Biophysical journal最新文献

{"title":"Diverse toxins exhibit a common binding mode to the nicotinic acetylcholine receptors.","authors":"Hung N Do, Jessica Z Kubicek-Sutherland, S Gnanakaran","doi":"10.1016/j.bpj.2025.02.022","DOIUrl":"10.1016/j.bpj.2025.02.022","url":null,"abstract":"<p><p>Nicotinic acetylcholine receptors (nAChRs) are critical ligand-gated ion channels in the human nervous system. They are targets for various neurotoxins produced by algae, plants, and animals. While many structures of nAChRs bound by neurotoxins have been published, the binding mechanism of toxins to the nAChRs remains unclear. In this work, we have performed extensive Gaussian accelerated molecular dynamics simulations on several Aplysia californica nAChRs in complex with α-conotoxins, strychnine, and pinnatoxins, as well as human nAChRs in complex with α-bungarotoxin and α-conotoxin, to determine the binding and dissociation pathways of the toxins to the nAChRs and the associated effects. We uncovered two common binding and dissociation pathways shared by toxins and nAChRs. In the first binding pathway, the toxins diffused from the bulk solvent to bind a region near the extracellular pore before moving downwards along the nAChRs to the nAChR orthosteric pocket. The second binding pathway involved a direct diffusion of the toxins from the bulk solvent into the nAChR orthosteric pocket. The dissociation pathways were the reverse of the observed binding pathways. Notably, we determined that the electrostatically bipolar interactions between the nAChR orthosteric pocket and toxins provided an explanation for the common binding mode shared by diverse toxins.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143522525","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":"Vesicle docking and fusion pore modulation by the neuronal calcium sensor Synaptotagmin-1.","authors":"Maria Tsemperouli, Sudheer Kumar Cheppali, Felix Rivera-Molina, David Chetrit, Ane Landajuela, Derek Toomre, Erdem Karatekin","doi":"10.1016/j.bpj.2025.02.013","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.02.013","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514666","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":"Image-Based Analysis of the Genome's Fractality During the Cell Cycle.","authors":"Suho Lee, Xutong Liu, Ivan Ziabkin, Alexandra Zidovska","doi":"10.1016/j.bpj.2025.02.014","DOIUrl":"10.1016/j.bpj.2025.02.014","url":null,"abstract":"<p><p>The human genome consists of about 2 m of DNA packed inside the cell nucleus barely 10 μm in diameter. DNA is complexed with histones, forming chromatin fiber, which folds inside the nucleus into loops, TADs, A/B compartments and chromosome territories. This organization is knot-free and self-similar across length scales, leading to a hypothesis that the genome presents a fractal globule, which was corroborated by chromosome conformation capture experiments. In addition, many microscopy techniques have been used to obtain the fractal dimension of the genome's spatial distribution from its images. However, different techniques often required that different definitions of fractal dimension be adapted, making the comparison of these results not trivial. In this study, we use spinning disc confocal microscopy to collect high-resolution images of nuclei in live human cells during the cell cycle. We then systematically compare existing image-based fractal analyses - including mass-scaling, box-counting, lacunarity and multifractal spectrum - by applying them to images of human cell nuclei and investigate changes in the genome's spatial organization during the cell cycle. Our data reveal that different image-based fractal measurements offer distinct metrics, highlighting different features of the genome's spatial organization. Yet, all these metrics consistently indicate the following trend for the changes in the genome's organization during the cell cycle: the genome being compactly packed in early G1 phase, followed by a decondensation throughout the G1 phase, and a subsequent condensation in the S and G2 phases. Our comprehensive comparison of image-based fractal analyses reconciles the perceived discrepancies between different methods. Moreover, our results offer new insights into the physical principles underlying the genome's organization and its changes during the cell cycle.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143498686","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":"FRETsael: Nanometer localization of biomolecular interactions using fluorescence lifetime imaging.","authors":"Yair Razvag, Paz Drori, Shalhevet Klemfner, Eran Meshorer, Eitan Lerner","doi":"10.1016/j.bpj.2025.02.017","DOIUrl":"10.1016/j.bpj.2025.02.017","url":null,"abstract":"<p><p>Super-resolution light microscopy techniques facilitate the observation of nm-sized biomolecules, which are 1-2 orders of magnitude smaller than the diffraction limit of light. Using super-resolution microscopy techniques, it is possible to observe fluorescence from two biomolecules in close proximity; however, not necessarily in direct interaction. Using FRETsael, we localize biomolecular interactions exhibiting FRET with nanometer accuracy, from two-color fluorescence lifetime imaging data. The concepts of FRETsael were tested first against simulations, in which the recovered localization accuracy is 20-30 nm for true-positive detections of FRET pairs. Further analysis of the simulation results reports the conditions in which true-positive rates are maximal. We then show the capabilities of FRETsael on simulated samples of actin-vinculin and ER-ribosome interactions, as well as experimental samples of actin-myosin two-color confocal imaging. Overall, the FRETsael approach paves the way toward studying biomolecular interactions with improved spatial resolution from laser scanning confocal two-color fluorescence lifetime imaging.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143456601","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":"Channel rectification made simple.","authors":"Harley T Kurata, Christopher N Rowley","doi":"10.1016/j.bpj.2025.01.013","DOIUrl":"10.1016/j.bpj.2025.01.013","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"587-589"},"PeriodicalIF":3.2,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11900148/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143036287","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":"Polarity sorting of actin filaments by motor-driven cargo transport.","authors":"Oghosa H Akenuwa, Steven M Abel","doi":"10.1016/j.bpj.2025.01.007","DOIUrl":"10.1016/j.bpj.2025.01.007","url":null,"abstract":"<p><p>During the active transport of cellular cargo, forces generated by cargo-associated molecular motors propel the cargo along cytoskeletal tracks. However, the forces impact not only the cargo, but also the underlying cytoskeletal filaments. To better understand the interplay between cargo transport and the organization of cytoskeletal filaments, we employ coarse-grained computer simulations to study actin filaments interacting with cargo-anchored myosin motors in a confined domain. We show that cargo transport can lead to the segregation of filaments into domains of preferred filament polarity separated by clusters of aggregated cargoes. The formation of polarity-sorted filament domains is enhanced by larger numbers of cargoes, more motors per cargo, and longer filaments. Analysis of individual trajectories reveals dynamic and heterogeneous behavior, including locally stable aggregates of cargoes that undergo rapid coalescence into larger clusters when sufficiently close. Our results provide insight into the impact of motor-driven organelle transport on actin filaments, which is relevant both in cells and in synthetic environments.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"704-716"},"PeriodicalIF":3.2,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11900188/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142999510","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":"Binuclear ruthenium complex linker length tunes DNA threading intercalation kinetics.","authors":"Ali A Almaqwashi, Micah J McCauley, Johanna Andersson, Ioulia Rouzina, Fredrik Westerlund, Per Lincoln, Mark C Williams","doi":"10.1016/j.bpj.2025.01.002","DOIUrl":"10.1016/j.bpj.2025.01.002","url":null,"abstract":"<p><p>Binuclear ruthenium complexes have been investigated for potential DNA-targeted therapeutic and diagnostic applications. Studies of DNA threading intercalation, in which DNA basepairs must be broken for intercalation, have revealed means of optimizing a model binuclear ruthenium complex to obtain reversible DNA-ligand assemblies with the desired properties of high affinity and slow kinetics. Here, we used single-molecule force spectroscopy to study a binuclear ruthenium complex with a longer semirigid linker relative to the model complex. Equilibrium results suggest a DNA affinity that is an order of magnitude higher than the parent binuclear ruthenium complex, likely due to a sterically relieved DNA threading intercalation mechanism. Notably, kinetics analysis shows that less DNA elongation is required for threading intercalation compared to the parent complex, and the association rate is two orders of magnitude faster. The ruthenium complex elongates the DNA duplex by ∼0.3 nm per bound ligand to reach the equilibrium intercalated state, with a significantly different energy landscape relative to the parent complex. Mechanical properties of the ligand-saturated DNA duplex show a higher persistence length, indicating that the longer semirigid linker provides enough molecular spacing to allow a single monomer to fully stack with basepairs, comparable to the monomeric parent ruthenium complex. The DNA basepairs in the equilibrium threading intercalated state are likely intact, and the ruthenium complex is shielded from the polar solution, providing measurable single-molecule confocal fluorescence signals. The obtained confocal fluorescence imaging of the bound dye confirms mostly uniform intercalation along the tethered DNA, consistent with other intercalators. The results of this study, along with previously examined ruthenium complex variants, illustrate tunable intercalation mechanisms guided by the rational design of therapeutic and diagnostic small molecules to target and modify the DNA duplex.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"667-676"},"PeriodicalIF":3.2,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11900151/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142963683","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":"Migrasome formation is initiated preferentially in tubular junctions by membrane tension.","authors":"Ben Zucker, Raviv Dharan, Dongju Wang, Li Yu, Raya Sorkin, Michael M Kozlov","doi":"10.1016/j.bpj.2024.12.029","DOIUrl":"10.1016/j.bpj.2024.12.029","url":null,"abstract":"<p><p>Migrasomes, the vesicle-like membrane microstructures, arise on the retraction fibers (RFs), the branched nanotubules pulled out of cell plasma membranes during cell migration and shaped by membrane tension. Migrasomes form in two steps: a local RF bulging is followed by a protein-dependent stabilization of the emerging spherical bulge. Here, we addressed theoretically and experimentally the previously unexplored mechanism of bulging of membrane tubular systems. We assumed that the bulging could be driven by increases in membrane tension and experimentally verified this hypothesis in live-cell and biomimetic systems. We exposed RF-generating live cells to a hypotonic medium, which produced water flows into the cells and a related increase in the membrane tension. We observed the formation of migrasome-like bulges with a preferential location in the RF branching sites. Next, we developed a biomimetic system of three membrane tubules pulled out of a giant plasma membrane vesicle (GPMV), connected by a junction, and subjected to pulling forces controlled by the GPMV membrane tension. An abrupt increase in the GPMV tension resulted in the generation of migrasome-like bulges mainly in the junctions. To understand the physical forces behind these observations, we considered theoretically the mechanical energy of a membrane system consisting of a three-way tubular junction with emerging tubular arms subjected to membrane tension. Substantiating our experimental observations, the energy minimization predicted a tension increase to drive the formation of membrane bulges, preferably in the junction site, independently of the way of the tension application. We generalized the model to derive universal criteria of bulging in branched membrane tubules.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"604-619"},"PeriodicalIF":3.2,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11900186/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142926386","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":"A Drosophila cardiac myosin increases jump muscle stretch activation and shortening deactivation.","authors":"Kaylyn M Bell, Alon T Brown, Sarah K Van Houten, Anna C Blice-Baum, William A Kronert, Amy K Loya, Jared Rafael T Camillo, Anthony Cammarato, David T Corr, Sanford I Bernstein, Douglas M Swank","doi":"10.1016/j.bpj.2025.01.001","DOIUrl":"10.1016/j.bpj.2025.01.001","url":null,"abstract":"<p><p>Stretch activation (SA), a delayed increase in force production after rapid muscle lengthening, is critical to the function of vertebrate cardiac muscle and insect asynchronous indirect flight muscle. SA enables or increases power generation in muscle types used in a cyclical manner. Recently, myosin isoform expression has been implicated as a mechanism for varying the amplitude of SA in some muscle types. For instance, we found that expressing a larval Drosophila myosin isoform in a muscle type with minimal SA, the Drosophila jump muscle, substantially increased SA amplitude and enabled positive cyclical power generation. To test whether other myosin isoforms could increase SA amplitude and whether the Drosophila heart benefits from SA, we identified two Drosophila cardiac myosin isoforms, CardM1 and CardM2, and expressed them in Drosophila jump muscle. CardM1, CardM2, and control jump muscle fibers all displayed the characteristic phase 3 of SA, with CardM2 SA amplitude ∼60% greater than that of CardM1 and control fibers. Increasing [P_i] from 0 to 16 mM increased CardM2 SA tension amplitude by 74%, yet had minimal or no effect on CardM1 or control muscle SA amplitude. CardM2 displayed the most prominent phase 3 dip when we induced shortening deactivation, a delayed decrease in force after muscle shortening. The magnitude of CardM2 shortening deactivation tension was ∼50% greater than control or CardM1 fibers. This, along with its greater stretch-activated tension, caused CardM2 to be the only isoform to produce positive power when its fiber length was sinusoidally oscillated. The results support our hypotheses that some myosin isoforms enable greater SA tension levels and suggest that the Drosophila heart is benefiting from SA and shortening deactivation in a manner similar to vertebrate hearts.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"651-666"},"PeriodicalIF":3.2,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11900181/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142969459","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":"Protein target search diffusion-association/dissociation free energy landscape around DNA binding site with flanking sequences.","authors":"Biao Wan, Jin Yu","doi":"10.1016/j.bpj.2025.01.005","DOIUrl":"10.1016/j.bpj.2025.01.005","url":null,"abstract":"<p><p>In this work we present a minimal structure-based model of protein diffusional search along local DNA amid protein binding and unbinding events on the DNA, taking into account protein-DNA electrostatic interactions and hydrogen-bonding (HB) interactions or contacts at the interface. We accordingly constructed the protein diffusion-association/dissociation free energy surface and mapped it to 1D as the protein slides along DNA, maintaining the protein-DNA interfacial HB contacts that presumably dictate the DNA sequence information detection. Upon DNA helical path correction, the protein 1D diffusion rates along local DNA can be physically derived to be consistent with experimental measurements. We also show that the sequence-dependent protein sliding or stepping patterns along DNA are regulated by collective interfacial HB dynamics, which also determines the ruggedness of the protein diffusion free energy landscape on the local DNA. In comparison, protein association or binding with DNA are generically dictated by the protein-DNA electrostatic interactions, with an interaction zone of nanometers around DNA. Extra degrees of freedom (DOFs) of the protein such as rotations and conformational fluctuations can be well accommodated within the protein-DNA electrostatic interaction zone. As such we demonstrate that the protein binding or association free energy profiling along DNA smoothens over the 1D diffusion free energy landscape, which leads to population variations for an order of magnitude upon a marginal free energetic smoothening around the specific or consensus sites. We further show that the protein unbinding or dissociation from a comparatively high-binding affinity DNA site is dominated by lateral diffusion to the flanking low-affinity sites. The results predict that experimental characterizations on the relative protein-DNA binding affinities or population profiling on the DNA are systematically and physically impacted by the extra DOFs of protein motions aside from 1D translation or helical tracking, as well as from flanking DNA sequences due to protein 1D diffusion and nonspecific binding/unbinding.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"677-692"},"PeriodicalIF":3.2,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11900189/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142999512","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}