Biophysical journal最新文献

{"title":"Squishy things: Mechanophenotyping of actin networks in minimal cell models","authors":"Nadab Wubshet","doi":"10.1016/j.bpj.2024.12.035","DOIUrl":"https://doi.org/10.1016/j.bpj.2024.12.035","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"49 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143027299","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":"Hypoosmotic stress shifts transcription of circadian genes.","authors":"Androniqi Qifti, Ayobami Adeeko, Madison Rennie, Elizabeth McGlaughlin, David McKinnon, Barbara Rosati, Suzanne Scarlata","doi":"10.1016/j.bpj.2024.12.027","DOIUrl":"10.1016/j.bpj.2024.12.027","url":null,"abstract":"<p><p>Cells respond to hypoosmotic stress by initial swelling followed by intracellular increases in the number of osmolytes and initiation of gene transcription that allow cells to adapt to the stress. Here, we have studied the genes that change expression under mild hypoosmotic stress for 12 and 24 h in rat cultured smooth muscle cells (WKO-3M22). We find shifts in the transcription of many genes, several of which are associated with circadian rhythm, such as per1, nr1d1, per2, dbp, and Ciart. To determine whether there is a connection between osmotic stress and circadian rhythm, we first subjected cells to hypoosmotic stress for 12 h, and find that Bmal1, a transcription factor whose nuclear localization promotes transit through the cell cycle, localizes to the cytoplasm, which may connect osmotic stress to cell cycle. Bmal1 nuclear localization recovers after 24 h and cell cycle resumes even though the osmotic stress remains elevated. We hypothesized that osmotic force is transmitted into the cell by deforming caveolae membrane domains releasing one of its structural proteins, cavin-1, which can travel to the nucleus and affect gene transcription. In support of this idea, we find that Bmal1 localization becomes independent of osmotic stress with cavin-1 downregulation, and Bmal1 localization is independent of osmotic stress in a cell line with low caveolae expression. These studies indicate that osmotic stress transiently arrests circadian rhythm and cell-cycle progression through caveolae deformation.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142926374","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":"Integrating mechanical and molecular perspectives in leukocyte adhesion: New computational insights","authors":"Min Lin","doi":"10.1016/j.bpj.2024.12.031","DOIUrl":"https://doi.org/10.1016/j.bpj.2024.12.031","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"20 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142939681","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":"Muscular expression of pezo-1 differentially influences swimming and crawling in C. elegans","authors":"Adina Fazyl, Mackenzie Jones, Damiano Marchiafava, Shifat Niha, Erin Sawilchik, Wolfgang Stein, Andrés Vidal-Gadea","doi":"10.1016/j.bpj.2024.12.032","DOIUrl":"https://doi.org/10.1016/j.bpj.2024.12.032","url":null,"abstract":"Mechanosensitive PIEZO ion channels are evolutionarily conserved proteins that are widely expressed in neuronal and muscular tissues. This study explores the role of the mechanoreceptor PEZO-1 in the body wall muscles of <ce:italic>Caenorhabditis elegans</ce:italic>, focusing on its influence on two locomotor behaviors, swimming and crawling. Using confocal imaging, we reveal that PEZO-1 localizes to the sarcolemma and plays a crucial role in modulating calcium dynamics, which is important for muscle contraction. When we knocked down <ce:italic>pezo-1</ce:italic> expression in striated muscles with RNA interference, calcium levels in head and tail muscles increased. However, we discovered differential effects on two locomotion modes displayed by <ce:italic>C. elegans</ce:italic>: while downregulation of <ce:italic>pezo-1</ce:italic> led to an increase in crawling speed, the overall trajectory of the calcium signal during the crawl cycle remained the same. In contrast, <ce:italic>pezo-1</ce:italic> downregulation caused a reduction in swimming speed, increased activation of the ventral tail muscles, and a disruption of dorsoventral movement asymmetry, a critical feature that enables propulsion in water. These alterations were correlated with impaired swimming posture and path curvature, suggesting that that PEZO-1 differentially modulates swimming and crawling behaviors.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"24 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142939683","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":"Understanding the coarse-grained free energy landscape of phospholipids and their phase separation","authors":"Patrick G. Sahrmann, Gregory A. Voth","doi":"10.1016/j.bpj.2024.12.030","DOIUrl":"https://doi.org/10.1016/j.bpj.2024.12.030","url":null,"abstract":"The cell membrane exhibits lateral heterogeneity due to the preferential association among the large number of lipid species that constitute the membrane. In particular, the preferential association of cholesterol (CHOL) with saturated lipids into ordered domains has been an area of intense investigation. The large spatiotemporal scales that comprise spontaneous domain formation largely precludes computational investigation via conventional all-atom molecular dynamics. We demonstrate here that molecular coarse-grained (CG) models, obtained from the bottom-up, i.e., via statistical mechanical renormalization of atomistic models, are capable of spontaneous assembly and phase separation for two model raft-like systems, DLiPC/DPPC/CHOL and DOPC/DPPC/CHOL. The resulting bottom-up CG models exhibit spontaneous self-assembly and phase separation and recapitulate the structural correlations of the underlying atomistic models. The accuracy and fast dynamics of these CG models constitute an effective means of bypassing the limited spatiotemporal scales of atomistic simulations. As the first bottom-up CG models of lipid phase separation, the CG models in this work provide an informative analysis for further construction of bottom-up CG models transferable across a range of lipid compositions.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"21 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142939735","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":"Functionally distinct SNARE motifs of SNAP25 cooperate in SNARE assembly and membrane fusion","authors":"Katelyn N. Kraichely, Connor R. Sandall, Binyong Liang, Volker Kiessling, Lukas K. Tamm","doi":"10.1016/j.bpj.2024.12.034","DOIUrl":"https://doi.org/10.1016/j.bpj.2024.12.034","url":null,"abstract":"Intracellular membrane traffic involves controlled membrane fission, and fusion and is essential for eukaryotic cell homeostasis. Most intracellular fusion is facilitated by Soluble <ce:italic>N</ce:italic>-ethylmaleimide sensitive factor attachment protein receptor (SNARE) proteins, which catalyze membrane merging by assembly of a coiled helical bundle of four 60- to 70-residue “SNARE motifs.” Perhaps no intracellular fusion reaction is as tightly regulated as that at the neuronal synapse, mediated by the synaptic vesicle SNARE Synaptobrevin-2 and the presynaptic plasma membrane SNAREs Syntaxin-1a and SNAP25. SNAP25 is different from its partner SNAREs: it contributes not one but two SNARE motifs to the final complex and instead of transmembrane domains is anchored in the membrane by post-translational palmitoylation of a long flexible linker between the SNARE motifs. Despite reports of structural and functional differences between the two SNARE motifs, many models of SNARE assembly and fusion consider SNAP25 to be a single functional unit and do not address how linking two distinct motifs in a single polypeptide contributes to synaptic SNARE assembly and fusion. To investigate whether SNAP25’s two SNARE motifs regulate each other’s folding and ability to assemble with other SNAREs, we determined their secondary structures in isolation and in the context of the whole protein by NMR spectroscopy and correlated the ability of the individual membrane-anchored SNARE motifs to interact with Syntaxin-1a and catalyze fusion in FRET-based binding and single-particle fusion assays, respectively. Our results demonstrate that the isolated N-terminal SNARE motif of SNAP25 promotes stronger Syntaxin-1a binding on membranes and more efficient fusion than wild-type SNAP25, while the C-terminal SNARE motif binds only transiently and facilitates kinetically delayed fusion. By comparing the functional properties of the single motifs to those of the full-length protein, we propose a new model of SNAP25 self-regulation in SNARE assembly and membrane fusion.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"67 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142939680","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":"Lattice light-sheet microscopy allows for super-resolution imaging of receptors in leaf tissue.","authors":"Jeremiah Traeger, Mengran Yang, Gary Stacey, Galya Orr, Dehong Hu","doi":"10.1016/j.bpj.2024.12.028","DOIUrl":"10.1016/j.bpj.2024.12.028","url":null,"abstract":"<p><p>Plant leaf tissues are difficult to image via fluorescence microscopy due to the presence of chlorophyll and other pigments, which provide large background fluorescence. Lattice light-sheet microscopy offers the advantage of using Bessel beams to illuminate a thin focal region of interest for microscopy, allowing for the excitation of fluorescent molecules within this region without surrounding chlorophyll-like objects outside of the region of interest. Here, we apply STORM super-resolution techniques to observe receptor-like kinases in Arabidopsis thaliana leaf cells. By applying this technique with lattice light-sheet microscopy, we can localize immune-response proteins at sub-100-nm length scales and reconstruct three-dimensional locations of proteins within individual leaf cells. Using this technique, we observed the effect of the ATP and flg22 elicitors, where we observed a significant degree of internalization of cognate receptors P2K1 and FLS2. We were also able to similarly observe differences in colocalization due to stimulation with these elicitors, whereby we observe proteins on the membrane becoming less colocalized as a result of stimulation, suggesting an immune-response mechanism involving receptor internalization via distinct pathways. These data show lattice light-sheet microscopy's capabilities for imaging tissue with problematic background fluorescence that otherwise makes super-resolution fluorescence microscopy difficult.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142913810","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":"Predicting RNA structure and dynamics with deep learning and solution scattering.","authors":"Edan Patt, Scott Classen, Michal Hammel, Dina Schneidman-Duhovny","doi":"10.1016/j.bpj.2024.12.024","DOIUrl":"10.1016/j.bpj.2024.12.024","url":null,"abstract":"<p><p>Advanced deep learning and statistical methods can predict structural models for RNA molecules. However, RNAs are flexible, and it remains difficult to describe their macromolecular conformations in solutions where varying conditions can induce conformational changes. Small-angle x-ray scattering (SAXS) in solution is an efficient technique to validate structural predictions by comparing the experimental SAXS profile with those calculated from predicted structures. There are two main challenges in comparing SAXS profiles to RNA structures: the absence of cations essential for stability and charge neutralization in predicted structures and the inadequacy of a single structure to represent RNA's conformational plasticity. We introduce a solution conformation predictor for RNA (SCOPER) to address these challenges. This pipeline integrates kinematics-based conformational sampling with the innovative deep learning model, IonNet, designed for predicting Mg²⁺ ion binding sites. Validated through benchmarking against 14 experimental data sets, SCOPER significantly improved the quality of SAXS profile fits by including Mg²⁺ ions and sampling of conformational plasticity. We observe that an increased content of monovalent and bivalent ions leads to decreased RNA plasticity. Therefore, carefully adjusting the plasticity and ion density is crucial to avoid overfitting experimental SAXS data. SCOPER is an efficient tool for accurately validating the solution state of RNAs given an initial, sufficiently accurate structure and provides the corrected atomistic model, including ions.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142891770","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":"Active Matter in the Nucleus: Chromatin Remodeling Drives Nuclear Force Dissipation.","authors":"Soham Ghosh","doi":"10.1016/j.bpj.2024.12.026","DOIUrl":"https://doi.org/10.1016/j.bpj.2024.12.026","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"17 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142887512","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":"Revealing an origin of temperature-dependent structural change in intrinsically disordered proteins.","authors":"Rintaro Inoue, Takashi Oda, Hiroshi Nakagawa, Taiki Tominaga, Takahisa Ikegami, Tsuyoshi Konuma, Hiroki Iwase, Yukinobu Kawakita, Mamoru Sato, Masaaki Sugiyama","doi":"10.1016/j.bpj.2024.12.022","DOIUrl":"10.1016/j.bpj.2024.12.022","url":null,"abstract":"<p><p>Intrinsically disordered proteins (IDPs) show structural changes stimulated by changes in external conditions. This study aims to reveal the temperature dependence of the structure and the dynamics of the intrinsically disordered region of the helicase-associated endonuclease for fork-structured DNA, one of the typical IDPs, using an integrative approach. Small-angle X-ray scattering (SAXS) and circular dichroism (CD) studies revealed that the radius of gyration and ellipticity at 222 nm remained constant up to 313-323 K, followed by a decline above this temperature range. NMR studies revealed the absence of a promotion of the α helix. As a result, SAXS, CD, and NMR data strongly suggest that these temperature-dependent structural changes were primarily due to a reduction in the content of the polyproline II (PPII) helix. Moreover, quasielastic neutron scattering studies revealed a slight change in the activation energy in a similar temperature range. Considering the concept of glass transition, it is posited that dynamical cooperativity between the PPII helix and water may play a significant role in these structural changes. The findings suggest that internal dynamics are crucial for regulating the structure of IDPs, highlighting the importance of considering dynamical cooperativity in future studies of protein behavior under varying temperature conditions.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142885150","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}