedded spheroids composed of 4T1 tumor cells or mouse tumor-derived CAF cell lines within 3D collagen gels and analyzed their invasion and collagen deformation. We found that 4T1s undergo greater invasion while generating lower collagen deformation compared to CAFs. Although force-driven collagen deformations are conventionally associated with higher cellular forces and invasion, here 4T1s specifically rely on actin-based protrusions, while CAFs rely on myosin-based contractility for collective invasion. In denser collagen, both cell types slowed their invasion, and selective pharmacological inhibitions show that Arp2/3 is required but myosin-II is dispensable for 4T1 invasion. Furthermore, depletion of CDH3 from 4T1s and DDR2 from CAFs reduces their ability to distinguish between collagen densities. For effective invasion, both cell types reorient and redistribute magnetically pre-aligned collagen fibers. With heterogenous cell populations of co-cultured CAFs and 4T1s, higher percentage of CAFs impeded invasion while increasing collagen fiber alignment. Overall, our findings demonstrate distinctive mechanisms of collective invasion adopted by 4T1 tumor cells and CAFs, one relying more on protrusions and the other on force-based collagen deformation. These results suggest that individually targeting cellular protrusions or contractility may not be universally applicable for all cell types or collagen densities, and a better cell type-dependent approach could enhance effectiveness of cancer therapies.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762696","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":"Predicted Functional Consequences of WNT Ligand Mutations in Colorectal Cancer.","authors":"Aamir Ahmed, David Shorthouse","doi":"10.1016/j.bpj.2025.03.030","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.030","url":null,"abstract":"<p><p>Mutations to WNT ligands in cancer are poorly understood. WNT ligands are a family of secreted proteins that trigger the activation of the WNT pathway with essential roles in cell development and carcinogenesis, particularly of the colorectal tract. Whilst the structure of WNT ligands has been elucidated, little is known about how mutations in these proteins affect colorectal cancer. Here we show that mutations in WNT ligands found in colorectal cancer show regional specificity and selectivity for particular conserved sequences. We further show that mutations in colorectal cancer are not selecting for changes in the binding affinity of the ligands to their receptor. We use clinical data to identify mutations to WNT5A as under selection and correlating with patient outcome in colorectal cancer, and by combining mutational data and folding energy calculations, elastic network modelling, and molecular dynamics simulations we show that these mutations alter its structural dynamics and flexibility. Thus we predict a novel structure-function relationship for mutations in WNT ligands in human cancers.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750759","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":"Single Molecule Measurements of Double-Stranded DNA Condensation.","authors":"Helena Gien, Ioulia Rouzina, Michael Morse, Micah J McCauley, Mark C Williams","doi":"10.1016/j.bpj.2025.03.033","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.033","url":null,"abstract":"<p><p>Electrostatically driven double stranded (ds)DNA condensation is critical in regulating many biological processes, including bacteriophage and virus replication and the packaging of chromosomal DNA in sperm heads. Here we review single-molecule (SM) measurements of dsDNA condensed by cationic proteins, polypeptides, and small multivalent cations. Optical tweezers (OT) measurements of dsDNA collapsed by cationic condensing agents reveal a critical condensing force unique to each condensing agent that is tunable with condensing agent concentration and ionic strength. DNA globules visualized via atomic force microscopy (AFM), transmission electron microscopy (TEM), and cryo-electron microscopy (CryoEM) reveal condensed dsDNA adopting several conformations including highly ordered toroids with a measurable central hole and, more recently, the maximally dense, yarn-ball like structures observed with dsDNA condensed by the HIV-1 nucleocapsid protein (NC). The combination of these approaches provides multifaceted insight into the shape and size of electrostatically condensed dsDNA globules and the kinetics of their formation and dissolution. We also review the physics of dsDNA condensation, including recent studies that show dsDNA globule size is tunable with ionic strength. Overall, this review provides important insights into understanding dsDNA condensate-regulated biological processes, as well as potential uses for gene delivery.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762698","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":"Accuracy of distance distributions and dynamics from single-molecule FRET.","authors":"Mark Nüesch, Miloš T Ivanović, Daniel Nettels, Robert B Best, Benjamin Schuler","doi":"10.1016/j.bpj.2025.03.028","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.028","url":null,"abstract":"<p><p>Single-molecule spectroscopy combined with Förster resonance energy transfer (FRET) is widely used to quantify distance dynamics and distributions in biomolecules. Most commonly, measurements are interpreted using simple analytical relations between experimental observables and the underlying distance distributions. However, these relations make simplifying assumptions, such as a separation of timescales between inter-dye distance dynamics, fluorescence lifetimes, and dye reorientation, the validity of which is notoriously difficult to assess from experimental data alone. Here, we use experimentally validated long-timescale, all-atom explicit-solvent molecular dynamics simulations of a disordered peptide with explicit fluorophores for testing these assumptions, in particular the separation of the relevant timescales and the description of chain dynamics in terms of diffusion in a potential of mean force. Our results allow us to quantitatively assess the resulting errors; they indicate that even outside the simple limiting regimes, the errors from common approximations in data analysis are generally smaller than the systematic uncertainty limiting the accuracy of FRET efficiencies. We also illustrate how the direct comparison between measured and simulated experimental data can be employed to optimize force field parameters and develop increasingly realistic simulation models.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750753","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":"A closed-loop system for millisecond readout and control of membrane tension.","authors":"Michael Sindoni, Jörg Grandl","doi":"10.1016/j.bpj.2025.03.025","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.025","url":null,"abstract":"<p><p>Characterizing the function of force-gated ion channels is essential for understanding their molecular mechanisms and how they are affected by disease-causing mutations, lipids, or small molecules. Pressure-clamp electrophysiology is a method that is established and widely used to characterize the mechanical sensitivity of force-gated ion channels. However, the physical stimulus many force-gated ion channels sense is not pressure, but membrane tension. Here, we further develop the approach of combining patch-clamp electrophysiology with differential interference contrast microscopy into a system that controls membrane tension in real time. The system uses machine learning object detection for millisecond analysis of membrane curvature and control of pipette pressure to produce a closed-loop membrane tension clamp. The analysis of membrane tension is fully automated and includes propagation of experimental errors, thereby increasing throughput and reducing bias. A dynamic control program clamps membrane tension with at least 93% accuracy and 0.3 mN/m precision. Additionally, the absence of tension drift enables averaging open probabilities of ion channels with low expression and/or unitary conductance over long durations. Using this system, we apply a tension step protocol and show that TMEM63A responds to tension with a tension of half-maximal activation of T₅₀ = 5.5±0.1 mN/m. Overall, this system allows for precise and efficient generation of tension-response relationships of force-gated ion channels.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750834","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":"A Discard-and-Restart MD algorithm for the sampling of protein intermediate states.","authors":"Alan Ianeselli, Jonathon Howard, Mark B Gerstein","doi":"10.1016/j.bpj.2025.03.024","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.024","url":null,"abstract":"<p><p>We introduce a Discard-and-Restart molecular dynamics (MD) algorithm tailored for the sampling of realistic protein intermediate states. It aids computational structure-based drug discovery by reducing the simulation times to compute a \"quick sketch\" of folding pathways by up to 2000x. The algorithm iteratively performs short MD simulations and measures their proximity to a target state via a collective variable (CV) loss, which can be defined in a flexible fashion, locally or globally. Using the loss, if the trajectory proceeds toward the target, the MD simulation continues. Otherwise, it is discarded, and a new MD simulation is restarted, with new initial velocities randomly drawn from a Maxwell-Boltzmann distribution. The discard-and-restart algorithm demonstrates efficacy and atomistic accuracy in capturing the folding pathways in several contexts: (1) fast-folding small protein domains; (2) the folding intermediate of the prion protein PrP; and (3) the spontaneous partial unfolding of α-Tubulin, a crucial event for microtubule severing. During each iteration of the algorithm, we can perform AI-based analysis of the transitory conformations to find potential binding pockets, which could represent druggable sites. Overall, our algorithm enables systematic and computationally efficient exploration of conformational landscapes, enhancing the design of ligands targeting dynamic protein states.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742016","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":"Perspectives: Comparison of Deep Learning Segmentation Models on Biophysical and Biomedical Data.","authors":"J Shepard Bryan, Pedro Pessoa, Meysam Tavakoli, Steve Pressé","doi":"10.1016/j.bpj.2025.03.023","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.023","url":null,"abstract":"<p><p>Deep learning based approaches are now widely used across biophysics to help automate a variety of tasks including image segmentation, feature selection, and deconvolution. However, the presence of multiple competing deep learning architectures, each with its own advantages and disadvantages, makes it challenging to select an architecture best suited for a specific application. As such, we present a comprehensive comparison of common models. Here, we focus on the task of segmentation assuming typical (often small) training dataset sizes available from biophysics experiments and compare the following four commonly used architectures: convolutional neural networks, U-Nets, vision transformers, and vision state space models. In doing so, we establish criteria for determining optimal conditions under which each model excels, thereby offering practical guidelines for researchers and practitioners in the field.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143750756","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":"Charge distribution and helicity tune the binding of septin's amphipathic helix domain to membranes.","authors":"Christopher J Edelmaier, Stephen J Klawa, S Mahsa Mofidi, Qunzhao Wang, Shreeya Bhonge, Ellysa J D Vogt, Brandy N Curtis, Wenzheng Shi, Sonya M Hanson, Daphne Klotsa, M Gregory Forest, Amy S Gladfelter, Ronit Freeman, Ehssan Nazockdast","doi":"10.1016/j.bpj.2025.03.008","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.008","url":null,"abstract":"<p><p>Amphipathic helices (AHs) are secondary structures that can facilitate binding of proteins to the membrane by folding into a helix with hydrophobic and hydrophilic faces that interact with the same surfaces in the lipid membrane. Septins are cytoskeletal proteins that preferentially bind to domains of micron-scale curvature on the cell membrane. Studies have shown that AH domains in septin are essential for curvature sensing. We present the first computational study of septin AH interactions with lipid bilayers. Using all-atom simulations and metadynamics-enhanced sampling, we study the effect of charge distribution at the flanking ends of septin AH on the energy for helical folding and its consequences on the binding configuration and affinity to the membrane. This is relevant to septins, since the net positive charge on the flanking C-terminal amino acids is a conserved property across several organisms. Simulations revealed that the energy barrier for folding in the neutral-capped AH is much larger than the charge-capped AH, leading to a small fraction of AH folding and integration to the membrane compared to a significantly folded configuration in the bound charge-capped AH. These observations are consistent with the binding measurements of synthetic AH constructs with variable helicity to lipid vesicles. Additionally, we examined an extended AH sequence including eight amino acids upstream and downstream of the AH to mimic the native protein. Again, simulations and experiments show that the extended peptide, with a net positive charge at C-terminus, adopts a strong helical configuration in solution, giving rise to a higher membrane affinity. Altogether, these results identify the energy cost for folding of AHs as a regulator of AH binding configuration and affinity and provide a basic template for parameterizing AH-membrane interactions as a starting point for the future multiscale simulations for septin-membrane interactions.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143778882","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":"Flow Sensitive Ion Channels in Vascular Endothelial Cells: Mechanisms of Activation and Roles in Mechanotransduction.","authors":"Katie M Beverley, Sang Joon Ahn, Irena Levitan","doi":"10.1016/j.bpj.2025.03.021","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.021","url":null,"abstract":"<p><p>The purpose of this review is to evaluate the current knowledge about the mechanisms by which mechanosensitive ion channels are activated by fluid shear stress in endothelial cells. We focus on three classes of endothelial ion channels that are most well studied for their sensitivity to flow and roles in mechanotransduction: inwardly-rectifying K⁺ channels, Piezo channels and TRPV channels. We also discuss the mechanisms by which these channels initiate and contribute to mechanosensitive signaling pathways. Three types of mechanisms have been described for flow-induced activation of ion channels: 1) through interaction with apical membrane flow sensors, such as glycocalyx, which is likely to be deformed by flow, 2) directly by sensing membrane stretch that is induced by shear stress, or 3) via flow-sensitive channel-channel or lipid channel interactions. We also demonstrate the physiological role of these channels and how they are related to cardiovascular and neurological diseases. Further studies are needed to determine how these channels function cooperatively to mediate the endothelial response to flow.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742018","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":"Agent-based model of the human colon to investigate mechanisms of pathogen colonization resistance.","authors":"Samantha Johanna Fletcher, Carly Ching, Mark Paladin Suprenant, Darash Desai, Muhammad Hamid Zaman","doi":"10.1016/j.bpj.2025.03.022","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.03.022","url":null,"abstract":"<p><p>Recent global burden of disease studies have shown that bacterial infections are responsible for over 13 million deaths worldwide, or one in every eight deaths, each year. Enteric diarrheal infections, in particular, pose a significant challenge and strain on healthcare systems as many are difficult to address pharmaceutically, and thus, rely primarily on the patient's own immune system and gut microbiome to fight the infection. Nonetheless, the specific mechanisms behind gut microbiome colonization resistance of enteric pathogens are not well-defined and microbiome diversity is difficult to represent and study experimentally. To address this gap, we have constructed an agent-based computational model of the colonic epithelium cross-section to investigate the colonic invasion of enteric pathogens. The model focuses on three main regions: epithelial layer, mucosal bilayer, and adjacent lumen, and utilizes four main cell types as agents: anaerobic bacteria, facultative anaerobic bacteria, human goblet cells, and pathogens. Utilizing this model, we are able to describe the healthy microbiome cell-localization and dynamics from our mucosal bilayer. In addition, we are also able to investigate the impact of host dietary fiber consumption and simulate pathogen invasion. The model exemplifies the possibility and potential to explore key gut microbiome colonization resistance mechanisms and environmental impacts on the gut microbiome using computational methods.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742017","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}