Biophysical journal最新文献

{"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":"565-573"},"PeriodicalIF":3.2,"publicationDate":"2025-02-04","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":"Metabolically intact nuclei are fluidized by the activity of the chromatin remodeling motor BRG1.","authors":"Fitzroy J Byfield, Behnaz Eftekhari, Kaeli Kaymak-Loveless, Kalpana Mandal, David Li, Rebecca G Wells, Wenjun Chen, Jasna Brujic, Giulia Bergamaschi, Gijs J L Wuite, Alison E Patteson, Paul A Janmey","doi":"10.1016/j.bpj.2024.11.3322","DOIUrl":"10.1016/j.bpj.2024.11.3322","url":null,"abstract":"<p><p>The structure and dynamics of the nucleus regulate cellular functions, with shape changes impacting cell motility. Although the nucleus is generally seen as the stiffest organelle in the cell, cells can nevertheless deform the nucleus to large strains by small mechanical stresses. Here, we show that the mechanical response of the cell nucleus exhibits active fluidization that is driven by the BRG1 motor of the SWI/SNF/BAF chromatin remodeling complex. Atomic force microscopy measurements show that the nucleus alters stiffness in response to the cell substrate stiffness, which is retained after the nucleus is isolated, and that the work of nuclear compression is mostly dissipated rather than elastically stored. Inhibiting BRG1 stiffens the nucleus and eliminates dissipation and nuclear remodeling both in isolated nuclei and in intact cells. These findings uncover a novel role of the BRG1 motor in nuclear mechanics, advancing our understanding of cell motility mechanisms.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"494-507"},"PeriodicalIF":3.2,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142765741","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":"540-548"},"PeriodicalIF":3.2,"publicationDate":"2025-02-04","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}

{"title":"Diet therapy abates mutant APC and KRas effects by reshaping plasma membrane cholesterol nanodomains.","authors":"Eunjoo Kim, Alfredo Erazo-Oliveras, Mónica Muñoz-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":"10.1016/j.bpj.2024.12.020","url":null,"abstract":"<p><p>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 1) colonocyte plasma membrane cholesterol homeostasis, order, and receptor nanoclustering, 2) colonocyte cell proliferation, and 3) 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. In addition, oncogene-induced loss of cholesterol homeostasis altered Fzd7, LRP6, and KRas cluster structure/organization. Notably, we show that the combination of chemoprotective 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.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"508-527"},"PeriodicalIF":3.2,"publicationDate":"2025-02-04","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}

{"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":"574-585"},"PeriodicalIF":3.2,"publicationDate":"2025-02-04","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":"549-564"},"PeriodicalIF":3.2,"publicationDate":"2025-02-04","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":"Trade-off movement between hydraulic resistance escape and shear stress escape by cancer cells.","authors":"Jialin Shi, Yiteng Jin, Shujing Wang, Chunxiong Luo","doi":"10.1016/j.bpj.2024.12.021","DOIUrl":"10.1016/j.bpj.2024.12.021","url":null,"abstract":"<p><p>In the circulatory system, the microenvironment surrounding cancer cells is complex and involves multiple coupled factors. We selected two core physical factors, shear stress and hydraulic resistance, and constructed a microfluidic device with dual negative inputs to study the trade-off movement behavior of cancer cells when facing coupled factors. We detected significant shear stress escape phenomena in the MDA-MB-231 cell line and qualitatively explained this behavior using a cellular force model. Through the dual validation of substrate anti-cell-adhesion modification and employment of the MCF-7 cell line, we further substantiated the predictability and feasibility of our model. This study provides an explanation for the trade-off underlying the direction-choosing mechanism of cancer cells when facing environmental selection.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"528-539"},"PeriodicalIF":3.2,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142885156","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":"Effects of molecular interaction and liver sinusoidal mechanical properties on leukocyte adhesions.","authors":"Jingchen Zhu, Shenbao Chen, Lüwen Zhou, Xiaobo Gong, Yuhong Cui, Yan Zhang, Mian Long, Shouqin Lü","doi":"10.1016/j.bpj.2024.11.3315","DOIUrl":"10.1016/j.bpj.2024.11.3315","url":null,"abstract":"<p><p>It is interesting to find pathologically that leukocytes, especially neutrophils, tend to adhere in the liver sinusoids dominantly but not in the postsinusoidal venules. While both views of receptor-ligand interactions and physical trapping are proposed for mediating leukocyte adhesion in liver sinusoids, integrated investigations for classifying their respective contributions are poorly presented. With a combination of Monte Carlo simulation and immersed boundary method, this study explored numerically the effects of molecular interaction kinetics and sinusoidal mechanical properties on leukocyte adhesion in liver sinusoid jointly. Results showed that, within the range of biological limitations, the lumen stenosis ratio, leukocyte stiffness, Disse space stiffness and endothelium permeability regulate the comprehensive adhesion process in a descending order of significance in the presence of receptor-ligand interactions. While leukocyte adhesions could be mutually promoted with proper combinations of leukocyte stiffness, lumen stenosis, and molecular interaction, the binding affinity is insensitive under the conditions with low leukocyte stiffness in normal lumen stenosis and high leukocyte stiffness in high lumen stenosis. This work deepens the understanding of recruitment mechanism of leukocyte in liver sinusoids.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":"480-493"},"PeriodicalIF":3.2,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142738149","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":"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, which can undergo Förster resonance energy transfer (FRET), 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 FRET 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 nm/ns - 10 nm/ns) and constant force (10 pN - 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":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","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":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Temperature Dependence of Membrane Viscosity of Ternary Lipid GUV with L_o Domains.","authors":"Julia Tanaka, Kenya Haga, Naohito Urakami, Masayuki Imai, Yuka Sakuma","doi":"10.1016/j.bpj.2025.01.024","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.01.024","url":null,"abstract":"<p><p>In the cell membrane, it is considered that saturated lipids and cholesterol organize liquid-ordered (L_o) domains in a sea of liquid-disordered (L_d) phase, and proteins relevant to cellular functions are localized in the L_o domains. Since the diffusion of transmembrane proteins is regulated by the membrane viscosity, we investigate the temperature dependence of the membrane viscosity of the ternary GUV composed of the saturated lipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), the unsaturated lipid 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and cholesterol (CHOL) to understand the effect of the phase separation on the membrane viscosity using microinjection technique. In the microinjection method, membrane viscosity is estimated by comparing the flow pattern induced on a spherical membrane with a hydrodynamic model. For phase-separated GUVs, the flow pattern is visualized by the motion of the domains. In this study, we developed a method to visualize the flow patterns of homogeneous GUVs above the phase separation temperature by using beads attached to the GUVs. We succeed to measure the membrane viscosity of ternary GUVs both above phase separation temperature and in the phase-separated region and find that the membrane viscosity decreases dramatically by the phase separation. In the phase-separated region, i.e., GUV with L_o domains, the membrane viscosity is determined by that of the L_d phase, η_Ld, and show weak temperature dependence compared with that of the DOPC single component GUV, which is a main component of the L_d phase. We revealed that the Moelwyn-Hughest (MH) model which takes into account the effects of the membrane composition, viscosity of pure component and interaction between components well describes the obtained membrane viscosity of the ternary GUV both above phase separation temperature and in the phase-separated region. The drastic decrease of the membrane viscosity by the phase separation plays an important role in regulating the mobility of constituents in multi-component membranes.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143188023","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}