Biophysical journal最新文献

{"title":"Molecular dynamics reveals how calcium drives hetero- versus homotrimerization of type I collagen","authors":"Emily J. Johnson,Shangze Xu,João V. de Souza,Anthony Evans,Agnieszka K. Bronowska,Elizabeth G. Canty-Laird","doi":"10.1016/j.bpj.2026.08.021","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.08.021","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"40 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148946642","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":"Localized ribosome access and distal tuning via the Listeria prfA RNA thermometer","authors":"Martin R. O’Steen,Jocelyn V. Chen,David H. Beier,Nils G. Walter,Sarah C. Keane","doi":"10.1016/j.bpj.2026.09.005","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.09.005","url":null,"abstract":"RNA thermometers (RNATs) are temperature-responsive structures in 5′ untranslated regions (UTRs) of some bacterial messenger RNA (mRNA) that control translation by modulating ribosome access. The Listeria monocytogenes prfA RNAT represses translation of PrfA (positive regulatory factor A), the master virulence regulator, at ambient temperature and activates it near the human host temperature (∼37 °C) by modulating ribosome binding site (RBS) accessibility. However, the prfA RNAT shares no homology with known RNAT classes, and its unfolding mechanism remains unclear. Here, we used analytical ultracentrifugation and single-molecule kinetic analysis of RNA transient structure (SiM-KARTS) to map prfA RNAT unfolding. SiM-KARTS analysis demonstrates that thermal opening occurs predominantly at the RBS, while the upper helix of the RNAT hairpin remains largely folded at 37 °C. The RBS binding kinetics increases with temperature in parallel with translation output, establishing a quantitative link between structural unfolding and function. Mutations in the upper helix impair thermal regulation, indicating that this region tunes switching even as it stays structured at host temperature. Together, these data reveal a hierarchical unfolding pathway in which initial RBS opening triggers activation, whereas the upper helix remotely tunes temperature sensitivity.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"36 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148915160","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":"Organization of Myosin H in the Apical Complex of Toxoplasma gondii Revealed by 3D Single-Molecule Super-Resolution Microscopy","authors":"Ashwin Balaji,Li-av Segev Zarko,Andrew E.S. Barentine,John C. Boothroyd,W.E. Moerner","doi":"10.1016/j.bpj.2026.09.012","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.09.012","url":null,"abstract":"Toxoplasma gondii is a single-celled eukaryotic parasite with prolific invasion capability. The parasite uses an apical complex comprised of proteinaceous structures and secretory organelles to efficiently enter host cells. As a result, the apical complex remains a vital structure of interest, with many studies dedicated to understanding its protein organization. One such protein is the motor Myosin H (MyoH), which is indispensable for parasite motility and host cell invasion. Given the small size of the complex, roughly a diffraction-limited volume in the visible, high-resolution techniques are required to make precise determinations of protein organization. In this work, we use 3D single-molecule localization microscopy in both traditionally fixed and gel-expanded parasites to localize the indispensable motor MyoH within the apical complex. Labeling of the N- and C-termini of MyoH in fixed parasites resolved the orientation of the motor protein in the apical complex, showing the motor head radially exterior to the tail. Two-color imaging of MyoH with tubulin in fixed parasites allowed for localization of the MyoH termini relative to the conoid, a barrel of tubulin-based fibrils in the apical complex, and showed the MyoH tail toward the interior face of the conoid and the head at the conoid exterior. Gel expansion showed improved labeling density for both tubulin and MyoH but altered MyoH localization, highlighting the nuanced effects of gel expansion on protein organization.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"16 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148915163","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":"Epileptic encephalopathy-related Kv2.1 mutants impair clustering but not neuronal excitability","authors":"Anne-Lise Paupiah,Melvyn Ginisty,Capucine Gendre,Marion Russeau,Imane Mouktine,Sabine Levi,Jean-Christophe Poncer,Marianne Renner","doi":"10.1016/j.bpj.2026.09.009","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.09.009","url":null,"abstract":"The voltage-gated potassium channel Kv2.1, encoded by the epileptic encephalopathy-associated gene KCNB1, is a primary driver of delayed-rectifier K+ currents in neurons. These currents contribute to high-frequency firing by preventing depolarization block due to Na+ channel inactivation. Wild-type (WT) channels are localized at the soma, proximal dendrites, and the initial segment of the axon, forming aggregates (clusters) via their C-terminal proximal restriction and clustering domain (PRC). This study investigated the biophysical and functional consequences of two C-terminal truncation mutations (Y529∗ and R579∗), identified in patients with epileptic encephalopathy, which disrupt this critical clustering domain. The mutations induced a change of Kv2.1 subcellular distribution towards distal dendrites and the axon. Cluster formation was impaired, though not abolished, in neurons expressing mutated subunits together with endogenous WT subunits. Consistent with this clustering deficit, single-molecule imaging revealed altered lateral diffusion of mutated channels. While WT channels remained largely immobile (stabilized), mutated forms exhibited intermittent diffusion punctuated by transient immobilization events. The percentage of stabilized trajectories was lower for mutated channels in the soma, dendrites and distal axons but not in the proximal portion of the axons. The differential diffusive behavior of WT and mutated channels was reproduced by diffusion-capture simulations considering channels with different numbers of PRC domains (i.e. heterotetramers with mutant subunits) and labile scaffolding interactions. Patch-clamp recordings revealed no significant difference in excitability between WT- and mutant-expressing neurons. However, we observed increased firing in both conditions compared to non-transfected neurons. Altogether, our results suggest that 1) mutated subunits form heterotetramers with endogenous WT subunits; 2) several PRC per channel are needed to efficiently immobilize Kv2.1 in large clusters; 3) increasing Kv2.1 channel expression level, independently of clustering, could drive neuronal hyperexcitability.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"11 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148908737","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":"Molecular dynamics simulations of a complex plasma membrane reveal finely-tuned sphingolipid hydrogen bonds","authors":"Tamir Dingjan,Hila Flumin,Anthony H. Futerman","doi":"10.1016/j.bpj.2026.09.010","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.09.010","url":null,"abstract":"The study of lipid bilayers has lagged behind that of other complex molecular assemblies due to the dynamic nature of lipid bilayers and the paucity of experimental techniques to study them in atomic detail. This is particularly true when analyzing interactions between lipid components of membranes. We now report a multi-resolution in silico analysis of a lipid bilayer based on the asymmetric lipid composition of the human erythrocyte plasma membrane. Our approach combines a coarse-grained bilayer simulation with resolution transformation to multiple smaller all-atom simulations. The coarse-grained simulation was consistent with previously published studies, as demonstrated by analysis of cholesterol translocation and neighbor enrichment. Subsequently, small patches from the coarse-grained simulations were transformed to all-atom resolution; quality control analysis of this data was again consistent with area per lipid and chain orientational order measurements of model bilayers. All-atom simulations permitted us to examine intermolecular and intramolecular hydrogen-bonding with a particular focus on sphingolipids, which unlike glycerophospholipids, donate hydrogen bonds in the bilayer interface region. We determined the relative contribution of each donor and acceptor hydrogen bond in lipid-lipid interactions and took advantage of atomic level resolution to study hydrogen-bonding for d-erythro-, 3-keto-, phyto- and dihydro-sphingolipids. Removing one of the hydrogen bond donors in sphingomyelin (SM) (by modeling 3-keto-SM rather than d-erythro-SM) resulted in an unexpected compensatory increase in hydrogen bond donation by the amide proton to neighboring SM. Phyto-SM increased hydrogen-bonding by the 3-position hydroxyl, while dihydro-SM reduced donation to cholesterol. Our results not only illustrate the usefulness of all-atom simulations to reveal membrane interactions less accessible by other methods, but also strengthen our recent suggestions that lipid bilayers are finely-tuned molecular assemblies in which atomic interactions play critical roles in maintaining and regulating membrane structure and function.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"51 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148915158","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":"A phase-field model for viscoelastic compressible tumor growth","authors":"Luise Zieger,Min Wu,Chaozhen Wei,John Lowengrub,Sebastian Aland","doi":"10.1016/j.bpj.2026.09.008","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.09.008","url":null,"abstract":"Growing tumors generate and respond to stress in their local microenvironment. Tissue re-arrangements can relax these mechanical stresses and make the tissue more fluid-like. Further, intricate coupling between mechanotransduction and biochemical signaling leads to complex patterns of growth. To predict the outcomes of these nonlinear interactions, we develop a phase-field model to simulate tumors growing into a surrounding medium taking into account their elastic and viscous properties as well as their compressibilities. We couple continuum modeling of the viscoelastic mechanics to the concentration of a diffusible growth-promoting nutrient in a mass conservative way. Additionally, the phase-field method is a stable and flexible way to describe the dynamics of arbitrarily shaped tumors. We demonstrate convergence of the phase-field model to a sharp interface model in radially symmetric geometries and can observe progression to stationary tumors. However, our results show that these stationary symmetric tumors are subject to symmetry-breaking instabilities in 2D and 3D driven by two primary mechanisms: (i) elastic buckling instabilities due to differential growth induced by the nutrient gradient and (ii) instabilities generated by apoptosis-related volumetric loss. Further, tissue fluidity and compressibility can lead to changes in tumor topologies. Our modeling framework provides a robust methodology for investigating how tissue mechanics and growth factor signaling influence the progression and invasive potential of solid tumors.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"10 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148902528","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":"A Biophysical Hypothesis for Compartment-Specific Conformational States of the IQSEC2 Intrinsically Disordered Protein","authors":"Michael Shokhen,Amnon Albeck,Nina S. Levy,Andrew P. Levy","doi":"10.1016/j.bpj.2026.09.007","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.09.007","url":null,"abstract":"The postsynaptic density (PSD) of neuronal synapses is a crowded, viscous membraneless compartment consisting of densely packed protein mixtures formed and maintained through liquid-liquid phase separation. A key regulator of synaptic function within the PSD is IQSEC2, an intrinsically disordered protein (IDP), which functions as a guanine nucleotide exchange factor (GEF), promoting the activation of the small GTPase ARF6 by catalyzing the exchange of ARF6 bound GDP for GTP. Experiments have shown that IQSEC2 is inactive in a folded state in the dendritic cytosol but can transiently adopt a catalytically active extended conformation in the PSD upon activation by neurotransmitter mediated calcium influx. In this study, we performed accelerated molecular dynamics (aMD) simulations of the IQSEC2 folding process in aqueous solvent and applied the Gibbs ergodic hypothesis formulated in statistical ensembles for post-processing and analysis of the results. We compared the effects of two sets of parameters on folding: a force field and a water model. The OPC water model optimized for proteins with disordered structure in the extended state in bulk aqueous solvent predicted an incorrect distorted 3D folded structure of IQSEC2. We propose that, due to fundamental biophysical differences between the dendritic cytosol and the postsynaptic density, there are two distinct classes of IDPs functioning in these different environments. These differences should be considered when optimizing force fields and parameters of water models for studying protein folding.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"1 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148899107","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":"Revisiting the mode of action of daptomycin considering the inoculum effect and a novel liposome-MIC-competition assay","authors":"Sarah Crocoll,Lennard Forssmann,Luisa Munz,Georg Häcker,Andreas Bechthold,Heiko Heerklotz","doi":"10.1016/j.bpj.2026.09.004","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.09.004","url":null,"abstract":"Daptomycin (DAP) is a cyclic lipopeptide drug for intravenous application against Gram-positive bacteria such as methicillin-resistant Staphylococcus aureus (MRSA). In spite of numerous studies, its mode of action remains controversial. This is partially due to the fact that no attention has been paid to the strong dependency of DAP activity on the cell count – referred to as the inoculum effect when minimal inhibitory concentrations (MICs) are concerned. The first objective is to quantify the inoculum effect of DAP acting against MRSA and, on this basis, review comparisons of data recorded at different cell counts. The data imply that the aqueous DAP concentration in equilibrium with minimally growth-inhibited MRSA is 0.24 μg/mL and the corresponding inhibitory drug load bound per bacterium is Rebac∗ = 1.0E+7. To directly compare phenomena observed at different cell counts, the samples must agree in Rebac∗; not in DAP concentration. The second objective has been to render data on liposomal model systems quantitatively comparable to in vivo data. This is achieved by the liposome-MIC-competition assay combining bacteria and liposomes in a single MIC experiment. It suggests an equivalent phosphatidylglycerol concentration of 3.5E-8 μM/(CFU/mL), giving rise to a re-assignment of model studies to comparable in vivo systems. Finally, the data obtained here are combined with common estimates regarding the lipid numbers per bacterium, suggesting that the majority of the bacteria-bound DAP is not localized in the membrane but most likely in the cell wall. Off-target binding is a crucial issue for membrane-active antibiotics.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"29 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148899104","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":"Actin filament assembly driven by distributive polymerases clustered on membrane surfaces","authors":"R. Dyche Mullins,Jane Kondev,Kristen Skruber","doi":"10.1016/j.bpj.2026.08.024","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.08.024","url":null,"abstract":"","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"24 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148893393","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":"Dimerization and Ligand Binding Rewire Allosteric Networks in SARS-CoV-2 Main Protease","authors":"Javier Sanlley Hernandez,Carla Calvó-Tusell,Fiona Kearns,Mac Kevin E. Braza,Rommie E. Amaro","doi":"10.1016/j.bpj.2026.08.023","DOIUrl":"https://doi.org/10.1016/j.bpj.2026.08.023","url":null,"abstract":"The SARS-CoV-2 main protease (MPro) is an essential enzyme for viral replication and a primary target for antiviral drug development. Despite extensive structural and biochemical characterization, the allosteric mechanisms by which dimerization informs conformational changes at active site lack an explicit comparison across the different states that identify key residues that connect substrate binding, dimerization, and catalytic activation. Here, we integrate microsecond time scale all-atom molecular dynamics (MD) simulations with dynamical network analysis to characterize how ligand binding and dimerization modulate the allosteric communication landscape of MPro. We performed triplicate 1-μs simulations of MPro in the monomer and dimer states. For each of these states, we simulated MPro in the apo state, as well as bound to a natural peptide substrate (nsp 15/16), the covalent inhibitor nirmatrelvir (Paxlovid) and the noncovalent inhibitor ensitrelvir (Xocova). Dynamical network analyses from the resulting simulations reveal that dimerization redirects the highest correlated motions from the interdomain loop towards the domain II and III interface. At the dimer interface, we identified N-terminal and domain II β-hairpin residues that act as central communication hubs creating networks that connect both chains in the dimer. Small molecule binding to the active site further modulates these networks in distinct ways: nirmatrelvir and peptide substrate binding results in the formation of allosteric networks within the oxyanion loop, while ensitrelvir-bound monomeric MPro results in a dimer-like network, suggesting an inhibitory “allosteric switch” mechanism that may hinder dimerization upon binding. Across all systems, domain III emerges as an allosteric “pivot”, providing a platform that allows the most relevant networks to connect inter-chain communication to the active site upon dimerization. Together, these findings define how correlated motion networks couple active-site dynamics to dimerization and ligand binding, providing molecular insight into the principles governing allosteric regulation in MPro. This framework highlights potential avenues for developing antivirals that target not only the catalytic site but also the communication pathways sustaining dimer stability and enzymatic function.","PeriodicalId":8922,"journal":{"name":"Biophysical journal","volume":"47 1","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148877400","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}