Biophysical journal最新文献

Migrasome formation is initiated preferentially in tubular junctions by membrane tension.

IF 3.2 3区生物学

Biophysical journal Pub Date : 2025-01-03 DOI: 10.1016/j.bpj.2024.12.029

Ben Zucker, Raviv Dharan, Dongju Wang, Li Yu, Raya Sorkin, Michael M Kozlov

{"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":"https://doi.org/10.1016/j.bpj.2024.12.029","url":null,"abstract":"Migrasomes, the vesicle-like membrane micro-structures, arise on the retraction fibers (RFs), the branched nano-tubules 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 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.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Hypo-osmotic stress shifts transcription of circadian genes.

IF 3.2 3区生物学

Biophysical journal Pub Date : 2025-01-02 DOI: 10.1016/j.bpj.2024.12.027

Androniqi Qifti, Ayobami Adeeko, Madison Rennie, Elizabeth McGlaughlin, David McKinnon, Barbara Rosati, Suzanne Scarlata

{"title":"Hypo-osmotic 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":"https://doi.org/10.1016/j.bpj.2024.12.027","url":null,"abstract":"Cells respond to hypo-osmotic 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 hypo-osmotic stress for 12 and 24 hours 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 hypo-osmotic stress for 12 hours, 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 hours 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 down-regulation, 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.","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}

引用次数: 0

Lattice Light-Sheet Microscopy Allows for Super-Resolution Imaging of Receptors in Leaf Tissue.

IF 3.2 3区生物学

Biophysical journal Pub Date : 2024-12-30 DOI: 10.1016/j.bpj.2024.12.028

Traeger Jeremiah, Yang Mengran, Stacey Gary, Orr Galya, Hu Dehong

{"title":"Lattice Light-Sheet Microscopy Allows for Super-Resolution Imaging of Receptors in Leaf Tissue.","authors":"Traeger Jeremiah, Yang Mengran, Stacey Gary, Orr Galya, Hu Dehong","doi":"10.1016/j.bpj.2024.12.028","DOIUrl":"https://doi.org/10.1016/j.bpj.2024.12.028","url":null,"abstract":"Plant leaf tissues are difficult to image via fluorescent microscopy due to the presence of chlorophyll and other pigments, which provide large background fluorescence. The 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 the lattice light-sheet microscopy, we can localize immune response proteins in 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, where 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 the lattice light-sheet microscopy's capabilities for imaging tissue with problematic background fluorescence that otherwise makes super-resolution fluorescence microscopy difficult.","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}

引用次数: 0

Active Matter in the Nucleus: Chromatin Remodeling Drives Nuclear Force Dissipation.

IF 3.4 3区生物学

Biophysical journal Pub Date : 2024-12-24 DOI: 10.1016/j.bpj.2024.12.026

Soham Ghosh

引用次数: 0

Amyloid beta Aβ1-40 activates Piezo1 channels in brain capillary endothelial cells.

IF 3.4 3区生物学

Biophysical journal Pub Date : 2024-12-24 DOI: 10.1016/j.bpj.2024.12.025

Xin Rui Lim,Luc Willemse,Osama F Harraz

{"title":"Amyloid beta Aβ1-40 activates Piezo1 channels in brain capillary endothelial cells.","authors":"Xin Rui Lim,Luc Willemse,Osama F Harraz","doi":"10.1016/j.bpj.2024.12.025","DOIUrl":"https://doi.org/10.1016/j.bpj.2024.12.025","url":null,"abstract":"Amyloid-beta (Aβ) peptide accumulation on blood vessels in the brain is a hallmark of neurodegeneration. While Aβ peptides constrict cerebral arteries and arterioles, their impact on capillaries is less understood. Aβ was recently shown to constrict brain capillaries through pericyte contraction, but whether-and if so how-Aβ affects endothelial cells (ECs) remains unknown. ECs represent the predominant vascular cell type in the cerebral circulation, and we recently showed that the mechanosensitive ion channel Piezo1 is functionally expressed in the plasma membrane of ECs. Since Aβ disrupts membrane structures, we hypothesized that Aβ1-40, the predominantly deposited isoform in the cerebral circulation, alters endothelial Piezo1 function. Using patch clamp electrophysiology and freshly isolated capillary ECs, we assessed the impact of Aβ1-40 peptide on single-channel Piezo1 activity. We show that Aβ1-40 increased Piezo1 open probability and the channel open time. Aβ1-40 effects were absent when Piezo1 was genetically deleted or when a superoxide dismutase/catalase mimetic was used. Further, Aβ1-40 enhanced Piezo1 mechanosensitivity and lowered the pressure of half-maximal Piezo1 activation. Our data collectively suggest that Aβ1-40 facilitates higher Piezo1-mediated cation influx in brain ECs. These novel findings have the potential to unravel the possible involvement of Piezo1 modulation in the pathophysiology of neurodegenerative diseases characterized by Aβ accumulation.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"8 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142887511","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}

引用次数: 0

Predicting RNA Structure and Dynamics with Deep Learning and Solution Scattering.

IF 3.2 3区生物学

Biophysical journal Pub Date : 2024-12-24 DOI: 10.1016/j.bpj.2024.12.024

Edan Patt, Scott Classen, Michal Hammel, Dina Schneidman-Duhovny

{"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":"https://doi.org/10.1016/j.bpj.2024.12.024","url":null,"abstract":"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 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 fourteen experimental datasets, 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.","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":"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}

引用次数: 0

Revealing an origin of temperature-dependent structural change in intrinsically disordered protein.

IF 3.2 3区生物学

Biophysical journal Pub Date : 2024-12-23 DOI: 10.1016/j.bpj.2024.12.022

Rintaro Inoue, Takashi Oda, Hiroshi Nakagawa, Taiki Tominaga, Takahisa Ikegami, Tsuyoshi Konuma, Hiroki Iwase, Yukinobu Kawakita, Mamoru Sato, Masaaki Sugiyama

{"title":"Revealing an origin of temperature-dependent structural change in intrinsically disordered protein.","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":"https://doi.org/10.1016/j.bpj.2024.12.022","url":null,"abstract":"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 dynamics of the intrinsically disordered region of Hef, 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. Nuclear magnetic resonance (NMR) studies revealed the absence of promotion of 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.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-23","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}

引用次数: 0

Vesicle docking and fusion pore modulation by the neuronal calcium sensor Synaptotagmin-1.

IF 3.2 3区生物学

Biophysical journal Pub Date : 2024-12-23 DOI: 10.1016/j.bpj.2024.12.023

Maria Tsemperouli, Sudheer Kumar Cheppali, Felix Rivera Molina, David Chetrit, Ane Landajuela, Derek Toomre, Erdem Karatekin

{"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.2024.12.023","DOIUrl":"https://doi.org/10.1016/j.bpj.2024.12.023","url":null,"abstract":"Synaptotagmin-1 (Syt1) is a major calcium sensor for rapid neurotransmitter release in neurons and hormone release in many neuroendocrine cells. It possesses two tandem cytosolic C2 domains that bind calcium, negatively charged phospholipids, and the neuronal SNARE complex. Calcium binding to Syt1 triggers exocytosis, but how this occurs is not well understood. Syt1 has additional roles in docking dense core vesicles (DCV) and synaptic vesicles (SV) to the plasma membrane (PM) and in regulating fusion pore dynamics. Thus, Syt1 perturbations could affect release through vesicle docking, fusion triggering, fusion pore regulation, or a combination of these. Here, using a human neuroendocrine cell line, we show that neutralization of highly conserved polybasic patches in either C2 domain of Syt1 impairs both DCV docking and efficient release of serotonin from DCVs. Interestingly, the same mutations resulted in larger fusion pores and faster release of serotonin during individual fusion events. Thus, Syt1's roles in vesicle docking, fusion triggering, and fusion pore control may be functionally related.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142885160","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}

引用次数: 0

Trade-off movement between hydraulic resistance escape and shear stress escape by cancer cells.

IF 3.2 3区生物学

Biophysical journal Pub Date : 2024-12-21 DOI: 10.1016/j.bpj.2024.12.021

Jialin Shi, Yiteng Jin, Shujing Wang, Chunxiong Luo

引用次数: 0

Diet therapy abates mutant APC and KRas effects by reshaping plasma membrane cholesterol nanodomains.

IF 3.2 3区生物学

Biophysical journal Pub Date : 2024-12-20 DOI: 10.1016/j.bpj.2024.12.020

Eunjoo Kim, Alfredo Erazo-Oliveras, Mónica Munoz-Vega, Natividad R Fuentes, Michael L Salinas, Miranda J George, Roger S Zoh, Martha E Hensel, Bhimanagouda S Patil, Ivan Ivanov, Nancy D Turner, Robert S Chapkin

{"title":"Diet therapy abates mutant APC and KRas effects by reshaping plasma membrane cholesterol nanodomains.","authors":"Eunjoo Kim, Alfredo Erazo-Oliveras, Mónica Munoz-Vega, Natividad R Fuentes, Michael L Salinas, Miranda J George, Roger S Zoh, Martha E Hensel, Bhimanagouda S Patil, Ivan Ivanov, Nancy D Turner, Robert S Chapkin","doi":"10.1016/j.bpj.2024.12.020","DOIUrl":"https://doi.org/10.1016/j.bpj.2024.12.020","url":null,"abstract":"Cholesterol-enriched plasma membrane domains are known to serve as signaling platforms in a diverse array of cellular processes. However, the link between cholesterol homeostasis and mutant APC-KRas-associated colorectal tumorigenesis remains to be established. Thus, we investigated the impact of Apc-Kras on (i) colonocyte plasma membrane cholesterol homeostasis, order, and receptor nanoclustering, (ii) colonocyte cell proliferation, and (iii) whether these effects are modulated by select membrane active dietaries (MADs). We observed that oncogenic APC-KRas increased membrane order by perturbing cholesterol homeostasis when cell proliferation is upregulated, in part by altering the expression of genes associated with cholesterol influx, export and de novo synthesis in mouse colorectal cancer (CRC) models and CRC patients. Additionally, oncogene-induced loss of cholesterol homeostasis altered Fzd7, LRP6 and KRas cluster structure/organization. Notably, we show that the combination of chemo-protective MADs, i.e., n-3 PUFAs and curcumin, reduced colonic membrane free cholesterol, order, receptor cluster size, cell proliferation and the number of dysplastic foci in mutant APC-KRas models. This work highlights the dynamic shaping of plasma membrane organization during colon tumorigenesis and the utility of membrane-targeted cancer therapy.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142871247","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}

引用次数: 0