Biophysical journal最新文献

{"title":"DNA Coronas Resist Nuclease Degradation.","authors":"Faisal Anees, Diego A Montoya, David S Pisetsky, Tariq Khan, Abhishek Kalpattu, Christine K Payne","doi":"10.1016/j.bpj.2025.05.028","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.05.028","url":null,"abstract":"<p><p>The interaction of cell-free DNA with biological particles has been linked to autoimmune diseases such as systemic lupus erythematosus, but mechanistic details are lacking. Our recent work has shown that DNA adsorbed on the surface of synthetic particles, forming a DNA \"corona,\" leads to an enhanced immunostimulatory response in macrophages, providing a model system to understand how DNA-particle interactions may lead to autoimmune diseases. This current study provides a detailed examination of DNA (500-600 base pairs and ∼10,000 base pairs) interacting with synthetic particles (40 nm - 10 μm) and planar surfaces. Of specific interest is how DNA adsorbed on the surface of particles is resistant to degradation by DNase 1, a common nuclease. DNA-particle complexes are characterized by a colorimetric DNA concentration assay (PicoGreen), spectroscopy (NanoDrop), dynamic light scattering (DLS), confocal fluorescence microscopy, and transmission electron microscopy (TEM). These studies show that the protective effect of the particle is size-dependent, with smaller (40 nm and 200 nm) particles providing less protection. Correlated with this lack of protection is significantly increased particle aggregation, suggesting that a DNA corona formed on the larger particles is protective, while particle aggregation, which dominates the smaller particles, is not protective. The formation of a ssDNA corona leads to the opposite protective effect with smaller (200 nm) particles leading to near complete protection of DNA from nuclease degradation. Overall, this study provides an important biophysical basis for the interaction of DNA with particles with the goal of guiding future in vitro and in vivo studies of cell-free DNA and particles in autoimmune disease.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144191433","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 Particle Tracking of Genetically Encoded Nanoparticles: Optimizing Expression for Cytoplasmic Diffusion Studies.","authors":"Elizaveta Korunova, Vitali Sikirzhystki, Jeffery L Twiss, Paula Vasquez, Michael Shtutman","doi":"10.1016/j.bpj.2025.05.025","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.05.025","url":null,"abstract":"<p><p>Single particle tracking (SPT) is a powerful technique for probing the diverse physical properties of the cytoplasm. Genetically encoded nanoparticles provide an especially convenient tool for such investigations, as they can be expressed and tracked in cells via fluorescence. Among these, 40-nm GEMs provide a unique opportunity to explore the cytoplasm. Their size corresponds to that of ribosomes and big protein complexes, allowing us to investigate the effects of the cytoplasm on the diffusivity of these objects while excluding the influence of chemical interactions during stressful events and pathological conditions. However, the effects of GEM expression levels on the measured cytoplasmic diffusivity remain largely uncharacterized in mammalian cells. To optimize the GEMs tracking and assess expression level effects, we developed doxycycline-inducible GEM expression system and compare it with a previously reported constitutive expression system. The inducible GEM expression system reduced the number of GEM particles from 2,000 to as low as 5-500 per average 2D cell cytoplasmic area, depending on doxycycline concentration and incubation time. This optimization enabled adjustment of particle density for imaging and improved homogeneity across the cell population. Moreover, we enhanced the analysis of GEM diffusivity by incorporating an effective diffusion coefficient that accounts for the type of motion and by quantifying motion heterogeneity through standard deviations of particle displacements within and between cells.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144191434","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":"RNA kink-turns are highly anisotropic with respect to lateral displacement of the flanking stems.","authors":"Eva Matoušková, Tomáš Dršata, Lucie Pfeiferová, Jiří Šponer, Kamila Réblová, Filip Lankaš","doi":"10.1016/j.bpj.2025.05.024","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.05.024","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144180165","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":"Modulation of striated muscle contractility by a high affinity myosin-targeting peptide.","authors":"Thomas Kampourakis, Negar Aboonasrshiraz, Theodore J Kalogeris, Rohit Singh, Dua'a Quedan, Motamed Qadan, Mozammel Hossain, Nasrin Taei, Michael Bih, Alysha Joseph, Kerry S McDonald, Douglas D Root","doi":"10.1016/j.bpj.2025.05.027","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.05.027","url":null,"abstract":"<p><p>Myosin-based regulation has emerged as a fundamental new concept governing both cardiac and skeletal muscle contractile function during both health and disease states. Myosin-targeted therapeutics have the potential to treat both heart failure with systolic or diastolic dysfunction based on either activating or inhibiting the function of myosin. In this study we developed a striated muscle myosin-specific high-affinity peptide targeted towards the proximal subfragment-2 (S2) region of the MYH7 myosin, which has been shown to undergo conformational changes associated with force generation by the myosin head domains. We characterized the peptide called 'Stabilizer' using a wide range of biochemical, biophysical and physiological methods, creating a multi-scale structure-activity relationship ranging from single molecule assays to contractile measurements in intact cardiac muscle cells. The 'Stabilizer' binds myosin S2 with low nanomolar affinity and strongly increases its mechanical stability as measured by single molecule gravitational force spectroscopy and Förester resonance energy transfer (FRET) measurements. The Stabilizer significantly inhibits myofibrilar contractility and ATPase activity, and reduces myosin crossbridge kinetics in demembranated cardiac muscle cells. Biochemical modification of the Stabilizer further allowed measurements in intact porcine cardiomyocytes showing decreased contraction and relaxation kinetics in the presence of the peptide. Our results show that myosin S2 targeting peptides are biologicals with potential therapeutic applications for muscle diseases. (208 words).</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144156242","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":"Microtubule polymerization generates microtentacles important in circulating tumor cell invasion.","authors":"Lucina Kainka, Reza Shaebani, Kathi Kaiser, Jonas Bosche, Ludger Santen, Franziska Lautenschläger","doi":"10.1016/j.bpj.2025.05.018","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.05.018","url":null,"abstract":"<p><p>Circulating tumor cells (CTCs) have crucial roles in the spread of tumors during metastasis. A decisive step is the extravasation of CTCs from the blood stream or lymph system, which depends on the ability of cells to attach to vessel walls. Recent work suggests that such adhesion is facilitated by microtubule (MT)-based membrane protrusions called microtentacles (McTNs). However, how McTNs facilitate such adhesion and how MTs can generate protrusions in CTCs remain unclear. By combining fluorescence recovery after photobleaching (FRAP) experiments and simulations we show that polymerization of MTs provides the main driving force for McTN formation, whereas the contribution of MTs sliding with respect to each other is minimal. Further, the forces exerted on the McTN tip result in curvature, as the MTs are anchored at the other end in the MT organizing center. When approaching vessel walls, McTN curvature is additionally influenced by the adhesion strength between the McTN and wall. Moreover, increasing McTN length, reducing its bending rigidity, or strengthening adhesion enhances the cell-wall contact area and, thus, promotes cell attachment to vessel walls. Our results demonstrate a link between the formation and function of McTNs, which may provide new insight into metastatic cancer diagnosis and therapy.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144156204","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":"Extending MMPBSA for membrane proteins: Addressing P2Y12R conformational changes upon ligand binding.","authors":"Cizhang Zhao,Tianhong Wang,Ray Luo","doi":"10.1016/j.bpj.2025.05.023","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.05.023","url":null,"abstract":"Membrane proteins play crucial roles in biological signaling and represent key targets in drug discovery, garnering significant experimental and computational attention. Recent advances in computational screening techniques have enabled the development of more accurate and efficient binding affinity calculation methods. Among these, the Molecular Mechanics Poisson Boltzmann Surface Area (MMPBSA) method has gained widespread adoption in large-scale simulations due to its computational efficiency. However, its application to membrane protein-ligand systems remains less developed compared to globular protein systems, primarily due to the additional complexity introduced by the membrane environment. In this study, we present enhanced capabilities in Amber that provide flexible and automatic options for calculating membrane placement parameters. Furthermore, we present the first application of ensemble simulations, combined with a multi-trajectory approach and entropy corrections, to enhance MMPBSA calculations for membrane protein systems. This novel methodology is particularly advantageous for systems exhibiting large ligand-induced conformational changes, significantly improving accuracy and sampling depth compared to traditional single-trajectory methods. We validate our approach using the human purinergic platelet receptor P2Y12R as a model system, chosen for its well-documented agonist-induced conformational changes and extensive experimental data, making it an ideal candidate for evaluating our enhanced simulation protocol.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"34 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-05-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144136821","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":"Characterization and structural basis for the brightness of mCLIFY: a novel monomeric and circularly permuted bright yellow fluorescent protein.","authors":"Him Shweta, Kushol Gupta, Yufeng Zhou, Xiaonan Cui, Selene Li, Zhe Lu, Yale E Goldman, Jody A Dantzig","doi":"10.1016/j.bpj.2025.05.012","DOIUrl":"10.1016/j.bpj.2025.05.012","url":null,"abstract":"<p><p>Ongoing improvements of genetically encoded fluorescent proteins have enhanced cellular localization studies and performance of bio-sensors, such as environmentally or mechanically sensitive FRET pairs, in cell biological and biophysical research. The brightest yellow fluorescent protein, widely used in these studies is YPet, derived from the jellyfish Aequorea victoria via the GFP derivative Venus. YPet dimerizes at concentrations used in cellular studies (K_D^1-2 = 3.4 μM) which impacts quantitative interpretation of emission intensity, rotational freedom, energy transfer and lifetime. Although YPet is nearly 30% brighter than Venus, no atomic structures of YPet have been reported to ascertain the structural differences leading to the higher brightness, possibly due to the tendency to dimerize or oligomerize. Here we report properties of a new YPet derivative, mCLIFY, a monomeric, bright, yellow, and long-lived fluorescent protein created by circular permutation of YPet and substitution of the amino acid residues thought to mediate dimerization. mCLIFY retains the advantageous photophysical properties of YPet but does not dimerize at least up to 40 μM concentration. We determined the atomic structure of mCLIFY at 1.57 Å resolution. Extensive characterization of the photophysical and structural properties of YPet and mCLIFY allowed us to elucidate the bases of their long lifetimes, enhanced brightness and the difference in propensity to dimerize.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126511","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":"Syntaxin 1A Transmembrane Domain Palmitoylation Induces a Fusogenic Conformation.","authors":"Dong An, Satyan Sharma, Manfred Lindau","doi":"10.1016/j.bpj.2025.05.022","DOIUrl":"10.1016/j.bpj.2025.05.022","url":null,"abstract":"<p><p>Neurotransmitter release is triggered by the fusion of synaptic vesicles with the plasma membrane, orchestrated by SNARE proteins Synaptobrevin 2 (Syb2), Syntaxin 1A (Stx1A), and SNAP25. Recent experimental studies showed that Stx1A palmitoylation of C271/C272 promotes spontaneous neurotransmitter release. However, the mechanistic role of SNARE transmembrane domain (TMD) palmitoylation in membrane fusion remains unclear. To investigate the structural and functional implications of TMD palmitoylation, we employed coarse-grained molecular dynamics simulations with the MARTINI force field. In simulations of individual SNAREs and of SNAP-25/Stx1A (t-SNARE) complexes in a membrane the palmitoyl chains of Syb2 and Stx1A localize to the membrane midplane, with Stx1A palmitoyl chains bending toward the extracellular leaflet. Non-palmitoylated Stx1A assumed a conformation where the SNARE domain was lying flat, adhering to the intracellular surface of the membrane. Stx1A dual palmitoylation induced dramatic changes, reducing the tilt of its TMD and stabilizing a more upright conformation of its SND. This conformation resembles the Stx1A conformation in a s Stx1A-SNAP25 t-SNARE complex, providing a potential mechanistic explanation of how Stx1A TMD palmitoylation facilitates early steps in SNARE complex formation and thus promotes spontaneous release. In simulations of the late steps of layers 5 to 8 SNARE complex zippering in a system of 4 SNARE complexes bridging a 10-nm nanodisc and a planar membrane, FPs spontaneously opened after a few hundred nanoseconds, preceded by distal leaflet lipid transfer and followed by FP flickering conductance before FP closure. At this stage, Stx1A TMD palmitoylation delayed lipid transfer and FP formation and decreased FP flicker open times, whereas the palmitoylation of Syb2 did not affect fusion pore dynamics. These findings suggest that after facilitation of priming before FP opening, Stx1A TMD palmitoylation, directly affects FP dynamics. These results highlight the essential role of SNARE TMD palmitoylation at multiple stages of neurotransmitter release.</p>","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":" ","pages":""},"PeriodicalIF":3.2,"publicationDate":"2025-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144135999","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":"Pairwise Encounters Boost Bacterial Motion by Transient Velocity Spikes.","authors":"Pu Feng,Chen Gui,Gancheng Wang,Lingling Wang,Jinglei Hu,Xiangjun Gong,Guangzhao Zhang","doi":"10.1016/j.bpj.2025.05.021","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.05.021","url":null,"abstract":"For swimming bacteria near surfaces, pairwise encounters inevitably occur and impact their social behavior. However, we know little about how the encounter events influence bacterial dynamics due to the limitations in tracking interplaying bacteria in 3D. Herein, we elucidated the motions of encountering E. coli using a combination of 3D holographic tracking experiments and hydrodynamic simulations. We find encounters with other cells induce transient yet remarkable fluctuations in the swimming speed and angle of E. coli, concurrently diminishing their temporal correlations, in contrast to solitary cells. Notably, bacteria approaching each other in a face-to-face fashion both accelerate, whereas they both decelerate during pursuits. Generally, the motion of a pair of smooth-swimming E. coli is dictated by the relative angle, velocity, and intercellular distance, as validated by hydrodynamic simulations. The presence of the surface mitigates the velocity spikes during the encounter process. Additionally, the encounter process influences the timing of tumbles, i.e., tumble tends to occur before the two bacteria get in close proximity. Despite the impact of one encounter being transient, we reveal that smooth-swimming E. coli gains propulsion advantage from the encounter, thus providing insights into bacterial physiology and guidance for designing active microdevices.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"25 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144122192","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":"Extrinsic heterogeneity: Collectivity in isotropic conformational fluctuations of chromosomes.","authors":"Takuya Nara,Haruko Takahashi,Akinori Awazu,Yutaka Kikuchi","doi":"10.1016/j.bpj.2025.05.020","DOIUrl":"https://doi.org/10.1016/j.bpj.2025.05.020","url":null,"abstract":"Eukaryotic interphase chromosomes maintain a three-dimensional conformation within the nucleus and undergo fluctuations. However, the analysis of chromosome conformational fluctuations has been mainly limited to chromosome conformation capture data that record the contact frequencies between chromosomal regions. Herein, we investigated chromosome fluctuations as polymers based on experimental data from sequential fluorescence in situ hybridization (seqFISH)+ using a multiomics methodology. To describe the principal modes of chromosome fluctuations, we applied principal component analysis to the three-dimensional conformation information of single chromosomes in 446 mouse embryonic stem cells (mESCs) obtained from seqFISH+ data analysis for spatial genomics and signals of nuclear factors (histone marks, repeat DNAs, and proteins in interchromosomal nuclear compartments). We found that chromosome fluctuations exhibit both isotropic and anisotropic modes. The isotropic conformational fluctuations of all chromosome types tended to synchronize each other, reflecting extrinsic heterogeneity in chromosome conformation that is independent of the cell cycle. In contrast, anisotropic conformational fluctuations, occurring in a spindle-like shape, were associated with the interactions between repeat DNAs and nuclear factors. These results highlight the importance of dissecting cell cycle-independent nuclear organization based on the conformational folding of chromosomes and the interactions between genomic regions and nuclear factors.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"2 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144122187","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}