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<title>bioRxiv Subject Collection: Biophysics</title>
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This feed contains articles for bioRxiv Subject Collection "Biophysics"
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<link>https://www.biorxiv.org</link>
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<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.11.751012v1?rss=1">
<title>
<![CDATA[
Inhibitors of HIV-1 maturation modulate conformational dynamics and heterogeneity of the immature Gag lattice 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.11.751012v1?rss=1
</link>
<description><![CDATA[
HIV-1 maturation requires the viral protease to cleave the Gag polyprotein into its constituent domains. Subsequent conformational and morphological changes result in a mature, infectious virion. Prior studies support a hypothesis in which Gag conformational dynamics and the heterogeneity of the immature Gag lattice enable proteolytic and morphological maturation. We developed a single-molecule Forster resonance energy transfer imaging approach to probe, in real time, the conformational dynamics of individual Gag molecules within immature HIV-1 virions. Our results capture Gag's conformational landscape and the spatial heterogeneity of the immature lattice. We evaluated inhibitors of maturation to identify immature lattice features that are modulated to disrupt maturation. Maturation inhibitors that act through diverse mechanisms, including lenacapavir and compounds that alter viral membrane composition, arrest Gag dynamics and reduce the spatial heterogeneity of the lattice. These observations support a model in which Gag dynamics and immature lattice organization regulate HIV-1 maturation.
]]></description>
<dc:creator><![CDATA[ Nandi, T., Wong, M., Waheed, A. A., Freed, E. O., Schiffer, C. A., Munro, J. B. ]]></dc:creator>
<dc:date>2026-09-12</dc:date>
<dc:identifier>doi:10.64898/2026.09.11.751012</dc:identifier>
<dc:title><![CDATA[Inhibitors of HIV-1 maturation modulate conformational dynamics and heterogeneity of the immature Gag lattice]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-12</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.11.750570v1?rss=1">
<title>
<![CDATA[
Plasmodium falciparum Myosin B is a slow motor optimized for force generation 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.11.750570v1?rss=1
</link>
<description><![CDATA[
Malaria is a disease caused by apicomplexan parasites of the genus Plasmodium. These organisms express two atypical class-XIV myosins: Myosin A (MyoA), a core component of the glideosome expressed throughout the entire lifecycle, and Myosin B (MyoB), which is restricted to invasive stages and localizes to the apical region. Here, we determine the crystal structure of Plasmodium falciparum MyoB (PfMyoB) in the Rigor state and identify its essential light chain as the same subunit bound to MyoA. Combining structural analysis, molecular dynamics simulations and in vitro kinetic and motility assays, we show that PfMyoB is a slow motor optimized for force production during invasion. The N-terminal extensions of PfMyoA and PfMyoB exert distinct effects on each motor s mechanochemistry. Altogether, these findings reveal how Plasmodium myosins have evolved specialized functions during the complex parasite lifecycle and provide insight into developing multi-target inhibitors of erythrocytic invasion based on the PfMyoA inhibitor KNX-002.
]]></description>
<dc:creator><![CDATA[ Robblee, J. P., Moussaoui, D., Bookwalter, C. S., Auguin, D., Fagnant, P. M., MacFarlane, J. E., Previs, M. J., Houdusse, A., Trybus, K. M., Robert-Paganin, J. ]]></dc:creator>
<dc:date>2026-09-12</dc:date>
<dc:identifier>doi:10.64898/2026.09.11.750570</dc:identifier>
<dc:title><![CDATA[Plasmodium falciparum Myosin B is a slow motor optimized for force generation]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-12</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.11.751009v1?rss=1">
<title>
<![CDATA[
Kinetic asymmetry drives directionality in an ATP-binding cassette transporter 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.11.751009v1?rss=1
</link>
<description><![CDATA[
How ATP binding and hydrolysis directionally reshape the conformational landscape remains unknown for ATP-binding cassette (ABC) transporters. Here, we identify two conserved ionic locks within the nucleotide-binding domains that govern transition barriers and energy transduction: an intra-subunit inward-facing (IF)-lock and an inter-subunit outward-facing (OF)-lock. Mg2+-ATP acts as a molecular key that disrupts the IF-lock, driving the forward transition. Following ATP hydrolysis, release of the {gamma}-phosphate, which, together with Mg2+, forms the pivot of the OF-lock, initiates the reverse transition. Directionality arises from kinetic asymmetry, driven by an anticorrelated exchange of the rate-limiting step between the consensus nucleotide-binding site and the transmembrane domains during forward and reverse transitions, respectively. Conservation of these molecular locks reveals a universal blueprint for ATP-driven mechanical transduction across the ABC superfamily.
]]></description>
<dc:creator><![CDATA[ Rudolph, M., Batebi, H., Pramod, M., Barth, K., Hirschberg, C., Tampe, R., Netz, R. R., Joseph, B. ]]></dc:creator>
<dc:date>2026-09-12</dc:date>
<dc:identifier>doi:10.64898/2026.09.11.751009</dc:identifier>
<dc:title><![CDATA[Kinetic asymmetry drives directionality in an ATP-binding cassette transporter]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-12</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.08.750297v1?rss=1">
<title>
<![CDATA[
Specimen-Dependent Sampling and Signal Limitations Govern the Effectiveness of Low-Magnification Super-Resolution in Cryo-EM 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.08.750297v1?rss=1
</link>
<description><![CDATA[
Single-particle cryo-EM routinely delivers near-atomic structures; however, optimizing data collection requires a delicate balance among magnification, sampling bandwidth, and particle throughput. Although low-magnification super-resolution imaging can recover information beyond the physical Nyquist limit, its benefit varies substantially among specimens. This variability suggests that the effectiveness of super-resolution may depend on whether reconstruction is limited by detector sampling bandwidth or by the recoverable particle signal. However, the conditions that distinguish these two regimes remain poorly defined. Here, we systematically compared super-resolution and physical-pixel workflows at two magnifications using apoferritin (APO) and malate synthase G (MSG) as representative specimens with contrasting molecular size, symmetry, and image contrast. At low magnification, APO exhibited sampling-limited behavior, with super-resolution processing achieving 1.72 Angstrom compared with 2.74 Angstrom for physical-pixel processing. In contrast, MSG exhibited predominantly signal-limited behavior under the same conditions, yielding comparable resolutions of 3.05 Angstrom and 2.98 Angstrom for super-resolution and physical-pixel processing, respectively, despite the increased sampling bandwidth. These contrasting responses were further supported by particle-number saturation, per-particle motion correction, and Q-score analyses, which provided complementary evidence for the underlying sampling-limited and signal-limited regimes. Together, these results provide a practical framework for assessing whether reconstruction quality is predominantly constrained by sampling bandwidth or recoverable particle signal and offer a rational basis for balancing achievable resolution and particle throughput when selecting acquisition strategies.
]]></description>
<dc:creator><![CDATA[ Wang, C.-H., Wu, K.-P., Chang, Y. C. ]]></dc:creator>
<dc:date>2026-09-12</dc:date>
<dc:identifier>doi:10.64898/2026.09.08.750297</dc:identifier>
<dc:title><![CDATA[Specimen-Dependent Sampling and Signal Limitations Govern the Effectiveness of Low-Magnification Super-Resolution in Cryo-EM]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-12</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.05.749092v1?rss=1">
<title>
<![CDATA[
Evidence of Chemical Wave-Electric Field Interaction in Bacterial Cells 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.05.749092v1?rss=1
</link>
<description><![CDATA[
Charge neutrality is widely assumed in living cells, yet this approximation breaks down in micron-scale bacteria where charge imbalance and spatial confinement are significant. Using Poisson-Nernst-Planck modeling, we show that unequal cation-anion effectiveness and bounded geometry generate extended intracellular diffuse layers and steady electric fields. We demonstrate that such fields couple directly to intracellular chemical waves, focusing on the Min-protein oscillator of Escherichia coli. Electric-field-driven transport skews the dispersion-mode structure, induces mode crossings, and selectively amplifies Turing and Hopf-Turing instabilities over intermediate length scales, constraining the permitted {omega}-k spectrum and setting optimal wavelengths and modal growth-rate velocities. Experiments in wild-type, anucleate, and antibiotic-treated cells, together with simulations of nucleoid-dependent charge density and field strength, quantitatively validate these predictions and explain observed pattern asymmetries and frequency modulations. Crucially, asymmetric wave-field coupling promotes quasi-periodicity through controlled mode competition, enhancing robustness to noise, cell-size variation, and growth. These findings identify intracellular electric fields as active regulators of biochemical patterning and suggest a general role for wave-field interactions in cellular self-organization.
]]></description>
<dc:creator><![CDATA[ Shen, J.-P., Chou, C.-F. ]]></dc:creator>
<dc:date>2026-09-12</dc:date>
<dc:identifier>doi:10.64898/2026.09.05.749092</dc:identifier>
<dc:title><![CDATA[Evidence of Chemical Wave-Electric Field Interaction in Bacterial Cells]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-12</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.10.749994v1?rss=1">
<title>
<![CDATA[
Conformational Switching between ON and OFF States Proceeds through Multiple Pathways in the SAM-III Translational Riboswitch 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.10.749994v1?rss=1
</link>
<description><![CDATA[
Gene regulation by translational riboswitches relies on repeated and reversible conformational switching between ON (apo) and OFF (holo) states. The switching mechanism often involves significant structural rearrangement, and the role of the metal ions in this mechanism is unclear. Using molecular dynamics simulations, we studied the switching transition of a translational riboswitch that regulates the concentration of S-adenosyl methionine (SAM), the `universal methyl donor'. We show that Mg2+ ions are essential for stabilizing the ON-state, and the three-way junction exhibits a `breathing-like' dynamic interconversion between open and closed modes. The riboswitch has a low population of a holo-like READY (R) state with a partially organized SAM-binding pocket prior to ligand binding. Multiple intermediates are observed in the switching landscape, contributing to the gradual stepwise structural transition between the ON and R states, and proceeding through multiple competing pathways. Interestingly, Mg2+ ions influence the dominant pathway for the ON to R state transition, whereas the reverse transition shows a weak dependence. These results provide broad insights into the function of translational riboswitches, which repeatedly and rapidly respond to changes in metabolite concentrations, in contrast to transcriptional riboswitches.
]]></description>
<dc:creator><![CDATA[ Mondal, D., Chowdhury, S. P., Reddy, G. ]]></dc:creator>
<dc:date>2026-09-11</dc:date>
<dc:identifier>doi:10.64898/2026.09.10.749994</dc:identifier>
<dc:title><![CDATA[Conformational Switching between ON and OFF States Proceeds through Multiple Pathways in the SAM-III Translational Riboswitch]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-11</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.10.750674v1?rss=1">
<title>
<![CDATA[
Predicting Capsid Protein Binding Sites in Single-Stranded RNA Viruses Using Machine Learning from Local Geometric Features 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.10.750674v1?rss=1
</link>
<description><![CDATA[
Selective recognition of viral RNA by capsid proteins is essential for genome packaging during the assembly of single-stranded RNA (ssRNA) viruses. However, identification of capsid protein binding sites in the RNA genome remains challenging because current experimental techniques are labor-intensive and low-throughput, motivating the development of computational approaches. Here, we present a sequence-based framework that integrates RNA tertiary structural modeling, local geometric feature extraction, and machine learning to predict capsid protein binding sites. Using the Qbeta; bacteriophage as a proof-of-concept system, we constructed a benchmark dataset of experimentally identified binding and non-binding RNA fragments. We designed a set of geometric descriptors to characterize the local structural features of the RNA backbone. When repeatedly trained and tested with these geometric descriptors on different subsets of the benchmark dataset, the neural network showed a strong ability to distinguish capsid protein binding sites from non-binding RNA fragments, achieving an area under the receiver operating characteristic curve (AUC) of 0.88 in a 5-fold cross-validation. To evaluate whether the model can predict RNA binding sites without experimental structures, we applied it to local geometric features derived from AlphaFold-predicted RNA structures. Despite substantial structural differences between predicted and experimentally determined models, the classifier retained considerable predictive performance (AUC = 0.75), indicating that approximate RNA tertiary structures may still preserve biologically meaningful information for capsid binding site prediction. Furthermore, the failed predictions suggest that viral genome packaging is not only governed by intrinsic RNA structural features, but also by additional dynamic factors beyond static RNA conformations. In summary, our findings provide new mechanistic insights into RNA-capsid interactions and establish a foundation for extending this approach to diverse ssRNA viruses.
]]></description>
<dc:creator><![CDATA[ Wu, Y. M., Zhang, J. ]]></dc:creator>
<dc:date>2026-09-11</dc:date>
<dc:identifier>doi:10.64898/2026.09.10.750674</dc:identifier>
<dc:title><![CDATA[Predicting Capsid Protein Binding Sites in Single-Stranded RNA Viruses Using Machine Learning from Local Geometric Features]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-11</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.09.750331v1?rss=1">
<title>
<![CDATA[
Processing, analysing and modelling kinetic data in the era of high-throughput single-molecule biophysics 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.09.750331v1?rss=1
</link>
<description><![CDATA[
Biomolecular reactions are often composed of multiple stochastic, reversible and branched transition paths over intermediates, leading to rich dynamics. Single-molecule biophysics has revolutionized our view of biology by revealing the heterogeneity in realized paths and pointing to the importance of rare events. The recent development of high-throughput single-molecule biophysics techniques now allow to quantitatively study this heterogeneity and characterize even the rarest kinetic events. Processing, analyzing and modelling high-throughput single-molecule data has been the focus of several reports, but are often difficult to implement for non-experts. Here, we provide a guide to extract the most from transitions in single-molecule biophysics data using a first-passage time framework and maximum likelihood estimation. We specifically focused on parameter sweeps in systems with one or two characteristic timescales, and show how they can be analyzed in terms of a minimal kinetic model and its dependence on enzyme/substrate concentration, force and temperature. We introduce a general framework to perform data-driven modelling on single- and two-state models and illustrate it with concrete examples. We also provide programs with graphical user interfaces to perform such analysis on raw data, in the hope that it will empower experimental single-molecule biophysicists to extract the most out of their data.
]]></description>
<dc:creator><![CDATA[ America, P., Klein, M., Dulin, D., Depken, M. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.09.750331</dc:identifier>
<dc:title><![CDATA[Processing, analysing and modelling kinetic data in the era of high-throughput single-molecule biophysics]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.09.750541v1?rss=1">
<title>
<![CDATA[
Affinity and distance dependence of SLiM-mediated dephosphorylation by protein phosphatase 1 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.09.750541v1?rss=1
</link>
<description><![CDATA[
Protein phosphatases counterbalance kinases by dephosphorylating phospho-proteins to regulate signaling pathways. But unlike kinases, their shallow catalytic groove has limited selectivity for the phospho-peptide motifs. Phosphatases such as protein phosphatase-1 (PP1) recognize their substrates through short linear motifs (SLiMs) within intrinsically disordered regions, yet the mechanism of SLiM-mediated recruitment remains unclear. We developed an intrinsically disordered phospho-protein substrate to enable quantitative modelling of tethered PP1 catalysis by varying SLiM affinity and distance. We show that a PP1-binding SLiM linked to a phospho-peptide by a flexible spacer is sufficient to enhance dephosphorylation. Dephosphorylation occurs most efficiently at a spacing of 20-30 residues, in agreement with predictions from theoretical polymer models. Low micromolar dissociation constants are most efficient for dephosphorylation, which can be modelled numerically as a trade-off between substrate binding and substrate inhibition. Bivalent SLiMs enhance or decrease catalysis depending on the combined affinity. Together, these results define a quantitative and generalizable framework for how linear motifs direct dephosphorylation by PP1.
]]></description>
<dc:creator><![CDATA[ Lande, E. S., Kjaergaard, M. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.09.750541</dc:identifier>
<dc:title><![CDATA[Affinity and distance dependence of SLiM-mediated dephosphorylation by protein phosphatase 1]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.07.749823v1?rss=1">
<title>
<![CDATA[
Individual mouse mitotic chromosomes exhibit cell type-specific differences in biomechanical properties 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.07.749823v1?rss=1
</link>
<description><![CDATA[
Cyclic episodes of chromosome compaction and de-condensation are features of eukaryotic cell division that aid mitotic segregation and help prevent aneuploidy. While biophysical data on mitotic chromosome structure has been previously obtained, heterogeneity within samples can confound analyses and precludes direct like-for-like comparisons. To circumvent this, we employed advanced flow cytometry to purify specific metaphase chromosomes with biotinylated telomeres from stably engineered mouse cells. We show that ESC-derived metaphase chromosomes 3 and 19 display distinct properties but share a conserved force-dependent mechanical response. In contrast, chromosome equivalents isolated from NSCs and preB cells show markedly different force-dependent responses, reflecting progressive differentiation stages. Covalent crosslinking of ESC-derived chromosomes alters biomechanical properties to mimic equivalents from more differentiated cells. Collectively, these results highlight the need to isolate specific, homogeneous metaphase chromosome samples to accurately decipher their complex behaviours.
]]></description>
<dc:creator><![CDATA[ Brown, K. E., Patra, S., Dimond, A., Ray, K. K., Cheriyamkunnel, S., Patel, B., Gim, D. H., Whilding, C., Llobet Ayala, M., Kilic, M. E., Rueda, D. S., Fisher, A. G. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.07.749823</dc:identifier>
<dc:title><![CDATA[Individual mouse mitotic chromosomes exhibit cell type-specific differences in biomechanical properties]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.05.749623v1?rss=1">
<title>
<![CDATA[
Thermorheological mapping and molecular insights into salt-dependent gel-like network formation in Mortierella alpina chitin-like exopolysaccharide solutions 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.05.749623v1?rss=1
</link>
<description><![CDATA[
Fungal chitin-like exopolysaccharides are promising fermentation-derived materials, however the molecular-level determinants of their salt- and temperature-dependent gel-like behavior remain poorly understood. Here, a previously characterized Mortierella alpina exopolysaccharide was re-examined by integrating oscillatory rheology with all-atom molecular dynamics simulations. Frequency sweeps across 5-15 mg mL-1, two ionic media (0.154 mol L-1 NaCl and 0.28 mol L-1 LiCl), and 10-60 C were used to map liquid-like, transitional, and elastic-dominated regimes. Increasing concentration strengthened network behavior, but the two salts followed distinct pathways: NaCl promoted a more coherent progression toward elastic dominance and more thermorheologically compatible relaxation behavior, whereas LiCl produced a high-dissipation intermediate regime and stronger temperature dependence. Simulations of a minimal multichain model comprising eight GlcNAc10 oligomers at approximately 15.8 mg mL-1 showed that NaCl favored larger, more compact assemblies despite weak and short-lived Na+-oxygen coordination. LiCl formed sharper, longer-lived first-shell contacts but maintained smaller and more expanded assemblies. Ion-mediated interchain bridges were sparse and transient. The combined results show that local cation binding strength does not directly predict collective network formation and support a dynamic physical-network mechanism governed by salt-specific coupling among hydration, ion exchange, chain packing, and reversible interchain association.
]]></description>
<dc:creator><![CDATA[ Goyzueta-Mamani, L. D., Barazorda-Ccahuana, H. L., Noseda, M. D., Alves de Freitas, R., Soccol, C. R., de Carvalho, J. C. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.05.749623</dc:identifier>
<dc:title><![CDATA[Thermorheological mapping and molecular insights into salt-dependent gel-like network formation in Mortierella alpina chitin-like exopolysaccharide solutions]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.08.748679v1?rss=1">
<title>
<![CDATA[
Solvent-Isotope Effects in Biomolecular Phase Separation and Fibrillation of Disordered Proteins and Peptides 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.08.748679v1?rss=1
</link>
<description><![CDATA[
Heavy water (D2O) is widely used in biomolecular spectroscopy and imaging, often under the assumption that it is an inert replacement for H2O. However, D2O differs subtly in hydrogen-bonding, viscosity, and dielectric properties, which can alter biomolecular interactions and self-assembly. Here, we test how solvent isotope substitution modulates protein/peptide phase separation and amyloid formation in multiple intrinsically disordered systems. Using turbidity-based phase diagrams and microscopy, we quantify how D2O shifts protein-RNA complex coacervation boundaries and alters condensate morphology. Droplet recovery measurements indicate significant solvent-dependent changes in condensate material properties. We further evaluate amyloid formation kinetics, in the presence or absence of a cofactor, supported by orthogonal structural characterization, and assess the functional consequences of tau fibrils using a tau biosensor seeding assay with explicitly defined seed delivery conditions. Together, these results show that D2O can systematically bias liquid-liquid phase separation and aggregation readouts and should be treated as an active experimental variable rather than a neutral solvent substitute.
]]></description>
<dc:creator><![CDATA[ Singh, H., Yeager, Z., Herlory, M., Mahapatra, S., Walczak, M. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.08.748679</dc:identifier>
<dc:title><![CDATA[Solvent-Isotope Effects in Biomolecular Phase Separation and Fibrillation of Disordered Proteins and Peptides]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.09.750393v1?rss=1">
<title>
<![CDATA[
A Bidomain Boundary Element-Cable Method for Modeling Neuronal Responses to Electric Fields 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.09.750393v1?rss=1
</link>
<description><![CDATA[
Objective: Extracellular electric fields critically influence neural activity through both exogenous neuromodulation and endogenous ephaptic coupling. While conventional cable models efficiently simulate membrane dynamics, they fail to capture bidirectional, field-mediated interactions self-consistently, and fully coupled volumetric methods require computationally prohibitive 3D meshing. We present Cable-BEM, a hybrid wire-kernel bidomain boundary element method designed to resolve these limitations. Approach: By analytically integrating boundary integral kernels around cylindrical neuronal compartments, Cable-BEM fully couples intracellular, extracellular, and membrane dynamics while strictly retaining the highly efficient 1D degrees of freedom of traditional cable equations. The system is advanced using a semi-implicit Crank-Nicolson scheme. To overcome the dense nature of the resulting integral operators, we implement an Adaptive Cross Approximation (ACA) and Hierarchical Off-Diagonal Low-Rank (HODLR) compression scheme. Main result: The solver was rigorously validated against full-surface bidomain boundary element method (BEM) reference implementations, demonstrating tight agreement in activation thresholds (within 1.3% relative error) across diverse stimulation geometries. The ACA-HODLR compression scheme achieved substantial memory footprint reductions-by a factor of up to 4.6 for large 225-cell networks- without sacrificing numerical accuracy. Furthermore, we utilized the framework to resolve subtle, distance-dependent ephaptic interactions, successfully demonstrating the progressive phase synchronization of biophysically realistic, multi-compartment Purkinje cells. Significance: Cable-BEM provides a computationally scalable, mesh-free framework that establishes a powerful and practical foundation for investigating complex field-mediated phenomena in large-scale, multicellular neuronal networks.
]]></description>
<dc:creator><![CDATA[ Sabino, V., Walenciak, A., Gomez, L. J. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.09.750393</dc:identifier>
<dc:title><![CDATA[A Bidomain Boundary Element-Cable Method for Modeling Neuronal Responses to Electric Fields]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.07.749827v1?rss=1">
<title>
<![CDATA[
Single-shot light-field microscopy captures delivery-dependent dye and autofluorescence patterns in Caenorhabditis elegans 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.07.749827v1?rss=1
</link>
<description><![CDATA[
Three-dimensional imaging of live Caenorhabditis elegans commonly relies on sequential z-stack acquisition, which can be slow and susceptible to movement and photobleaching. Here, we used light-field microscopy to capture dye and delivery-dependent fluorescence patterns across intact adult worms in a single exposure per channel. With a 40x/1.20 NA water-immersion objective, each reconstructed dataset contained 121 axial slices spanning 109 {micro}m at 0.91 {micro}m spacing. In a representative adult, nematode signal extended from 40.88 to 85.4 {micro}m, corresponding to approximately 44.5 {micro}m of captured axial depth without sequential z scanning. Three fluorescence channels were acquired with a summed exposure time of 112 ms across a 685 x 1010 {micro}m field of view. FM1-43 labelled intestinal, cuticular and vesicular structures, FM4-64 highlighted ingested bacteria and intestinal compartments, and Nile Red revealed vesicular and broader whole-organism fluorescence. Intrinsic blue and green autofluorescence signals were also resolved. These observations demonstrate rapid single-shot acquisition of whole-organism three-dimensional fluorescence information and show how delivery route influences the spatial distribution of commonly used fluorescent probes in C. elegans.
]]></description>
<dc:creator><![CDATA[ Markus, R., Rea, E., Berfi, N. A., Taresco, V., Hudson, C., White, D. R. A., Chauhan, V. M. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.07.749827</dc:identifier>
<dc:title><![CDATA[Single-shot light-field microscopy captures delivery-dependent dye and autofluorescence patterns in Caenorhabditis elegans]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.09.750406v1?rss=1">
<title>
<![CDATA[
A multiscale modeling framework for transport of PEGylated lipid nanoparticle through the extracellular matrix 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.09.750406v1?rss=1
</link>
<description><![CDATA[
Lipid nanoparticles (LNPs) are one of the leading platforms for delivering nucleic acid therapeutics, yet their efficacy is limited by physicochemical interactions with the extracellular matrix (ECM) that trap the particles before they reach target cells. PEGylated nanoparticles mitigate these interactions by forming a protective steric layer on their surfaces. However, there is a lack of a predictive tool that gives mechanistic insights about how PEG surface density governs the underlying interaction and results in enhanced diffusive transport of LNPs through the ECM. Here, we present a multiscale hierarchical computational framework that couples all-atom constant pH molecular dynamics (CpHMD) with a highly coarse-grained model of the complete LNP within a crosslinked hyaluronic acid (HA) network. These atomistic simulations resolve the free energy of interaction between the LNP surface and HA chains across varying PEG lipid compositions, and integrate these free energy profiles to inform the coarse-grained simulations of LNP transport through the matrix. This work highlights that even a slightly PEGylated surface depletes the near-contact shell between the LNP and HA chains, which disrupts their adhesive interactions. These protective PEG layers produce a sharp, non-linear enhancement in LNP diffusivities, with just 1% PEG increasing the diffusivity nearly eight-fold relative to bare LNPs, which remain trapped in the matrix structures. This work provides a quantitative estimate of how PEG surface density governs LNP transport through the ECM, which offers predictive guidance for engineering LNP surface properties in target-specific drug delivery.
]]></description>
<dc:creator><![CDATA[ Nakate, P., Colston, K. J., Schneebeli, S. T., Ardekani, A. M. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.09.750406</dc:identifier>
<dc:title><![CDATA[A multiscale modeling framework for transport of PEGylated lipid nanoparticle through the extracellular matrix]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.06.749741v1?rss=1">
<title>
<![CDATA[
Complementary roles of human protamine 1 and spermine in giant DNA compaction 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.06.749741v1?rss=1
</link>
<description><![CDATA[
During sperm maturation, protamines progressively replace histones and compact the paternal genome. Spermine (SPM), a naturally occurring tetravalent polyamine that induces DNA compaction, is also abundant in seminal fluid. However, how SPM and protamines jointly influence higher-order structural transitions of giant DNA remains poorly understood. Here, we investigated the cooperative effects of human protamine 1 (PRM1) and SPM using single-molecule fluorescence microscopy. PRM1 induced a continuous conformational transition from coil to globule through intermediate conformations, whereas SPM induced a discrete coil-globule transition. Notably, under coexistence conditions with low concentrations of PRM1, SPM promoted structural progression along the PRM1-induced continuous folding pathway toward the fully compact globule state. Quantitative analysis supported these observations and demonstrated distinct yet cooperative modes of DNA compaction by PRM1 and SPM. These findings demonstrate complementary roles of human PRM1 and SPM in giant DNA compaction and provide a physicochemical framework for understanding genome compaction during sperm maturation.
]]></description>
<dc:creator><![CDATA[ Nishio, T., Kato, Y. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.06.749741</dc:identifier>
<dc:title><![CDATA[Complementary roles of human protamine 1 and spermine in giant DNA compaction]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.09.750262v1?rss=1">
<title>
<![CDATA[
Thermal fractuations assist high-speed rotation of the bacterial flagellar motor at low load 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.09.750262v1?rss=1
</link>
<description><![CDATA[
The bacterial flagellar motor is a proton-driven rotary nanomachine that converts ion flow into mechanical motion. Proton-coupled rotation of the MotA5-MotB2 stator complex generates torque, yet how this process drives high-speed rotation remains unclear. Here we use single-molecule nanophotometry to resolve stepwise rotation under low-load conditions. Lowering intracellular pH selectively prolongs dwell times without affecting step durations, indicating that proton dissociation triggers torque generation. Structural analysis further suggests that the rotor disengages from the stator before completing the elementary step angle (~11 degree), implying that the power stroke alone is insufficient. Notably, the rotational diffusion coefficient of stator-less motors closely matches that inferred from wild-type motors at low load. These findings support a model in which intrinsic thermal fluctuations compensate for the limited reach of the power stroke, enabling rapid rotation. Our results reveal a hybrid mechanism in which ion-driven conformational changes bias stochastic motion to achieve efficient energy transduction.
]]></description>
<dc:creator><![CDATA[ Nakamura, S., Morimoto, Y. V., Kami-ike, N., Minamino, T., Namba, K. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.09.750262</dc:identifier>
<dc:title><![CDATA[Thermal fractuations assist high-speed rotation of the bacterial flagellar motor at low load]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.07.749946v1?rss=1">
<title>
<![CDATA[
Characterization of Liquid-Liquid Phase Separation of Companion of Cellulose Synthases under Stress Mimicking Conditions 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.07.749946v1?rss=1
</link>
<description><![CDATA[
Companion of Cellulose Synthase (CC), has previously been shown to sustain cellulose synthesis during salt stress. However, the role of CCs in this process is not well-understood. In this study, we show that the intrinsically disordered N-terminal domain of Arabidopsis CC1 (CC1NTD) can undergo liquid-liquid phase separation (LLPS) under defined reducing conditions in the presence of trimethylamine N-oxide (TMAO), a naturally occurring plant stress osmolyte. The observed biomolecular condensates are enriched in CC1NTD and display liquid-like behavior, including spherical morphology, fusion, and dynamic exchange with the surrounding solution. We further show that TMAO compacts CC1NTD without inducing folding, that CC1NTD condensates recruit tubulin and accelerate microtubule polymerization while retaining dynamic properties. Additionally, we also studied the intrinsically disordered N-terminal domain of CC2, a closely related paralog to CC1. We found that CC2NTD remains disordered but does not phase separate independently under the same experimental conditions. However, it does partition into CC1NTD condensates. Together, these results define a condition-dependent condensate state for CC1NTD and link that state to tubulin-related function. Finally, we propose a novel mechanism for the formation and maintenance of stress-associated cellulose synthase compartments driven by LLPS of the disordered regions of CSC and accessory proteins.
]]></description>
<dc:creator><![CDATA[ Gurumoorthy, V., Zhang, Q., Leite, W., Hicks, A., Kolape, J., Lamichhane, R., O'Neill, H. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.07.749946</dc:identifier>
<dc:title><![CDATA[Characterization of Liquid-Liquid Phase Separation of Companion of Cellulose Synthases under Stress Mimicking Conditions]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.06.749717v1?rss=1">
<title>
<![CDATA[
Microfluidic Devices for Imaging and Biochemistry Analysis of Microbes Under Mechanical Pressure 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.06.749717v1?rss=1
</link>
<description><![CDATA[
Growth-induced pressure arises when proliferating cell populations are confined within rigid microenvironments and is increasingly recognized as a determinant of microbial physiology in soils, biofilms, and host tissues. We present two complementary microfluidic devices that confine microbes within polydimethylsiloxane (PDMS) chambers and apply defined, optically read-out growth-induced pressure of up to 1.5 MPa. The first, the self-closing (SC) chip, confines cells in multiple small chambers accommodating hundreds of cells; it provides excellent nutrient supply and rapid medium exchange, supports single-cell imaging, and allows multiplexing of cellular or chemical conditions. The second, the pressure-recovery (PR) chip, confines cells in a single 5 cm-long chamber accommodating hundreds of thousands of cells; a scalpel-cut step recovers live cells from the channel within minutes for bulk biochemical assays. The two devices share a single two-layer soft-lithography fabrication process and a common brightfield wall-displacement pressure readout. Together, they enable single-cell imaging and bulk biochemical analysis under matched, defined pressure conditions. We illustrate the protocol with two representative validations: rapid {beta}-estradiol-induced transcription in the SC chip, in which nascent transcription foci appear within 5 min independently of the applied pressure, and the PR chip, which produces uniform growth-induced pressure along the entire 5 cm channel and recovers between 0.1x10^6 and 1x10^6 cells per device in a pressure-tunable manner.
]]></description>
<dc:creator><![CDATA[ Kim, H., Nguyen, N., Alric, B., Albert, L., Delarue, M. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.06.749717</dc:identifier>
<dc:title><![CDATA[Microfluidic Devices for Imaging and Biochemistry Analysis of Microbes Under Mechanical Pressure]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.09.750526v1?rss=1">
<title>
<![CDATA[
Atomistic Insights into TRPC6/Caveolin-1 Interactions Interface via All- Atom Molecular Dynamics Simulations: Structural and Energetic Basis for Selective Modulation 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.09.750526v1?rss=1
</link>
<description><![CDATA[
The molecular determinants governing TRPC6 stabilization and its interaction with caveolin1 (CAV1) remain poorly defined, despite their critical role in caveolae organization and signaling. The absence of atomistic structural models has hindered a mechanistic understanding of how TRPC6 is recruited to, and stabilized within, caveolar microdomains. Here, we combine all-atom molecular dynamics simulations with MM/PBSA calculations to characterize the TRPC6-CAV1 complex at atomic resolution. To preserve a biologically realistic membrane environment, harmonic restraints were applied to transmembrane and membrane-embedded regions of both proteins, while the cytosolic TRPC6 N-terminus and solvent-exposed edges of the CAV1 scaffolding domain were kept fully flexible, allowing the putative caveolin-binding motif to explore conformational space and form dynamic contacts. This protocol maintained overall structural integrity while capturing physiologically relevant flexibility at the interaction surface. MM/PBSA analysis revealed a highly favorable binding free energy ({Delta}G-binding = -255.9 {+/-} 1.6 kJ/mol), dominated by electrostatic contributions and reinforced by hydrophobic and aromatic interactions. Per-residue energy decomposition identified an acidic patch in TRPC6 (residues 30-41) that engages a complementary basic, amphipathic segment in CAV1 (residues 85-106), defining a cooperative, reversible binding interface. These findings provide the first atomistic description of TRPC6 recruitment by CAV1 and establish a quantitative framework for the rational design of strategies to selectively modulate this interaction.
]]></description>
<dc:creator><![CDATA[ Polat, O. K., Bazsefidpar, S., Rodriguez, A., Mori, M. X., Mosadeghi, H., Israni, A. K., Koss, K. M. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.09.750526</dc:identifier>
<dc:title><![CDATA[Atomistic Insights into TRPC6/Caveolin-1 Interactions Interface via All- Atom Molecular Dynamics Simulations: Structural and Energetic Basis for Selective Modulation]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.09.750510v1?rss=1">
<title>
<![CDATA[
The ecological context of enzymatic variation 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.09.750510v1?rss=1
</link>
<description><![CDATA[
Among the challenges in understanding microbial ecosystems is the presence of physics at vastly different scales. Reactions, catalyzed by enzymes but regulated at the level of the cell, propel the flux of carbon and nitrogen through our atmosphere. Compounding this is the presence of pervasive enzyme sequence variation; this variation has been shown to contain coevolving modes of amino acids which encode the enzyme's evolutionary history. In this work, we take steps towards bridging the gap between the enzymatic variation present in an ecosystem and its subsequent activity. We employ the reduction of nitrate by NarG as a model system, which acts as an essential step in the nitrogen cycle by mediating both the return of di-nitrogen to the atmosphere and the assimilation of nitrate into biomass. Considering both metagenomic reconstructions as well as functional data from soil nitrate reducers, we find that sequence variants of enzymes obey predictable responses to environmental fluctuations. That is, while prior community-level metagenomic studies have characterized the response of bacterial strains to the environment, our study provides an enzyme variant level sequence-to-response map. Further, we demonstrate that a simple statistical model can predict the organismal phenotype from variant sequence; in soil samples not originally seen by that model, the prediction of a variant's reduction rate correlates with how much cells with that variant grow in abundance.
]]></description>
<dc:creator><![CDATA[ Landsittel, J. A., Howe, A., Kuehn, S., Lee, K. K., Mani, M. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.09.750510</dc:identifier>
<dc:title><![CDATA[The ecological context of enzymatic variation]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.09.750318v1?rss=1">
<title>
<![CDATA[
From flagellar motor behavior to bacterial swimming: defining a reference state for motility dynamics in Magnetospirillum gryphiswaldense 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.09.750318v1?rss=1
</link>
<description><![CDATA[
Cell motility is powered by the bacterial flagellar motor, a rotary nanomachine whose activity is dynamically modulated by external stimuli. In Magnetospirillum gryphiswaldense, magnetic and chemical inputs are thought to converge at the level of motility control, yet the mechanisms underlying chemotactic regulation remain poorly understood. Here, we seek to establish a quantitative reference-state of a model strain of magnetotactic bacteria through bacterial flagellar motor dynamics. To achieve this goal, magnetotaxis was kept as a natural factor by keeping the earth's magnetic field as the only source of magnetism. To avoid aerotaxis bias, oxygen gradients were removed by implementing two different constant oxygen conditions: environmental oxygen exposure, and limited oxygen exposure. Together, the tethered-cell bacterial flagellar rotational assay and the free-swimming assay in the absence of external stimuli presented in this paper establish a framework for investigating motor and cellular swimming adaptation to magnetic, aerotactic, and chemical signals. Under reference-state conditions, the bacterial flagellar motor showed a tendency to exhibit log-normal distributions for the time spent in each motor state: runs in different directions (counter-clockwise and clockwise), and pause. A semi-Markov reference-state model was developed to provide a quantitative description of bacterial flagellar motor dynamics. The model revealed that cell magnetic polarity modulates the transition pathways leading to the paused state, whereas oxygen, in the absence of a gradient, primarily regulates residence in each motility state.
]]></description>
<dc:creator><![CDATA[ Roesch Martinez, D. R., Delabre, G., Gachon, E. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.09.750318</dc:identifier>
<dc:title><![CDATA[From flagellar motor behavior to bacterial swimming: defining a reference state for motility dynamics in Magnetospirillum gryphiswaldense]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.08.750273v1?rss=1">
<title>
<![CDATA[
Cytosolic MagLOV Magnetofluorescence in Mammalian Cell Lines and Primary Neurons 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.08.750273v1?rss=1
</link>
<description><![CDATA[
Magnetic fields can influence the outcome of photochemical reactions through the radical pair mechanism, but whether this sensitivity extends to standard experimental conditions in mammalian cells has remained unclear. Here, we quantify the cytosolic magnetofluorescence of MagLOV, a genetically encoded, flavin-binding fluorescent protein, in mammalian cells, validated against extensive artifact controls. Excitation intensity and magnetic field strength differentially tune response kinetics and amplitude, respectively, with amplitude saturating above approximately 8 mT. Magnetic field-effect amplitude is further modulated by cellular culture state. This response generalizes across HEK293T, HeLa, U2OS, and A549 cells and primary mouse cortical neurons, with plateau amplitudes ranging from 1.4% to 2.7%. Together, these results establish that genetically encoded spin-dependent photochemistry can be quantitatively interrogated under standard mammalian live-cell imaging conditions, and generalizes across mammalian cell types.
]]></description>
<dc:creator><![CDATA[ Li, H., An, H., Hidalgo, E. C., Pavlic, A., Zhong, B. L., Plastina, F., Wu, D., Shapiro, M. G. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.08.750273</dc:identifier>
<dc:title><![CDATA[Cytosolic MagLOV Magnetofluorescence in Mammalian Cell Lines and Primary Neurons]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.07.749822v1?rss=1">
<title>
<![CDATA[
The Tensile Expansion Microscopy (TExM) cell stretcher: an iris expansion device integrated with automated real-time autofocus and tracking to super-resolve cells 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.07.749822v1?rss=1
</link>
<description><![CDATA[
Mechanical stretchers are used to physically expand biological samples for microscopic studies of mechanobiology. Existing stretchers suffer from limited strain capacity and non-quantifiable forces, along with focus drift and feature-tracking limitations during microscopy. We develop an iris-based cell stretcher that applies isotropic equibiaxial force to achieve aerial strain of 1664% that corresponds to 4.2x linear expansion for Tensile Expansion Microscopy (TExM), a super-resolution method which increases sample size above the diffraction limit of light. The TExM stretcher uses 3D-printed, printed circuit board (PCB) and cost-effective parts, is portable and automated. We verify the performance of the TExM cell stretcher using image analysis, achieving ~90% mechanical precision, a maximum of four degrees of arm angular deviation, precise speed control down to 0.01 cm/sec, and an average expansion resolution of 3.98 x 10^-3 x. Integrated strain gauge sensors confirm equal application of force by each arm of the stretcher throughout expansion and finite-element simulation and planar-polariscope photoelastic imaging characterize the uniform substrate stress distribution while indicating high stress at the substrate gripping area. An AutoTracking software in communication with the stretcher hardware and microscope enables continuous autofocus and feature tracking during TExM and fiducial markers verify uniform equibiaxial stretch. The stretcher is demonstrated with fixed NIH 3T3 fibroblasts and live HeLa cells, observing ~4x cellular expansion of fixed cell size and separation of live cell clusters, highlighting the potential of TExM cell stretcher for biological imaging.
]]></description>
<dc:creator><![CDATA[ Arampongpun, R., Shrikanth, T., Venkataramani, V., Latham, D. R., Zammali, M., Vakil, V., Kisley, L. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.07.749822</dc:identifier>
<dc:title><![CDATA[The Tensile Expansion Microscopy (TExM) cell stretcher: an iris expansion device integrated with automated real-time autofocus and tracking to super-resolve cells]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.07.749947v1?rss=1">
<title>
<![CDATA[
Structural basis of lipid-mediated self-regulation of Tissue Factor. 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.07.749947v1?rss=1
</link>
<description><![CDATA[
Tissue Factor (TF) is a tightly regulated transmembrane protein that maintains its encrypted state on the cell surface with an unknown conformation. Generation of TF conformational ensembles by the co-folding method using alphafold3 and boltz2 software revealed two mechanisms of TF self-regulation and corresponding conformational changes that were validated by Molecular Dynamics simulations. The first mechanism includes tilted and upright conformations of TF, whereas the second mechanism involves the spontaneous formation of TF oligomers, mostly dimers. The structural changes in TF responsible for both mechanisms were reversible and lipid-dependent. TF co-folding with phosphatidylserine resulted in approximately 90% of the TF extracellular domain in an upright conformation, enabling fast Factor VII (FVII) binding, while co-folding with phosphatidylcholine resulted in 60% of TF conformations tilted relative to the membrane surface and with a hidden FVII binding site. TF residues 210-219 (Linker Peptide) serve as a sensor that determines the TF conformation by interacting with the headgroups of phospholipids. TF self-association results in four types of homodimers with distinct relative orientations of extracellular domains and different accessibility of TF FVII binding sites. Approximately half of the dimers had accessible FVII binding sites, whereas in the remaining dimers, the FVII binding sites were partially or completely blocked. Co-folding of two TF sequences in the presence of cholesterol and phospholipids inhibited the dimerization and increased the number of TF monomers capable of FVII binding. These previously unknown TF conformations provide a structural basis for maintaining the encrypted and decrypted states of TF on the cell surface.
]]></description>
<dc:creator><![CDATA[ Iakhiaev, A. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.07.749947</dc:identifier>
<dc:title><![CDATA[Structural basis of lipid-mediated self-regulation of Tissue Factor.]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.04.749494v1?rss=1">
<title>
<![CDATA[
Large phospholipid-number asymmetry is not required to reproduce plasma membrane physical properties 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.04.749494v1?rss=1
</link>
<description><![CDATA[
Plasma membranes are compositionally asymmetric, but whether this lipid-type asymmetry is accompanied by a substantial phospholipid-number imbalance between leaflets remains debated. Here, we use microsecond all-atom molecular dynamics simulations to compare human red blood cell plasma membrane models with either strong phospholipid-number asymmetry and exoplasmic cholesterol enrichment or near-symmetric phospholipid and cholesterol numbers but preserved lipid-type asymmetry. Both asymmetric models reproduce a densely packed, ordered exoplasmic leaflet and a more fluid cytoplasmic leaflet. Strong phospholipid-number asymmetry, however, drives extensive cholesterol enrichment in the exoplasmic leaflet and amplifies membrane asymmetry, leading to large cholesterol-rich clusters, enhanced shallow hydrophobic exposure, reduced exoplasmic lipid mobility, lower ethanol permeability, and increased area compressibility. Comparison with available diffusion and alcohol-permeability measurements indicates that the strongly asymmetric model overestimates the immobilization and barrier properties of the exoplasmic leaflet, whereas the near-symmetric-number model better captures these dynamic observables. Our results suggest that lipid-type asymmetry is sufficient to reproduce many physical hallmarks of plasma membranes without requiring a large phospholipid-number imbalance.
]]></description>
<dc:creator><![CDATA[ Popov, C. R., Trollmann, M. F., Zhang, C., Böckmann, R. A. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.04.749494</dc:identifier>
<dc:title><![CDATA[Large phospholipid-number asymmetry is not required to reproduce plasma membrane physical properties]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.05.749365v1?rss=1">
<title>
<![CDATA[
Phosphoinositides protonation states dictate AKT1 binding with membrane 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.05.749365v1?rss=1
</link>
<description><![CDATA[
Phosphoinositides are key regulators of membrane-associated signaling, yet their electrostatic properties are commonly represented by a single nominal charge in molecular simulations and structural models. Using the essential protein kinase AKT1 as a model system, we show that phosphoinositide protonation microstates, both the degree and positional placement of protons, govern peripheral membrane-protein recognition. By integrating quantum-mechanics-derived headgroup parameters, microsecond-scale all-atom molecular dynamics, and umbrella-sampling free-energy calculations with the available solid-state NMR-derived lipid populations via Bayesian/Maximum Entropy reweighting, we account explicitly for the thermodynamic ensemble of phosphoinositide proto-nation states. This population-weighted free-energy framework provides a quantitative mechanistic rationale for the strict specificity of wild-type AKT1 toward PI(3, 4, 5)P3 and elucidates how the oncogenic sentry mutation (E17K) alters this specificity to enable high-affinity PIP2 binding. Furthermore, Proximity-based Labeling of Membrane Associated Proteins (PLiMAP) assays experimentally confirm that AKT1 pleckstrin homology domain binding to distinct phosphoinositide species is differentially sensitive to pH. Together, our findings establish a direct connection between phosphoinositide protonation equilibria, binding energetics, and AKT1 lipid specificity. Beyond AKT1, these results demonstrate that the dynamic protonation microstates of anionic phospholipids act as a functional regulatory layer governing peripheral membrane-protein recruitment across diverse cellular microenvironments.
]]></description>
<dc:creator><![CDATA[ Jha, K., Sarkar, M., Baratam, K., Nagesh, J., Pucadyil, T., Srivastava, A. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.05.749365</dc:identifier>
<dc:title><![CDATA[Phosphoinositides protonation states dictate AKT1 binding with membrane]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.07.749370v1?rss=1">
<title>
<![CDATA[
Residue-level predictions of the protein-protein interactions of the hepatitis B virus core and envelope proteins 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.07.749370v1?rss=1
</link>
<description><![CDATA[
We here predicted the interactions between the capsid (Cp) and envelope proteins (S/M/LHBs) of the hepatitis B virus using a recently established mutation-driven deep-learning model, as well as coevolution signatures that serve as markers of physical interactions and/or functional relationships. The sequence-based analyses reveal putative protein-protein interaction (PPI) hotspots in proteins, and identify abundant coevolved residues within and across proteins. We analyze the results with a focus on the intermolecular interactions between Cp and the large envelope protein LHBs, especially its disordered preS domain. We compare the predicted PPI interface sites to previous evidence on PPIs, derived from mutational analyses described in the literature. We equally integrate experimental NMR data that provide a rationale for the previous observation that spike-binding peptides inhibit core-envelope interactions. Our work sheds new light on the molecular mechanisms at play on HBV envelopment, and provides starting points for the experimental investigation of these interactions using structural and molecular virology approaches.
]]></description>
<dc:creator><![CDATA[ van Belleghem, C., Rescalli, S., Briday, M., Combet, C., Cano Contreras, M., Lecoq, L., Fogeron, M.-L., Carbone, A., Bockmann, A. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.07.749370</dc:identifier>
<dc:title><![CDATA[Residue-level predictions of the protein-protein interactions of the hepatitis B virus core and envelope proteins]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.07.749836v1?rss=1">
<title>
<![CDATA[
Clogging of particle suspensions in networks 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.07.749836v1?rss=1
</link>
<description><![CDATA[
In many biological, biomedical and industrial systems, particles are transported via fluids through confined networks, in which clogging can disrupt function. However, we lack a predictive theoretical framework that couples particle transport, suspension rheology and network flow resistance. Here, we develop a model and solution algorithm for particle suspension flow in networks based on vessel-level continuum modelling and particle distribution at nodes connecting vessels. We apply the model to study transport of dense particle suspensions in minimal and physiological biological networks. A key feature of our model is the coupling between particle volume fraction and particle flux: in line with the physics of dense suspensions, each network branch, or vessel, possesses a local carrying capacity for particle transport at an intermediate particle fraction between zero and the maximum packing fraction. If this flux capacity is reached, the vessel becomes flux-limited and particles can accumulate in upstream branches, causing them to enter a high-particle-fraction, high-resistance state that we refer to as 'clogged'. We show that these vessel flux limitations lead to network-level redistribution of particles, which can cause widespread clogging and emergent network-scale heterogeneity. By varying network topology, we find that in some regimes increasing network connectivity does not improve transport: paradoxically, additional pathways can promote clogging and reduce network-level particle flux, analogous to classic results in traffic flow networks. Our results provide a minimal mechanistic framework that links suspension physics, network topology, and transport failure in complex flow networks.
]]></description>
<dc:creator><![CDATA[ Neal, C. V., Hewitt, D. R., Pearce, P. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.07.749836</dc:identifier>
<dc:title><![CDATA[Clogging of particle suspensions in networks]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.09.07.749945v1?rss=1">
<title>
<![CDATA[
An integrated mass spectrometry strategy for quantifying the proteoform diversity of the extensively modified O-glycoprotein Osteopontin 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.09.07.749945v1?rss=1
</link>
<description><![CDATA[
O-glycosylation is among the most abundant and structurally diverse post-translational modifications in eukaryotes, yet its heterogeneity renders O-glycoproteins exceptionally difficult to characterize. To overcome these challenges, we have developed an integrated mass spectrometry (MS) strategy to define the proteoform landscape of O-glycoproteins and applied it to human osteopontin (OPN). OPN is a disease-associated extracellular matrix protein subject to extensive modification. By combining native MS with serial exoglycosidase digestions, we directly resolved truncation, phosphorylation, sulfation, and O-glycosylation of OPN. Matched glycoproteomic analyses, using tailored (glyco)protease combinations, allowed us to quantify glycan heterogeneity inaccessible to conventional trypsin-based approaches or protein-centric methods. We integrated these datasets using forward compositional simulations to infer the intact OPN proteoform distribution and benchmarked the resulting models against an experimental intact-mass distribution obtained by proton-transfer charge-reduction MS. This comparison revealed that bottom-up O-glycoproteomics systematically underestimates the true extent of glycan sialylation, whereas assuming (near-)complete sialylation accurately reproduced the experimental intact OPN mass distribution. Together, these results provide a comprehensive, quantitative view of OPN compositional diversity and demonstrate how intact-protein and peptide-level measurements can be reconciled to resolve highly heterogeneous glycoform populations. The workflow establishes a broadly applicable framework for characterizing extensively O-glycosylated and multiply modified proteins.
]]></description>
<dc:creator><![CDATA[ Zouboulis, K. C., Bennett, J. L., Daly, L. A., Burnap, S. A., Holden, E., Lutomski, C. A., Eyers, C. E., Robinson, C. V., Struwe, W. B., Benesch, J. L. P. ]]></dc:creator>
<dc:date>2026-09-10</dc:date>
<dc:identifier>doi:10.64898/2026.09.07.749945</dc:identifier>
<dc:title><![CDATA[An integrated mass spectrometry strategy for quantifying the proteoform diversity of the extensively modified O-glycoprotein Osteopontin]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-09-10</prism:publicationDate>
<prism:section></prism:section>
</item>
</rdf:RDF>
