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This feed contains articles for bioRxiv Subject Collection "Biophysics"
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<title>bioRxiv</title>
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<link>https://www.biorxiv.org</link>
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<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.13.718243v1?rss=1">
<title>
<![CDATA[
Topological defects and coherent myocardial chirality shape torsional heart contraction 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.13.718243v1?rss=1
</link>
<description><![CDATA[
The efficient pumping of the mammalian heart relies on torsional contractile motion generated by its highly ordered three-dimensional (3D) architecture of myocardial fibres. However, the topological principles governing how its complex geometry translates into contractile mechanics remain elusive. Here, we show that the mammalian heart forms a chiral nematic field, a biological analogue to 3D liquid crystals, whose topological organisation underlies its function. Analysis of 3D imaging data revealed disclination lines, continuous assemblies of topological defects characteristic of nematic systems, within the compact myocardium. Finite-element simulations reveal that these defects are not mere structural irregularities but can locally modulate contractile behaviour and reduce mechanical work. In heterotaxy hearts with reversed global anatomy (situs inversus), myocardial fibres retain a predominantly counter-clockwise twist, similar to that of the normal heart, but with a small clockwise component near the base. This decoupling of tissue-level chirality from systemic left-right patterning suggests that cardiac twist is an intrinsic property of the myocardial fibre. Mechanical simulations of situs inversus heart demonstrate that the coherence of transmural chirality, rather than its specific orientation, is critical for contractile efficiency. Together, these findings establish the heart as a topological material and reveal how organised chiral fields generate robust organ-level mechanical function.
]]></description>
<dc:creator><![CDATA[ Kawahira, N., Yamamoto, T., Washio, T., Nakajima, Y., Yashiro, K., Xu, V., Kawaguchi, K., Nakano, A. ]]></dc:creator>
<dc:date>2026-04-16</dc:date>
<dc:identifier>doi:10.64898/2026.04.13.718243</dc:identifier>
<dc:title><![CDATA[Topological defects and coherent myocardial chirality shape torsional heart contraction]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-16</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.15.718739v1?rss=1">
<title>
<![CDATA[
The dynamic and heterogeneous structure of the non-canonical inflammasome 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.15.718739v1?rss=1
</link>
<description><![CDATA[
Inflammasomes are high molecular weight complexes that play an integral role in the innate immune system, triggering an inflammatory cascade to protect against cellular stresses such as pathogenic bacteria. Both canonical and non-canonical inflammasomes have been described in the literature and detailed structural studies of many components of the more complex and larger canonical versions have been reported. In contrast, corresponding structures of the non-canonical inflammasome have not emerged even though it consists of only two components: lipopolysaccharide (LPS) from gram-negative bacteria, and one of caspase-4 or caspase-5 in humans or caspase-11 in mice. Here we determine the stoichiometry of the non-canonical inflammasome using size-exclusion chromatography coupled with UV, refractive index, and light-scattering measurements, showing that the non-canonical inflammasome is heterogeneous, comprised of three major complexes with different numbers of LPS and caspase molecules. Solution Nuclear Magnetic Resonance (NMR) spectroscopy studies of the N-terminal Caspase Activation and Recruitment Domain (CARD) of caspase-11, that binds LPS, show that it is largely unstructured in the absence of lipid, with pervasive dynamics on the s-ms timescale. Formation of this complex increases the alpha-helical content of the CARD but the dynamics persist, multiple conformers are formed, and tertiary contacts are transient, consistent with formation of a molten globule. Our NMR results establish that the protease domain of caspase-11 is monomeric in isolation. As proteolysis is linked with dimerization, the protease domains are inactive in this state, but upon formation of the non-canonical inflammasome dimerization occurs, priming the complex for rapid processing of substrates.
]]></description>
<dc:creator><![CDATA[ Sever, A. I., Aramini, J. M., Bonin, J. P., Zhao, H., Wang, H., Rubinstein, J. L., Schuck, P., Kay, L. E. ]]></dc:creator>
<dc:date>2026-04-16</dc:date>
<dc:identifier>doi:10.64898/2026.04.15.718739</dc:identifier>
<dc:title><![CDATA[The dynamic and heterogeneous structure of the non-canonical inflammasome]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-16</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.14.718453v1?rss=1">
<title>
<![CDATA[
Biomolecular condensates provide a unique environment for redox-mediated protein crosslinking 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.14.718453v1?rss=1
</link>
<description><![CDATA[
Biomolecular condensates, often formed through liquid-liquid phase separation, are dynamic cellular compartments. Here, we demonstrate that a wide range of fluorescently tagged proteins undergo inadvertent, condensate-mediated crosslinking, resulting in rapid solidification of condensates under common fluorescence imaging conditions. The process is driven by excitation-induced, short-lived reactive oxygen species (ROS), whose otherwise limited crosslinking potential becomes uniquely enabled in the dense phase. In live cells, excitation-induced ROS potently trigger stress granule formation, while the ROS-driven solidification of condensates is modulated by compartment-dependent antioxidant buffering. Our findings demonstrate that condensates create a distinct environment that enables ROS chemistry unlikely to occur in the bulk cytosol. Furthermore, the cellular redox level can be a general regulator of condensate rheology. Beyond biological insights, our findings underscore the need for scrutiny when examining fluorophore-labeled condensates.
]]></description>
<dc:creator><![CDATA[ Wang, H., Favetta, B., Wang, J., Hoffmann, C., Maloku, E., Xia, Y., Baum, J., Milovanovic, D., Schuster, B. S., Shi, Z. ]]></dc:creator>
<dc:date>2026-04-16</dc:date>
<dc:identifier>doi:10.64898/2026.04.14.718453</dc:identifier>
<dc:title><![CDATA[Biomolecular condensates provide a unique environment for redox-mediated protein crosslinking]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-16</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.14.718443v1?rss=1">
<title>
<![CDATA[
Differential effects of α-Synuclein monomers and seeds on the material properties of Tau condensates 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.14.718443v1?rss=1
</link>
<description><![CDATA[
Tau and -Synuclein (Syn) frequently co-aggregate in various neurodegenerative disorders. Recently, Tau has been shown to form dynamic, liquid-like condensates that can recruit Syn, and potentially serve as a precursor to pathological aggregation. However, the quantitative impact of Syn on the material properties of these condensates remains elusive. Here, we measure the viscosity and interfacial tension of Tau condensates and determine how these properties are modulated by Syn monomers and fibril seeds. We find that while both forms of Syn partition efficiently into Tau condensates, they exert vastly different effects on the condensate's material state. The viscosity of Tau condensates remains unchanged in the presence of Syn monomers at concentrations up to 200 M, accompanied by a moderate reduction in the condensates' interfacial tension. In contrast, the addition of only 5 M Syn fibril seeds triggers rapid solidification of Tau condensates, manifested by a nearly 100-fold increase in condensate viscosity within one hour. These findings provide quantitative insights into condensate mechanics, highlighting the unique capacity of Syn seeds to drive the liquid-to-solid transition of Tau condensates that may underlie the formation of pathological aggregates.
]]></description>
<dc:creator><![CDATA[ Sharma, B., Wang, J., Retana, P. C., Baum, J., Shi, Z. ]]></dc:creator>
<dc:date>2026-04-16</dc:date>
<dc:identifier>doi:10.64898/2026.04.14.718443</dc:identifier>
<dc:title><![CDATA[Differential effects of α-Synuclein monomers and seeds on the material properties of Tau condensates]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-16</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.14.718414v1?rss=1">
<title>
<![CDATA[
Asymmetric Hydration and Protonation Switching of Dual Aspartates Drive Flagellar Rotation 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.14.718414v1?rss=1
</link>
<description><![CDATA[
The bacterial flagellar motor is an intricate nanomachine that transforms chemical energy from ion gradients into mechanical rotation, enabling bacterial movement. While stator unit architectures are conserved across species, the molecular link connecting ion translocation to rotational force generation remains elusive. In this study, we refined the cryo-EM structures of MotAB from Campylobacter jejuni (CjMotAB) and integrated a suite of approaches-including single-structure based pKa predictors and free energy perturbation (FEP) calculations, as well as standard and constant-pH molecular dynamics (CpHMD) simulations of various structural models representing the plugged, unplugged, and plug-removed states with different protonation states of D22 to dissect its rotational mechanism. Based on pKa calculations, the D22 residues in chains F and G of MotB were identified as proton carriers supporting the previous hypotheses. Importantly, we observed asymmetric hydration patterns of the two D22 residues in the MotB dimer, along with their hydrogen bonding interactions with MotA T189, which contribute to functional specialization. Our findings reveal that MotA rotation requires two essential prerequisites: plug removal and alternating D22 protonation switching, coupled with dynamic gauche-trans conformational changes in the sidechain of D22. This work clarifies how protonation dynamics and structural asymmetry synergistically regulate CjMotAB rotation, advancing our understanding of bacterial flagellar motor function and providing a foundational framework for investigating diverse ion-driven biological motors.
]]></description>
<dc:creator><![CDATA[ Luo, J., Hu, H., Cai, Z., chen, S., Lao, Y., Xiu, P., Taylor, N., Huang, Y., Wang, Y. ]]></dc:creator>
<dc:date>2026-04-16</dc:date>
<dc:identifier>doi:10.64898/2026.04.14.718414</dc:identifier>
<dc:title><![CDATA[Asymmetric Hydration and Protonation Switching of Dual Aspartates Drive Flagellar Rotation]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-16</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.15.718738v1?rss=1">
<title>
<![CDATA[
Quantitative and mutational analysis of soluble HIV-1 Vpu and calmodulin interactions 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.15.718738v1?rss=1
</link>
<description><![CDATA[
The HIV-1 Vpu protein aids viral adaptation by influencing host cell pathways via protein interactions. While Vpu is mainly found in plasma and endomembranes, we recently discovered a soluble form that forms a stable, equimolar complex with Ca2+-bound calmodulin (Ca2+-CaM), potentially affecting Vpu cellular trafficking. Here, to determine the binding affinity and identify regions of soluble Vpu involved in CaM binding, we used ensemble Forster Resonance Energy Transfer (eFRET). We tested Cy3-labeled full-length (FL) Vpu, a C-terminal fragment (helices 2 and 3), and a Cy3-labeled FL Vpu V22A/W23Y mutant with substitutions in Vpu helix 1. All Vpu variants were labeled at residue L42C, and Ca2+-CaM was tagged with Cy5 at residue S39C. eFRET analysis of 100 nM Cy3-Vpu variants mixed with Cy5-Ca2+-CaM (in the range 100-600 nM) revealed dissociation constants (Kd) and binding energies (deltaG) for heterocomplexes. FL Vpu-Ca2+-CaM showed high stability (Kd ~40 nM, deltaG ~10.1 kcal/mol), while the truncated C-terminal region and V22A/W23Y mutant formed less stable complexes with Ca2+-CaM (Kd ~200 nM and 800 nM, deltaG ~9 kcal/mol and ~8.3 kcal/mol). This, a binding hot spot in Vpu CaM-binding motif in helix 1 was identified, which may control the stability of Vpu-Ca2+-CaM complex and Vpu insertion in the membrane: We hypothesize that upon delivery to the membrane, the hydrophobic helix 1 of Vpu dissociates from Ca2+-CaM and inserts in the lipid bilayer; thereafter, CaM dissociates from Vpu facilitated by the reduced Vpu-Ca2+-CaM complex stability. The findings from this study advance our understanding of HIV-1 Vpu interactions with cellular components and may aid the development of antivirals.
]]></description>
<dc:creator><![CDATA[ Ogunbowale, A., Hadadianpour, E., Ishola, O., Islam, M. M., Ramos, N., Saffarian Delkhosh, A., Georgieva, E. R. ]]></dc:creator>
<dc:date>2026-04-16</dc:date>
<dc:identifier>doi:10.64898/2026.04.15.718738</dc:identifier>
<dc:title><![CDATA[Quantitative and mutational analysis of soluble HIV-1 Vpu and calmodulin interactions]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-16</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.15.718748v1?rss=1">
<title>
<![CDATA[
Protein entanglement misfolding determines divergent fates: proteasomal degradation or persistence in near-native misfolded states 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.15.718748v1?rss=1
</link>
<description><![CDATA[
A novel class of protein misfolding, involving changes in entanglement status, occurs across the cytosolic proteome of a bacterium and likely occurs in many other organisms. Here, we examine if this class of misfolding has measurable downstream consequences for protein homeostasis. Specifically, we test the hypothesis that proteins that misfold in this way are more likely to be degraded by the ubiquitin-proteosome system immediately after synthesis. We do this by cross-referencing protein structural information with ubiquitin mass spectrometry (Ubq-MS) data from human fibroblast cells. Ubq-MS identifies proteins that have been covalently modified with ubiquitin in a particular pattern and is a cellular signal for that protein to be degraded by the proteosome. We find that nascent proteins with native entanglements, which were previously shown to be twice as likely to misfold, are 93% (95% Confidence Interval: [44%, 160%]) more likely to be tagged with ubiquitin and targeted to the proteasome compared to proteins that do not contain such entanglements. Simulating the folding of these proteins using a coarse-grained model, we find that the ubiquitin-tagged proteins containing native entanglements are four times more likely to misfold than the non-ubiquitinated proteins that are devoid of entanglements. These results indicate that entanglement misfolding, primarily involving a failure to form native entanglements, leads to an increased likelihood that those proteins will be degraded in human cells. Finally, we estimate that approximately one-third of the globular proteome likely misfolds in this way but bypasses proteasomal degradation because their misfolded states are structurally similar to their native ensemble. These consequences for protein degradation are likely common across organisms as entanglement misfolding is inherent to the polymeric nature of proteins.
]]></description>
<dc:creator><![CDATA[ Jiang, Y., Jain, A., Ghaemmaghami, S., O'Brien, E. P. ]]></dc:creator>
<dc:date>2026-04-16</dc:date>
<dc:identifier>doi:10.64898/2026.04.15.718748</dc:identifier>
<dc:title><![CDATA[Protein entanglement misfolding determines divergent fates: proteasomal degradation or persistence in near-native misfolded states]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-16</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.15.718817v1?rss=1">
<title>
<![CDATA[
Influence of Lipomannan and Lipoarabinomannan Concentration on Mycobacterial Inner Membranes Characterized by All-atom Simulations 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.15.718817v1?rss=1
</link>
<description><![CDATA[
Mycobacteria are responsible for causing severe illnesses like tuberculosis and leprosy in humans. Studying the mycobacteria cell envelope presents a significant challenge due to its intricate lipid compositions and structural variations and also its harmful nature in a typical experiment setting. In this study, we use all-atom molecular dynamics simulation to study mycobacterial inner membranes (MIMs). By incorporating different types of phosphatidyl-myo-inositol-mannosides (PIMs) and their glycoconjugates such as lipomannans (LM) and lipoarabinomannans (LAM) lipoglycans, we have constructed both symmetric and asymmetric membrane systems to study the MIM structure and dynamics under varying compositions of each lipid type. Our results show that the phospholipid/PIM-rich inner leaflet remains a stable, fluid bilayer, and the outer leaflet structure and dynamics are heavily governed by lipoglycan surface density. Importantly, as LM/LAM concentration increases, the polysaccharide chains shift from flexible, membrane-lying orientations to a compact brush-like state aligned with the membrane normal. This crowding significantly reduces the solvent-accessible volume and limits direct interactions between LM/LAM sugars and the outer leaflet surface. Furthermore, we observe that high lipoglycan presence in the outer leaflet slows lipid diffusion across the entire bilayer, demonstrating a dynamic coupling between the two leaflets. By resolving these LM/LAM sugar-level dynamics and their impact on membrane-wide properties, this study provides a molecular framework for future MIM modeling and simulation with various (peripheral) membrane proteins to better understand how the MIM functions as a regulated physical barrier and a platform for mycobacterial virulence.
]]></description>
<dc:creator><![CDATA[ Lee, H., Rygh, N., Chavent, M., Im, W. ]]></dc:creator>
<dc:date>2026-04-16</dc:date>
<dc:identifier>doi:10.64898/2026.04.15.718817</dc:identifier>
<dc:title><![CDATA[Influence of Lipomannan and Lipoarabinomannan Concentration on Mycobacterial Inner Membranes Characterized by All-atom Simulations]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-16</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.13.718244v1?rss=1">
<title>
<![CDATA[
Resolving the Activation Mechanism of the Human 20S Proteasome 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.13.718244v1?rss=1
</link>
<description><![CDATA[
Proteasome activators (PAs) bind the -subunits of the human 20S proteasome (h20S), opening the gates and allowing entry of substrate proteins. Aging is associated with diminished proteasome activity, leading to interest in understanding this activation mechanism. Evolving models have been proposed regarding PAs C-terminal tails, yet the critical molecular contacts for gate-opening are unclear. Here, we show a conserved leucine in the 5th position (P5) of the C-terminus is essential for h20S gate opening. By engineering C-termini in a model activator, PA26E102A, we show mutations to P5 systematically modulate proteasome activity in vitro and in cells. Structures of PA26E102A:h20S complexes at 2.7-3.2 [A] resolution identify interactions between P5 and a conserved arginine in the h20S, leading to partial or full gate opening. These results clarify the essential contacts required for h20S gate opening, potentially enabling design of proteasome activation therapies.
]]></description>
<dc:creator><![CDATA[ Ryder, B. D., Yan, N. L., Trejos-Vidal, D., Martinez-Botia, P., Braxton, J. R., Lim, A., Felstead, H., Andrews, S., Tse, E., De Melo, A. A., Skidmore, J., Prado, M. A., Southworth, D. R., Gestwicki, J. E. ]]></dc:creator>
<dc:date>2026-04-15</dc:date>
<dc:identifier>doi:10.64898/2026.04.13.718244</dc:identifier>
<dc:title><![CDATA[Resolving the Activation Mechanism of the Human 20S Proteasome]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-15</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.13.718213v1?rss=1">
<title>
<![CDATA[
Heterotrimeric G proteins exhibit subtype-specific mobility differences in live cells 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.13.718213v1?rss=1
</link>
<description><![CDATA[
Heterotrimeric G proteins are key signal transducers in all eukaryotic cells. They are responsible for unification and amplification of perceived extracellular chemical and physical stimuli. Heterotrimeric G proteins are peripheral membrane proteins attached to the inner leaflet of the plasma membrane. Despite numerous available studies, many biophysical aspects regulating G protein signaling, including mobility in the membrane, are insufficiently understood. Here, using single-molecule imaging, we show that different subtypes of heterotrimeric G proteins show high diversity in their mobility in the membrane. We demonstrate that the nature of the G subunit defines the mobility of a heterotrimer. Our results indicate that heterotrimers containing G12 and G13 subunits have remarkably reduced mobility compared to those with Gi/o, Gs, and Gq subunits. These findings identify subtype-specific lateral membrane mobility of G proteins as a factor affecting their signaling dynamics in living cells.
]]></description>
<dc:creator><![CDATA[ Kuchynka, O., Kovalchuk, A., Nussbaumer, M., Sviridova, E., Fessl, T., Bondar, A. ]]></dc:creator>
<dc:date>2026-04-15</dc:date>
<dc:identifier>doi:10.64898/2026.04.13.718213</dc:identifier>
<dc:title><![CDATA[Heterotrimeric G proteins exhibit subtype-specific mobility differences in live cells]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-15</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.14.718163v1?rss=1">
<title>
<![CDATA[
Atomic structure and dynamics of the mechanosensitive channel MscL from E. coli by cryo-EM and solid-state NMR 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.14.718163v1?rss=1
</link>
<description><![CDATA[
Mechanosensitive channels are central to cellular responses to membrane tension, yet the structural basis of their gating remains incompletely understood. Here, we determine the structures of wild-type and G22S mutants of MscL from E. coli (EcMscL) by cryo-EM in peptide-based lipid nanodiscs and complement them with solid-state NMR measurements in liposomes to capture their dynamics in a native-like membrane environment. The cryo-EM structures reveal a closed conformation, whereas analysis of the low-threshold G22S mutant by NMR uncovers widespread conformational changes in both cytoplasmic and periplasmic regions. These data indicate enhanced dynamics and conformational heterogeneity in the mutant, revealing the early transitions from the closed towards the open state. Together, our results establish a synergistic framework integrating cryo-EM and NMR to resolve both structure and dynamics of mechanosensitive channels, and identify lipid-protein interactions as key determinants of MscL gating and mechanosensitivity. Our study further provides a quantitative benchmark for computational investigations of mechanogating and lays the foundation for the rational design of channels with tunable gating kinetics.
]]></description>
<dc:creator><![CDATA[ Xiao, T., Kovinko, A., Shi, C., Sawczyc, H., Qoraj, D., Öster, C., Sprink, T., Lange, S., Kosteletos, S., Sun, H., Roderer, D., Chen, S., Lange, A. ]]></dc:creator>
<dc:date>2026-04-15</dc:date>
<dc:identifier>doi:10.64898/2026.04.14.718163</dc:identifier>
<dc:title><![CDATA[Atomic structure and dynamics of the mechanosensitive channel MscL from E. coli by cryo-EM and solid-state NMR]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-15</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.13.718267v1?rss=1">
<title>
<![CDATA[
Far-from-equilibrium assembly of multimers through DNA-based catalytic templating 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.13.718267v1?rss=1
</link>
<description><![CDATA[
On-demand assembly of arbitrary, sequence-defined polymers from a pool of monomers is a major challenge in modern chemistry, towards which limited progress has been made. By contrast, biological systems routinely use information-bearing DNA and RNA templates to catalytically synthesize a precise, far-from-equilibrium ensemble of nucleic acid and protein sequences from the available pools of NTPs or aminoacyl-tRNAs. Inspired by these biological examples, we introduce an enzyme-free DNA strand displacement network in which single-stranded DNA sequences template the assembly of specific non-covalent DNA multimers of up to length five, under isothermal and autonomous conditions. The templates demonstrate significant turnover, bypassing product inhibition. They can thereby catalyse the formation of a far-from-equilibrium ensemble of long-lived metastable products that are not otherwise addressable.
]]></description>
<dc:creator><![CDATA[ Mukherjee, R., Mitra, M., Jurinovic, K., Juritz, J., Ouldridge, T. E. ]]></dc:creator>
<dc:date>2026-04-15</dc:date>
<dc:identifier>doi:10.64898/2026.04.13.718267</dc:identifier>
<dc:title><![CDATA[Far-from-equilibrium assembly of multimers through DNA-based catalytic templating]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-15</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.13.718311v1?rss=1">
<title>
<![CDATA[
From Pixel to Wave: A Geometric Complementary Code for Hierarchical Pixel-Based Morphometry 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.13.718311v1?rss=1
</link>
<description><![CDATA[
This paper introduces a geometric complementary code (GCC) that bridges discrete digital pixel graphics with continuous analog wave mechanics in a geometric morphometrics framework. By oscillating four shaded cubic pixels in a Cartesian grid, an emergent pattern resembling a face-centered cubic (FCC) unit cell lattice appears. This pattern is modeled first in lattice space incorporating polarities of the sagittal, transverse, and coronal planes traditionally applied to Cartesian space and subsequently in Cartesian space as a topographic medium. In the Cartesian model, topographic values divide into rise values, where the grid converges toward elevated features along the Y-axis, and run values, where it flares within terrain dips. This produces a surface grid that undulates like a propagating wave. Across both models, a polar continuum emerges, oscillating between crossed and uncrossed polarities at micro- and macro-grid scales when applied at the topographic tile level. Each tile oscillates to generate counter-oscillatory perspectives across the macro-grid, dynamically shifting between approaching-point and vanishing-point modes. The GCC functions as a hierarchical pixel-based morphometry. It begins with pixel-scale analysis in a single ZX plane, advances to atomic-scale resolution across four ZX planes, and extends to topographic tile-scale across 16 ZX planes. This progression reveals a geometric expansion of FCC patterns within a nested 2 by 2 matrix processor. Grounded in a consistent Pythagorean grid-count relationship, the framework maps discrete pixel states onto continuous wave-like surface behavior. By addressing limitations in current geometric morphometrics where 3D scanning and semilandmark methods remain anchored in discrete landmarks or sparse points rather than detailed continuous topographic dimensions the GCC offers a novel hierarchical bridge between digital and analog domains.
]]></description>
<dc:creator><![CDATA[ Marcil, W. A. ]]></dc:creator>
<dc:date>2026-04-15</dc:date>
<dc:identifier>doi:10.64898/2026.04.13.718311</dc:identifier>
<dc:title><![CDATA[From Pixel to Wave: A Geometric Complementary Code for Hierarchical Pixel-Based Morphometry]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-15</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.14.717675v1?rss=1">
<title>
<![CDATA[
On-lamella super-resolution cryo-CLEM for cryo-ET enabled by vacuum-free ultra-stable cryogenic fluorescence microscopy 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.14.717675v1?rss=1
</link>
<description><![CDATA[
Cryogenic correlative light and electron microscopy (cryo-CLEM) combines specific fluorescence labelling of proteins inside cells with structural information at the angstrom-level. The introduction of super-resolution fluorescence methods in the field of cryogenic fluorescence microscopy is a necessary step to bridge the large resolution gap between the different imaging modalities. However, there are many challenges hindering the full potential of cryogenic super-resolution correlative light and electron microscopy and seamless integration with structural cell biology. One of the main limiting factors is a lack of dedicated cryogenic fluorescence microscopy systems with sufficient mechanical stability to enable the collection of high-quality super-resolution data and full compatibility with vitrified specimens for cryo-electron tomography. Here, we address this by developing a vacuum-free ultra-stable cryogenic optical microscope (VULCROM). VULCROM is a dedicated super-resolution cryo-CLEM (cryo-SR-CLEM) setup that combines the stability of a vacuum-insulated cryostat with the flexibility and modularity of an open microscopy system. We demonstrate that VULCROM enables detailed investigations of single-molecule cryo-photo-physics across timescales spanning milliseconds to hours. We furthermore demonstrate its suitability for routine cryo-SR-CLEM with a resolution in the 10 nm range in distinct vitrified biological specimen types. We resolve the nanoscale architecture of YFP-labelled PML bodies within the nucleus of mammalian cells and the distribution of ATG9-eGFP in its cellular structural context in a cryo-lift-out lamella of N. benthamiana plant tissue. Owing to its vacuum-free design, VULCROM can be readily adapted for diverse correlative workflows and other cryo-light microscopy applications.
]]></description>
<dc:creator><![CDATA[ Falckenhayn, J., Duong, V. Q., Prabhakar, N., Harley, I., Yuen, E. L. H., Bozkurt, T. O., Carter, S. D., Prazak, V., Kaufmann, R. ]]></dc:creator>
<dc:date>2026-04-15</dc:date>
<dc:identifier>doi:10.64898/2026.04.14.717675</dc:identifier>
<dc:title><![CDATA[On-lamella super-resolution cryo-CLEM for cryo-ET enabled by vacuum-free ultra-stable cryogenic fluorescence microscopy]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-15</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.13.717683v1?rss=1">
<title>
<![CDATA[
Single-molecule imaging and tracking on clinical liquid biopsies reveals cancer biomarkers nanoscale organization and heterogeneity 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.13.717683v1?rss=1
</link>
<description><![CDATA[
Single-molecule imaging and tracking have revealed fundamental biological mechanisms at the molecular scale, yet their application to clinical research remains limited by technical complexity and sample preparation incompatible with patient-derived specimens. As a result, we lack information with molecular-scale resolution of clinically relevant biomarkers. Here, we develop a workflow enabling Points Accumulation in Nanoscale Topography (PAINT) combined with single-particle tracking (SPT) on clinical liquid biopsies, allowing analysis of biomarker nanoscale organization at the single-molecule level in cancer patients. Our approach features a sample preparation tailored to liquid biopsies and requires no fixation, covalent labelling, or genetic modification, making single-molecule imaging compatible with hospital clinical workflows. We demonstrate the method's diversity by imaging liquid biopsies from blood, bone marrow aspirates, and pleural effusions across different cancer types. PAINT-SPT captures both the expression and mobility of clinically relevant membrane receptor biomarkers, revealing pronounced inter- and intra-patient heterogeneity at the molecular and cellular levels. We discover that individual patients exhibit distinct molecular mobility fingerprints that reflect biomarker interaction states and correlate with clinical diagnostic readouts. Furthermore, these fingerprints distinguish healthy from cancer cells, enabling the development of a classifier that accurately identifies cancer cells based on their single-molecule behaviour. Together, our results establish a route to investigate patient-derived clinical samples at the single-molecule level and open new opportunities to understand cancer biology and biomarker function beyond ensemble-averaged measurements.
]]></description>
<dc:creator><![CDATA[ Tholen, M. M. E., Riera Brillas, R., Hijzelaar, T. H. W., Cao, H., Cortopassi, F., Moers, M. E., Veta, M., Cruijsen, M. J., van de Kerkhof, D., Scharnhorst, V., Albertazzi, L. ]]></dc:creator>
<dc:date>2026-04-15</dc:date>
<dc:identifier>doi:10.64898/2026.04.13.717683</dc:identifier>
<dc:title><![CDATA[Single-molecule imaging and tracking on clinical liquid biopsies reveals cancer biomarkers nanoscale organization and heterogeneity]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-15</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.12.718068v1?rss=1">
<title>
<![CDATA[
Multifractal Fluctuations in Electrogram Dynamics Distinguish Atrial Fibrillation Phenotype, Drug Response, and Imminent Termination: Implications for Mechanism and Treatment. 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.12.718068v1?rss=1
</link>
<description><![CDATA[
Background Atrial fibrillation (AF) is maintained by complex dynamics, clinically characterised by bursting periods of organization and disorganization in intracardiac electrograms. We have previously postulated that cardiac conduction behaves like a critical system, where phase shift from organised rhythm to AF is a phase transition at the critical point. We thus hypothesized that using multifractal analysis of AF electrograms could potentially quantify non-stationary fluctuations, revealing novel mechanistic insights into the cardiac critical system and examine potential clinically relevant markers of AF dynamics, phenotype and treatment response. Objectives To determine whether multifractal analysis of AF electrograms can (i) Distinguish paroxysmal (PAF0 and non-paroxysmal AF (NPAF), (ii) predict response to pharmacologic modulation, and (iii) identify imminent spontaneous termination, thereby acting as marker of proximity to criticality along complex system phase spectrum. Methods We analysed >1.4 million seconds of high-density bipolar electrograms from 106 patients (paroxysmal n{approx}52, non-paroxysmal n{approx}54) undergoing left atrial mapping with a 24-bipole HD-Grid catheter at standardized sites (RENEWAL AF-ANZCTR ACTRN12619001172190)). Multifractal analysis using the Wavelet Transform Modulus Maxima Method (WTMM) was applied to a burst-energy observable to derive log-normal multifractal parameters c0 (support dimension), c1 (spectrum location), and c2 (fluctuations). Hierarchical mixed-effects models accounted for channels nested within locations within patients. A flecainide sub-study (n=15) provided paired pre/post-infusion recordings, and 27 spontaneous termination events in 15 patients were analysed using 60-s pre-termination windows. Spatial texture of c2 was quantified by variogram-derived correlation length and sill. Results AF electrograms exhibited robust multifractality confirming multifractal fluctuations as an intrinsic property of AF. Non-paroxysmal AF showed significantly reduced fluctuations versus paroxysmal AF (c2: {beta}=-0.01, p=0.001), indicating a paradoxical loss of fluctuations with disease progression. Flecainide selectively increased fluctuations in paroxysmal AF ({Delta}c2 = +0.04, p<0.01; {Delta}c0 = +0.06, p<0.01) but had no significant effect on fluctuations (c2) in non-paroxysmal AF, revealing phenotype-dependent drug response. Immediately prior to spontaneous AF termination, fluctuations increased significantly compared with sustained AF (c2: 0.198 vs 0.181, p=0.024). Spatial variogram analysis revealed heterogenous patterns in paroxysmal AF, whereas non-paroxysmal AF displayed a homogenised, flattened fluctuations landscape. Conclusions Atrial fibrillation exhibits robust multifractal dynamics rather than random electrical activity. Reduced fluctuations characterizes non-paroxysmal AF, whereas higher fluctuations is observed in paroxysmal AF, during flecainide modulation, and immediately prior to spontaneous termination. These findings suggest that multifractal fluctuations (c2) reflects the dynamical state of AF and may serve as a quantitative biomarker of disease progression, pharmacologic responsiveness, and proximity to termination.
]]></description>
<dc:creator><![CDATA[ Chapman, D. G., Ganesan, A. N., Strong, C., Tonchev, I., Lorensini, S., Shahrbabaki, S. S. ]]></dc:creator>
<dc:date>2026-04-15</dc:date>
<dc:identifier>doi:10.64898/2026.04.12.718068</dc:identifier>
<dc:title><![CDATA[Multifractal Fluctuations in Electrogram Dynamics Distinguish Atrial Fibrillation Phenotype, Drug Response, and Imminent Termination: Implications for Mechanism and Treatment.]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-15</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.13.718064v1?rss=1">
<title>
<![CDATA[
Emergence of rigidity percolation and critical behavior in tunable protein condensates 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.13.718064v1?rss=1
</link>
<description><![CDATA[
Multivalent proteins are known to form complex networks within biomolecular condensates, yet the mechanisms governing the emergence and evolution of these networks remain poorly understood. Here, we utilize a synthetic protein chimera system with tunable interactions to investigate the transition from liquid-like droplets to networked condensates. By employing single amino-acid substitutions, we generated a series of mutants with varying protein-binding strengths. As the interaction strength increases, the condensates undergo a sharp rigidity percolation transition, characterized by a more than 200-fold increase in both elastic modulus and viscosity. Near this transition, we identify a critical scaling relation in the condensate elasticity, providing robust evidence for a percolation-driven assembly mechanism. Furthermore, we demonstrate that this network architecture is fundamentally linked to biological functions. The introduction of disease associated mutations disrupts the network, significantly softening the condensates and rendering them fluid-like. Our findings reveal that network percolation and criticality in protein condensates can be sensitively regulated by single-amino-acid substitutions, underscoring their essential role in maintaining structural integrity and supporting physiological function.
]]></description>
<dc:creator><![CDATA[ Liao, Z., Jia, B., Xu, Y., Shen, Z., Zhang, M., Tong, P. ]]></dc:creator>
<dc:date>2026-04-14</dc:date>
<dc:identifier>doi:10.64898/2026.04.13.718064</dc:identifier>
<dc:title><![CDATA[Emergence of rigidity percolation and critical behavior in tunable protein condensates]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-14</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.13.717819v1?rss=1">
<title>
<![CDATA[
Escherichia coli K12 exhibits a ~50% longer lag phase, but no difference in log phase growth rate, under hypomagnetic conditions (19 nT) 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.13.717819v1?rss=1
</link>
<description><![CDATA[
Previous investigations have explored the effects of hypermagnetic fields, that is, fields in excess of the Earth's background geomagnetic field strength of approximately 50 , on Escherichia coli (E. coli). Conversely, this study investigates the effects of hypomagnetic field conditions, that is, fields below the geomagnetic background intensity, on the growth of E. coli K12 by using a hypomagnetic chamber to shield cultures, with a measured residual magnetic field inside the chamber of 19 nT. When grown in rich media from a semi-anaerobic, stationary-phase starting culture under geomagnetic and hypomagnetic conditions, the lag phases of E. coli were approximately 86 minutes and 132 minutes, respectively. Despite this increase in lag phase, exceeding two E. coli doubling times, the log-phase growth rate of E. coli was identical under both geomagnetic and hypomagnetic conditions. In addition to demonstrating a biologically relevant sensitivity to magnetic field parameters in the hypomagnetic direction, this represents a much greater absolute magnetosensitivity, with a deviation of only 50 T between the hypomagnetic and geomagnetic conditions, than has previously been demonstrated for E. coli.
]]></description>
<dc:creator><![CDATA[ Montague, M., Lodesani, A., Aiello, C. D. ]]></dc:creator>
<dc:date>2026-04-14</dc:date>
<dc:identifier>doi:10.64898/2026.04.13.717819</dc:identifier>
<dc:title><![CDATA[Escherichia coli K12 exhibits a ~50% longer lag phase, but no difference in log phase growth rate, under hypomagnetic conditions (19 nT)]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-14</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.11.717930v1?rss=1">
<title>
<![CDATA[
Quantifying Mg2+ dependence on conformational equilibrium in the two-state 7SK RNA stem-loop 3 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.11.717930v1?rss=1
</link>
<description><![CDATA[
RNA structural heterogeneity is increasingly recognized as essential for RNA function, yet quantitative understanding of intrinsic RNA structural dynamics and how cellular conditions modulate these dynamics remains limited. 7SK RNA is an abundant eukaryotic noncoding RNA that assembles with protein cofactors to form the 7SK ribonucleoprotein (RNP), a dynamic complex that regulates transcription elongation. In particular, the 7SK RNA stem-loop 3 (SL3) domain is a critical hub for protein recruitment that is required for 7SK RNP function. We recently discovered that SL3 undergoes exchange between two equally populated yet structurally distinct conformers, named SL3e and SL3a, providing a model system to understand RNA conformational equilibria. Here, we combined quantitative dimethyl sulfate mutational profiling with sequencing (qDMS-MaPseq), solution NMR spectroscopy, and isothermal titration calorimetry (ITC) experiments to gain quantitative insights into SL3 equilibria under varying ionic conditions. We find that Mg2+ shifts the SL3 conformational equilibrium from 52%:48% to 67%:33% populations, with ITC experiments showing ~2-fold higher affinity for the SL3e conformer, providing the thermodynamic basis for this population shift. NMR 1H-1H NOESY experiments show that Mg2+ stabilizes an A-form helical geometry in the distal end of the SL3e conformer that contains multiple noncanonical base pairs. Validating our combined approach, NMR and DMS-MaPseq Mg2+-induced perturbation data are highly correlated for nucleobase moieties at the Watson-Crick face (R2 = 0.87). From this work, we identify a characteristic DMS reactivity signature for A{middle dot}C wobble base pairs from DMS-MaPseq MgCl2 titration experiments, expanding the utility of chemical probing for detecting noncanonical base pairs. Our findings demonstrate how modest differences in cation affinity between conformational states can modulate RNA population ensembles. More broadly, this work establishes a generalizable thermodynamic framework to quantitatively dissect ion-dependent conformational equilibria in structurally heterogeneous RNAs and advances structural understanding of the essential SL3 regulatory element in the 7SK RNP.
]]></description>
<dc:creator><![CDATA[ Owusu Ansah, S., Camara, M. B., Eichhorn, C. D. ]]></dc:creator>
<dc:date>2026-04-14</dc:date>
<dc:identifier>doi:10.64898/2026.04.11.717930</dc:identifier>
<dc:title><![CDATA[Quantifying Mg2+ dependence on conformational equilibrium in the two-state 7SK RNA stem-loop 3]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-14</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.11.717946v1?rss=1">
<title>
<![CDATA[
Mechanical interaction enables a collective mode of protocell proliferation 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.11.717946v1?rss=1
</link>
<description><![CDATA[
The proliferation of primitive life-forms (known as protocells) without sophisticated cell-division molecular machineries has been an intriguing question in evolutionary biology, synthetic biology, and living matter physics. While various modes of protocell proliferation at the individual level have been proposed, the growth dynamics of protocell colonies (i.e., protocolonies) received less attention. Here we chose to study this question in protocolonies consisting of densely packed protocells derived from wall-deficient L-form bacteria. We discovered that protocolonies proliferated robustly under spatial confinement, while isolated protocells failed to divide and eventually experienced membrane rupture due to imbalance of surface and volume growth. Combining results from quantitative imaging and computational modeling, we attributed this unexpected finding to mechanical shearing between densely packed protocells driven by their growth activities; such mechanical shearing enhances cell deformation, thereby enabling cell division and sustaining population growth in a protocolony. Our study reveals a unique role of self-generated mechanical stresses in the lifestyle of primitive life-forms. The findings may help to understand and control the collective growth dynamics of synthetic protocells or active droplets.
]]></description>
<dc:creator><![CDATA[ Wu, Y., Li, Y. ]]></dc:creator>
<dc:date>2026-04-14</dc:date>
<dc:identifier>doi:10.64898/2026.04.11.717946</dc:identifier>
<dc:title><![CDATA[Mechanical interaction enables a collective mode of protocell proliferation]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-14</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.11.717926v1?rss=1">
<title>
<![CDATA[
Engineered Channel Asymmetry Extends Hydrogen-Bonding Networks for Proton Conduction 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.11.717926v1?rss=1
</link>
<description><![CDATA[
The precise and selective transport of protons across cellular membranes relies on the dynamic formation and dissipation of hydrogen-bonding networks involving water molecules, protein sidechains, and backbone carbonyls. As in aqueous solution, protons are conducted over long distances along chains of hydrogen-bonded water molecules within narrow protein pores. To engineer proton-conductive pathways, therefore, we must explicitly account for the dynamic behavior of these networks. In previous work, we showed that incorporation of polar Gln residues into hydrophobic pores drives formation of transient, single-file water wires that enable proton-selective transport. Here, we sought to enhance conduction by introducing targeted Ile-to-Ser substitutions to extend connectivity across the pore. We find that the position of Ser relative to Gln modulates sidechain dynamics and, in turn, channel hydration. Although increased polarity reduces hydrophobic length and enhances hydration, these effects alone do not explain the observed conduction rates. Instead, asymmetry in the arrangement and dynamics of polar sidechains emerges as a key determinant of proton conductivity. Together, these results demonstrate that proton conduction is governed not only by pore polarity and hydration, but also by the dynamic and asymmetric organization of hydrogen-bonding networks. This work establishes design principles for engineering proton-selective channels and reveals how asymmetry enables efficient proton transport across biological membranes.
]]></description>
<dc:creator><![CDATA[ Jacob, N. P., Silverman, V. T., Prida Ajo, G., Kratochvil, H. T. ]]></dc:creator>
<dc:date>2026-04-14</dc:date>
<dc:identifier>doi:10.64898/2026.04.11.717926</dc:identifier>
<dc:title><![CDATA[Engineered Channel Asymmetry Extends Hydrogen-Bonding Networks for Proton Conduction]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-14</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.10.717862v1?rss=1">
<title>
<![CDATA[
Single-particle light scattering reveals the dynamic heterogeneity of biomolecular condensates 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.10.717862v1?rss=1
</link>
<description><![CDATA[
Biomolecular condensates are membraneless cellular compartments that form through weak, multivalent interactions. These condensates are typically submicrometer structures whose biological functions depend sensitively on physical properties such as size, composition, internal concentration and interfacial properties. Despite recent progress in characterizing these systems, high-throughput, label-free, and quantitative measurements of these parameters at the single-condensate level and at submicron length scales are lacking. Here, we employ an off-axis holographic imaging technique to simultaneously quantify the size, protein concentration, interfacial structure, and hydrodynamic drag of submicrometer condensates formed by the N-terminal domain of Ddx4 and synthetic polymers, with a throughput of hundreds of condensates per minute. We find that Ddx4-LCD forms two morphologically distinct classes of condensates: one class with a sharp interface and another with a broad interface. The relative abundance of these classes changes in response to ionic strength and as a function of time, revealing a dynamic heterogeneity even in single component condensates. By characterizing condensates formed by zwitterionic polymers, we show that the presence of two populations can be reproduced in systems with two types of stickers, but not in systems with one sticker type. Our results reveal that, while obscured in ensemble-based or monoparametric measurements, chemically identical systems at the molecular level can encode multiple coexisting condensate states at the mesoscale, arising from heterogeneity in interaction motifs. These findings identify interaction heterogeneity as a key factor governing interfacial organization in multivalent condensates.
]]></description>
<dc:creator><![CDATA[ Rodriguez, B. G., Makasewicz, K., Tesei, G., Arosio, P., Volpe, G., Midtvedt, D. S. ]]></dc:creator>
<dc:date>2026-04-14</dc:date>
<dc:identifier>doi:10.64898/2026.04.10.717862</dc:identifier>
<dc:title><![CDATA[Single-particle light scattering reveals the dynamic heterogeneity of biomolecular condensates]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-14</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.10.717621v1?rss=1">
<title>
<![CDATA[
Third Harmonic Generation Microscopy Reveals Structure and Mucus Dynamics in Human Airway Epithelium Models 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.10.717621v1?rss=1
</link>
<description><![CDATA[
Airway epithelium plays a major role as the primary interface between human body and the external environment, acting both as a physical and functional barrier. In vitro airway models that reproduce the epithelium architecture are therefore a valuable tool for studying infection, inflammation, and transport processes. In this work, we present a label-free, non-invasive method to visualize and measure mucociliary transport in air-liquid human models using third-harmonic generation (THG) microscopy with an optical parametric amplifier laser source at 1300 nm. By exploiting the intrinsic nonlinear contrast at optical heterogeneities, THG provides high resolution images of both epithelial structures and of the overlying mucus layer without the need for fluorescence staining or sample processing. Time-lapse THG imaging reveals depth-dependent transport dynamics within the mucus, offering new insights into mucociliary transport mechanism. Our approach offers a physiologically relevant way to assess mucociliary function in vitro and could support studies on respiratory diseases, drug delivery and efficacy, and epithelial remodeling.
]]></description>
<dc:creator><![CDATA[ Kim, D., Latshaw, A., Balkota, M., Wiggert, M., Alata, M., Huang, S., Constant, S., Maechler, P., Vanden Berghe, P., Bonacina, L. ]]></dc:creator>
<dc:date>2026-04-14</dc:date>
<dc:identifier>doi:10.64898/2026.04.10.717621</dc:identifier>
<dc:title><![CDATA[Third Harmonic Generation Microscopy Reveals Structure and Mucus Dynamics in Human Airway Epithelium Models]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-14</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.10.717851v1?rss=1">
<title>
<![CDATA[
How Generative Models Approach Molecular Conformational Sampling 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.10.717851v1?rss=1
</link>
<description><![CDATA[
Characterising equilibrium conformational ensembles with deep generative models requires assessing not only whether a model reproduces the target distribution, but also the mechanism of how it arrives here. Here we examine two distinct routes to generative conformational sampling---stochastic relaxation and deterministic transport---through a study of denoising diffusion probabilistic models (DDPM) and rectified-flow (RF) models across molecular systems of increasing complexity. Using systems of increasing complexity, including a multimodal two-dimensional potential, the folded mini-protein Trp-cage, and a high-dimensional dihedral subspace of the intrinsically disordered protein -synuclein, we show that the key distinction between these paradigms lies not only in endpoint fidelity but in how distributional error is resolved during sampling. Diffusion models converge via pronounced late-stage stochastic relaxation and exhibits robust recovery of configurational breadth across neural architectures. Rectified flow approaches the target more gradually through deterministic transport and therefore depends much more strongly on architectural expressivity, particularly in heterogeneous high-dimensional landscapes. Analyses of entropy and moment evolution further show that diffusion more reliably restores both ensemble location and fluctuation structure, whereas RF requires Transformer-level feature mixing to represent the transport geometry accurately. These results establish convergence mechanism as a key design principle for generative sampling.
]]></description>
<dc:creator><![CDATA[ B E, N., Mondal, J. ]]></dc:creator>
<dc:date>2026-04-14</dc:date>
<dc:identifier>doi:10.64898/2026.04.10.717851</dc:identifier>
<dc:title><![CDATA[How Generative Models Approach Molecular Conformational Sampling]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-14</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.10.717806v1?rss=1">
<title>
<![CDATA[
Contemporaneity of the past in stochastic intergenerational homeostasis 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.10.717806v1?rss=1
</link>
<description><![CDATA[
What recurring patterns of behaviors are hidden in the stochastic intergenerational dynamics of individual bacterial cells in different environments? Embracing the inherently stochastic nature of the homeostasis process, first we reconceptualize homeostasis as representing a "standing pattern of variation in trajectory space" of a naturally occurring adaptive complex system (rather than the simple "set-point" of a self-regulating apparatus), then delineate two mechanistically distinct potential routes to achieving homeostasis (either elastic, reflexive, memory-free adaptation or plastic, reflective, memoryful adaptation) and show that both schemes are simultaneously utilized during multigenerational stochastic growth and division of an individual cell. From experimental data we identify an intergenerational scaling law which directly yields the exact stochastic map governing stochastic intergenerational cell size homeostasis of individual bacterial cells. Its broad applicability across bacterial species, growth conditions, and microenvironments suggests that the organizational motif representing the nature of coupling of growth to division is effectively the same in all of these scenarios, despite apparent differences in actualization through molecular circuitry. The precise parameters characterizing the intergenerational scaling law vary from condition to condition and provide early hints of two tradeoffs: precision-speed and precision-energy.
]]></description>
<dc:creator><![CDATA[ Joshi, K., Ziegler, K. F., Wright, C. S., Spiers, E., Crosser, J. T., Roy, S., Gandhi, R., Stonecipher, J., Eschker, S., Biswas, R. R., Iyer-Biswas, S. ]]></dc:creator>
<dc:date>2026-04-14</dc:date>
<dc:identifier>doi:10.64898/2026.04.10.717806</dc:identifier>
<dc:title><![CDATA[Contemporaneity of the past in stochastic intergenerational homeostasis]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-14</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.10.717811v1?rss=1">
<title>
<![CDATA[
Dynamic myosin 10 coupling to DCC and β1 integrin is mediated by intrinsically disordered regions during filopodial transport and patterning 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.10.717811v1?rss=1
</link>
<description><![CDATA[
Intrinsically disordered regions (IDRs) are key mediators of protein-protein interactions. IDRs are important components of Myosin 10 (Myo10) and cargo complexes that influence neuronal development and cell growth, yet how IDRs dictate Myo10's cargo affinity and selectivity is not fully understood. Here, we investigate how the actin motor protein Myo10 engages two distinct cargo receptors, DCC and {beta}1 integrin, in cellular protrusions known as filopodia. Using hydrogen-deuterium exchange mass spectrometry (HDX-MS), cross-linking mass spectrometry (XL-MS), live-cell imaging, and super-resolution microscopy, we show that Myo10 decodes IDR elements through two complementary mechanisms: disorder-to-order transitions and "fuzzy" binding. The cytoplasmic portion of DCC binds Myo10 via a weakly helical P3 motif that acts as a preformed recognition element, while additional disordered motifs contribute to affinity through dynamic, weak interactions. In contrast, the {beta}1 integrin tail interacts with Myo10 through short NPxY motifs that remain disordered. Both cargos engage a common Myo10 surface but also contact distinct sites. Super-resolution DNA-PAINT imaging reveals distinct patterning of cargo with Myo10 along and around filopodia. Concentration measurements show that DCC is primarily bound while {beta}1 integrin exhibits a broader range of occupancy along the filopodial shaft. Multiple additive weak contacts and a shared binding site implies that DCC can out-compete integrin for Myo10 binding, which causes redistribution of active {beta}1 integrin from the filopodial tip to the shaft. Our findings illustrate a tunable, multivalent binding strategy that allows Myo10 to selectively coordinate diverse signaling cargos, demonstrating how regulated disorder within IDRs is one mechanism underlying cargo binding and cellular signaling.
]]></description>
<dc:creator><![CDATA[ Shangguan, J., Reinhardt, S., Weng, S. H. S., Jungmann, R., Sosnick, T. R., Rock, R. S. ]]></dc:creator>
<dc:date>2026-04-14</dc:date>
<dc:identifier>doi:10.64898/2026.04.10.717811</dc:identifier>
<dc:title><![CDATA[Dynamic myosin 10 coupling to DCC and β1 integrin is mediated by intrinsically disordered regions during filopodial transport and patterning]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-14</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.10.717705v1?rss=1">
<title>
<![CDATA[
Tau-Mediated Cytoskeletal Stabilization Modulates Cell Mechanics and Vulnerability to Mechanical Strain 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.10.717705v1?rss=1
</link>
<description><![CDATA[
Cells experience mechanical loading across a broad range of loading rates, from low strain rates that are generated during morphogenesis and tissue remodelling, to high and injurious strain rates that are sustained during ventilation induced lung injury, blast-induced injury, and impact-induced traumatic brain injury. Cell survival under high strain rate loading conditions depends on the ability of the cytoskeleton and plasma membrane to sustain mechanical load without permanent damage. The activity of different cytoskeletal and membrane regulatory proteins could therefore modulate cell susceptibility to injury, but the underlying mechanisms of injury at high strain rate are poorly understood. Tau is a microtubule associated protein best known for its role in stabilizing microtubules in neurons and as a marker of neurodegenerative disease. Here, we investigated how Tau expression, phosphorylation, and microtubule binding modulates cell viscoelastic behaviour and membrane integrity during high strain-rate uniaxial stretch. We show that Tau expression and dephosphorylation stabilize microtubules and causes increases in cell stiffness, suppresses cytoskeletal fluidity, and heightens susceptibility to stretch-induced membrane poration. Interestingly, we also find that these effects cannot be explained by microtubule stabilization by Tau alone. Actin architecture acts as a key determinant of injury vulnerability at high strain rate, highlighting the importance of cytoskeletal fluidity and microtubule actin crosstalk for rapid force dissipation.
]]></description>
<dc:creator><![CDATA[ Kang, G., Aljapur, V., Petel, O. E., Harris, A. R. ]]></dc:creator>
<dc:date>2026-04-14</dc:date>
<dc:identifier>doi:10.64898/2026.04.10.717705</dc:identifier>
<dc:title><![CDATA[Tau-Mediated Cytoskeletal Stabilization Modulates Cell Mechanics and Vulnerability to Mechanical Strain]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-14</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.10.717625v1?rss=1">
<title>
<![CDATA[
Mechanical properties of DNA double-crossover motifs 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.10.717625v1?rss=1
</link>
<description><![CDATA[
DNA double-crossover (DX) molecules, comprising two Holliday junctions connected by two duplex arms, are fundamental building blocks of DNA nanostructures, but their mechanical properties remain poorly understood. Here we investigate the elasticity of isolated antiparallel DX motifs with 18 to 22 base pairs between the crossovers. Using mechanical models parameterized by extensive all-atom molecular dynamics simulations, we demonstrate that the bending rigidity of the duplexes within a DX motif is highly anisotropic, and that this anisotropy results from long-range elastic couplings involving all the duplex base pairs between the crossovers. The duplex stretch modulus decreases due to localized defects, while the twist stiffness is close to that of an isolated duplex. The DX core as a whole follows an analytical beam theory in bending but not in torsion. Our results extend beyond local elastic models of DNA nanostructures and pave the way for probing peculiar mechanical properties of other key motifs for DNA and RNA nanotechnology.
]]></description>
<dc:creator><![CDATA[ Matouskova, E., Cuker, M., Lankas, F. ]]></dc:creator>
<dc:date>2026-04-14</dc:date>
<dc:identifier>doi:10.64898/2026.04.10.717625</dc:identifier>
<dc:title><![CDATA[Mechanical properties of DNA double-crossover motifs]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-14</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.10.717728v1?rss=1">
<title>
<![CDATA[
Polymorphic structures of rapidly twisting 40-residue amyloid-β fibrils 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.10.717728v1?rss=1
</link>
<description><![CDATA[
Fibrils formed by 40- and 42-residue amyloid-{beta} peptides (A{beta}40 and A{beta}42) are polymorphic, containing molecular structures that vary with growth conditions in ways that are not fully understood. Here we use cryogenic electron microscopy to characterize the structure of rapidly twisting A{beta}40 fibrils, for which the distance between apparent width minima in electron microscope images ("cross-over distances") is approximately 25 nm. From samples grown under a single set of growth conditions, we obtain high-resolution structures for three different rapidly twisting polymorphs. Although their cross-over distances are similar, the three rapidly twisting polymorphs differ in twist handedness, symmetry, molecular conformations, and intermolecular contacts. Two of the rapidly twisting polymorphs resemble slowly twisting A{beta}40 polymorphs that have been described previously, including polymorphs extracted from brain tissue of Alzheimer's disease patients or created by seeded growth from amyloid in brain tissue, but with shorter conformationally ordered segments and other specific conformational differences. These results contribute to our understanding of amyloid polymorphism, connections between morphology and molecular structure, and relationships between brain-derived and in vitro-grown fibrils.
]]></description>
<dc:creator><![CDATA[ Larimi, M. G., Thurber, K. R., Tycko, R. ]]></dc:creator>
<dc:date>2026-04-14</dc:date>
<dc:identifier>doi:10.64898/2026.04.10.717728</dc:identifier>
<dc:title><![CDATA[Polymorphic structures of rapidly twisting 40-residue amyloid-β fibrils]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-14</prism:publicationDate>
<prism:section></prism:section>
</item>
<item rdf:about="https://www.biorxiv.org/content/10.64898/2026.04.10.717701v1?rss=1">
<title>
<![CDATA[
The influence of tension-compression switches on brain anisotropic modelling 
]]>
</title>
<link>
https://www.biorxiv.org/content/10.64898/2026.04.10.717701v1?rss=1
</link>
<description><![CDATA[
Finite element (FE) head models are valuable tools for investigating brain injury mechanics, with their reliability critically dependent on accurate material modelling. White matter (WM) is often considered mechanically anisotropic due to its aligned axonal fiber architecture and is commonly represented using fiber-reinforced hyperelastic formulations such as the Gasser-Ogden-Holzapfel (GOH) model. A fundamental assumption of the GOH model is that fibers contribute only in tension and not in compression, requiring the use of tension-compression switches. However, inconsistencies were noted in the formulation of tension-compression switches with the influence on computational biomechanics unknown. To address this knowledge gap, three commonly used switching schemes - differing in both the switching parameter and the treatment of compressed fibers - were theoretically elaborated and numerical implementation within the GOH framework to simulate the mechanical anisotropy of WM in impact simulations. Results from the case-based and group-level analyses demonstrated that both the switching parameter and the treatment of compressed fibers affected WM deformation. Significant cross-scheme strain differences were noted in the first principal strain at the element level and fiber strain at the fiber level. These findings highlighted the mechanical role of tension-compression switch in the GOH-based brain modelling and advocated the adoption of fiber stretch itself as the switching parameter to discriminate the tensile and compressive fibers. The current study provides important guidance for the anisotropic constitutive models in brain tissue and calls for direct verification of the tension-compression switch hypothesis in axonal fibers.
]]></description>
<dc:creator><![CDATA[ Li, C., Zhou, Z. ]]></dc:creator>
<dc:date>2026-04-14</dc:date>
<dc:identifier>doi:10.64898/2026.04.10.717701</dc:identifier>
<dc:title><![CDATA[The influence of tension-compression switches on brain anisotropic modelling]]></dc:title>
<dc:publisher>Cold Spring Harbor Laboratory</dc:publisher>
<prism:publicationDate>2026-04-14</prism:publicationDate>
<prism:section></prism:section>
</item>
</rdf:RDF>
