Biophysical Journal

Recent genetic and bioinformatic studies have led to the discovery that many bacterial species encode the genes required to produce sphingolipids. Shotgun lipidomic studies have identified numerous sphingolipid species with novel structures that do not exist in eukaryotic organisms. The impacts of these lipids on the biophysical properties of bacterial membranes have not yet been determined. In this study, we purify a novel anionic bacterial sphingolipid, ceramide phosphoglycerate (CPG), and investigate its effect on membrane zeta potential and bending stiffness. CPG and its precursor, ceramide 1-phosphate (C1P), are shown to increase the magnitude of the membrane zeta potential. These sphingolipids also increase the stiffness of these membranes, with CPG increasing rigidity more than C1P or ceramide. This work provides experimental and computational methods of lipid isolation and characterization that may be broadly applicable to a variety of uncharacterized bacterial sphingolipids. SIGNIFICANCEThe diversity of bacterial sphingolipids far exceeds those found in eukaryotes. However, the function and biophysical properties of these lipids are unknown. Characterization of these lipids is a challenge as they are not commercially available. In this study, we developed experimental methods to purify the anionic sphingolipid ceramide phosphoglycerate and incorporate it into liposomes for analysis. Furthermore, we built computational tools to determine the bending stiffness of sphingolipid-containing vesicles from thermal fluctuation data.

In muscle cells, desmin intermediate filaments form a cytoskeletal network that maintains the structural integrity and mechanical coupling of myofibrils. Dominant missense mutations in desmin cause myopathies characterized by intracellular protein aggregation. To explore the process of aggregate formation, we investigate the assembly kinetics of wild-type desmin and four disease-associated variants (N342D, L345P, R350P, and R406W) using dual-wavelength stopped-flow spectroscopy, complemented by atomic force microscopy and molecular dynamics simulations. At low ionic strength, all proteins form uniform tetramers. Increasing the ionic strength initiates assembly byrapid lateral association of tetramers into unit-length filaments (ULFs), followed by longitudinal elongation and radial filament compaction. R406W forms ULFs with wild-type-like kinetics, whereas N342D, L345P, and R350P exhibit delayed lateral assembly. After short filaments have formed, all four mutants diverge from productive filament maturation, but through distinct pathways. Quantitative analysis of atomic force microscopy images together with kinetic modelling of the spectroscopic data shows that wild-type filaments elongate continuously, whereas R406W filaments progressively associate into fibrillar clusters and cease elongating. By contrast, N342D, L345P, and R350P rapidly collapse into globular complexes that subsequently coalesce into larger aggregates. Molecular dynamics simulations indicate that the mutations differentially destabilize coil 2, which leads to local structural perturbations and mutation-specific assembly defects. Together, these findings identify early filament maturation - when elongating ULF-derived filaments would normally undergo radial compaction to form stable, mature filaments - as a critical time point in desmin assembly. At this stage, pathogenic mutations redirect the internal reorganization of the filament from productive stabilization toward mutation-specific structural collapse and aggregation. SignificanceDominant mutations in the intermediate filament protein desmin cause myofibrillar myopathies characterized by protein aggregation and progressive muscle degeneration. Using in vitro filament-assembly experiments, we identify intrinsic assembly defects of disease-associated desmin mutants. Mutant proteins initially enter the normal assembly pathway, albeit with delayed kinetics. They subsequently fail at an early maturation step in which short filaments would normally reorganize to sustain productive elongation. Instead, mutant proteins form morphologically distinct aggregates. Similar structural abnormalities occur when mutant proteins co-assemble with wild-type desmin. Our findings identify the radial compaction phase during early longitudinal assembly as a critical checkpoint that determines whether desmin assembly yields functional intermediate filaments or is redirected into pathogenic aggregation pathways.

There is a vast literature on the voltage gating of ion channels, with a fairly large fraction concerned with potassium channels, especially of the KV1 family, including Shaker. Experimental evidence derived from protein structure has been interpreted to give gating mechanisms that largely disregard water. We propose that the K+ ion, in order to pass through the gating region and enter the cavity pore, must be largely dehydrated. Competitive interactions of each single hydration shell water at the gate, with counterions, protein, or other water molecules, can remove one water at a time. There are several such interactions for the ion hydration shell; for the ion to pass through the gating region, there must be enough such interactions to leave the ion with at most two hydrating water molecules, in which case the gate is open. Protein conformational changes are secondary, small, and mostly unimportant. The hypothesis has a second part: protons, previously shown to be candidate carriers of the gating current (Kariev and Green, JPC B, 2019, Membranes, 2022, 2024) are capable of reaching the gate; adding four protons to the gate prevents dehydration, leaving the ion with at least three hydrating water molecules, enough to block passage. Quantum calculations presented here support the dehydration part of the hypothesis; they also mostly support the second part, concerning the protons, but further work will be required to fully confirm this. The hypothesis explains the experimental finding that the P475D mutant is essentially constitutively open, while the P475S mutant, with a wider gate opening, is closed at all relevant potentials; the computations presented here show the mechanism for this in detail, further confirming the first part of the hypothesis, and largely but not completely confirming the second part, concerning protons, while showing where further work is needed. This mechanism can also qualitatively account for flicker noise and fluctuations, and their consequences.

Lipid droplets (LDs) are cellular organelles responsible for lipid storage and metabolism. The mechanism of biogenesis of LDs involves phase separation of neutral lipids from the surrounding phospholipids, which generates oil lenses embedded in lipid bilayers, also known as nascent LDs. As nascent LDs grow, at some point they bud out of the bilayer, forming nearly spherical droplets. Nascent LDs have different propensity to bud, and it has been proposed that their shape provides information on such propensity; however, LD shape is difficult to determine experimentally. Here we studied the shape of lipid droplets using MD simulations at the coarse-grained level, and compared it to the predictions by an established theory. Our general system setup features an oil lens embedded into a flat, periodic bilayer. We found that the shape of simulated nascent LDs resembles a spherical cap (i.e., it has constant curvature over most of the surface), in excellent agreement with the theory, already for very small droplet sizes. The aspect ratio (height/radius) of nascent LDs increases with increasing LD volume, increasing membrane softness, and increasing surface tension between oil and water, also in agreement with theoretical predictions; however, it remains lower than 1 (i.e., the ratio for a sphere) for LDs of up to 40 nm in diameter. Fitting the simulated LD shapes with a theoretical shape equation suggests that a non-zero surface tension is present in both the monolayer and in the bilayer region. The existence of a relatively high surface tension in the bilayer region is confirmed by local stress calculations, and indicates that the periodic system setup does not reproduce the properties of nascent LDs in the endoplasmic reticulum, where the bilayer tension is two orders of magnitude lower. However, the simulations provide a microscopic view into the properties of droplet embedded vesicles.

Weak magnetic fields affect many biological processes across the tree of life, though the precise molecular sensors and pathways involved in such magnetoresponses remain mostly uncharacterized. Fluorescence is a useful tool for investigating magnetic field effects in flavoproteins, as their chromophores fluorescence intensity can be shown to depend on the spin states of electronic radical pairs. Here, we describe a four-state ordinary differential equation model to understand what parameter sets result in fluorescence contrast between spin states in photocycles with singlet and triplet radical pairs. We conclude that only certain sets of parameters result in the fluorescence intensity being a good proxy measurement for singlet yield. In particular, we observe that the illumination intensity required to obtain fluorescence contrast depends on the rate of the slow spin-independent radical termination reactions that recover ground-state oxidized fluorophores. Moreover, to observe a magnetic field effect in fluorescence intensity when an external magnetic field modulates the singlet yield, the illumination intensity must be strong enough such that photoexcitation is not the rate-limiting step. This understanding suggests that flavoproteins that do not exhibit magnetic field effects in their fluorescence emission under certain experimental setups may still be sensitive to weak magnetic fields in terms of function, as magnetosensitivity in fluorescence depends strongly on illumination conditions.

Dynamic conformational changes in intracellular domains fundamentally affect the function and pharmacology of many membrane proteins. For example, sodium influx through the cardiac voltage-gated sodium channel (NaV1.5) is rapidly terminated through conformational changes that result in pore closure, a transition known as inactivation. Inactivation involves NaV1.5 intracellular regions, particularly the DIII-DIV linker containing the IFM particle (Isoleucine-Phenylalanine-Methionine) and its dysfunction is a major cause of cardiac arrythmias. However, the conformational changes involved in inactivation and their modulation by auxiliary proteins and clinically used drugs remain incompletely characterized, partly because live-cell, site-specific labeling of intracellular regions with small fluorescent dyes remains challenging. Here, we combine live-cell protein semi-synthesis with voltage-clamp fluorometry (VCF), to track intracellular conformational dynamics of the cardiac sodium channel NaV1.5 and monitor their voltage dependence and kinetics in real time. We identify intracellular conformational changes involved in both fast and steady-state inactivation of NaV1.5 and show that both lidocaine and auxiliary proteins affect the kinetics of conformational changes of the DIII-DIV linker. Our work establishes the combination of protein semi-synthesis and voltage-clamp fluorometry as a powerful approach to dissect intracellular conformational changes in membrane proteins.

Membrane fusion is an essential process in cells that requires a balance of lipid composition to establish biophysical properties conducive to topology changes. During fusion, lipids of opposing membranes must invert and overcome energy barriers associated with forming highly curved stalk and pore intermediates. While theoretical work has modelled the effect of lipid intrinsic curvature on stalk formation, quantifying the relationship experimentally has proven to be a challenge due to the inability to vary lipid curvature without concomitantly changing other properties that affect fusion. Here we address this hurdle by using hydrostatic pressure to modulate lipid intrinsic curvature independently of chemical composition. Using high-pressure stopped-flow fluorimetry, we measured rates of calcium-mediated lipid mixing between populations of vesicles, a process that is strongly inhibited by pressure. We correlated mean lipid intrinsic curvature across pressure with lipid mixing rates by incorporating complementary small-angle x-ray scattering measurements for each individual lipid component. This analysis showed that lipid mixing rates, a proxy for hemifusion, across compositional and pressure regimes are determined by changes in lipid spontaneous curvature. Consistent with previous theoretical models, we find a linear relation between lipid intrinsic curvature and the hemifusion stalk formation energy, offering direct experimental support for the stalk hypothesis. Significance statementMembrane fusion proceeds through a hemifusion stalk intermediate whose formation energy depends on lipid intrinsic curvature, a central prediction of the stalk hypothesis that has lacked direct experimental support. Previous tests relied on changes in lipid composition that affect multiple membrane properties, confounding the contribution of curvature alone. Here we use hydrostatic pressure to tune lipid curvature independently of chemical composition and calibrate its effects with high-pressure SAXS. Hemifusion rates across three lipid compositions and four pressures collapse into a single exponential dependence on mean spontaneous curvature, yielding a linear relation between curvature and energy consistent with continuum elastic theory. This work quantifies how lipid composition tunes fusion kinetics, suggesting that small changes in lipid curvature may strongly affect fusogenicity.

Staphyloxanthin (STX) is a carotenoid synthesized by the human pathogen Staphylococcus aureus. The golden color of this bacterium is due to this carotenoid. STX protects Staphylococcus aureus from oxidative stress by scavenging free radical species. Furthermore, STX has been shown to mechanically strengthen the Staphylococcus aureus membrane and to form microdomains that recruit antibiotic-resistance factors. Thus, inhibition of STX is a promising strategy for intervening against multidrug-resistant strains of this pathogen. However, the molecular mechanisms by which STX regulates the membrane structure and function of Staphylococcus aureus remain unclear. More specifically, the localization of STX within phosphatidylglycerol (PG) bilayers, the primary phospholipid of this bacteriums membrane, and how this localization drives macroscopic biophysical changes remain unresolved questions. Here, we addressed this issue by integrating molecular dynamics (MD) simulations, X-ray scattering experiments, and fluorescence spectroscopy. We developed an atomistic model of STX, which was validated against X-ray scattering data and which is suitable for all-atom MD simulations. We demonstrate that STX significantly increases lipid packing and acyl chain order of STX-PG bilayer mixtures. In addition, STX self-assembles into clusters, where the long and rigid conjugated triterpenoid chain interdigitates across both leaflets, modifying locally the density of the surrounding PG molecules. These findings provide a molecular explanation to the reduced headgroup spacing and core dynamics observed in fluorescence experiments and are consistent with the formation of structurally-distinct STX-enriched microdomains. Notably, STX reduces the gel-to-liquid crystalline phase transition temperature, indicating a general stabilizing effect for the fluid phase of PG lipids of varying length. Overall, our findings provide molecular insights into how STX enhances membrane mechanical integrity. It will be highly interesting to establish how the membrane remodeling effects observed here connect with STXs dual roles, acting as an antioxidant and preventing pore formation and other mechanical perturbations induced by antimicrobial molecules.

Protein oligomerization equilibria are central to many biological processes and are often highly sensitive to environmental conditions such as ionic strength, pH, and ligand binding. Quantitative characterization of these equilibria remains experimentally challenging because stable protein complexes frequently dissociate only at concentrations that are difficult to access with conventional biophysical methods. Fluorescence correlation spectroscopy (FCS) is uniquely suited to this problem, as it provides direct access to diffusion coefficients of fluorescently labeled proteins at nanomolar concentrations. However, the quantitative interpretation of FCS data from oligomeric systems requires a rigorous mathematical framework and careful experimental practice that have not previously been described in sufficient detail to guide implementation. Here, we provide a comprehensive description of the experimental workflow and analytical framework for determining dissociation equilibrium constants by FCS, covering instrument calibration, sample preparation, data quality control, after-pulse correction, and nonlinear least-squares fitting. We discuss common sources of error and provide practical guidance on critical experimental considerations including surface passivation, buffer preparation, equilibration time, and the role of labeling efficiency. Using the homotrimeric sliding clamp PCNA as a model system, we demonstrate the complete workflow under a range of KCl concentrations and show that moderate ionic strength stabilizes the PCNA trimer while very high salt partially destabilizes the complex. The approach is general and applicable to any reversible protein self-association reaction accessible by fluorescence detection at low protein concentrations.

Reaction diffusion (RD) systems play a fundamental role in numerous biochemical and biophysical processes. Here, we present a novel analytical framework for solving RD equations by applying the Wentzel Kramers Brillouin Jeffreys (WKBJ) formalism to Ca nanodomains generated by individual membrane channels, a widely used paradigm for intracellular Ca signaling. Previous models have primarily focused on stationary Ca nanodomains while neglecting diffusion and saturation of intracellular Ca buffers and sensors. In contrast, we derive analytical solutions without these simplifying assumptions. Our analysis demonstrates that sustained Ca influx generates continuously expanding distributions of free Ca, whereas Ca bound buffers and sensors propagate as traveling waves. These predictions are supported experimentally by measurements of one-dimensional fluorescence profiles produced by single-channel activity and two-dimensional profiles generated by whole cell Ca currents. The analytical framework developed here readily extends Michaelis Menten type kinetics to reaction diffusion systems and may therefore be broadly applicable to biochemical and biophysical processes in which diffusion cannot be neglected.

Diffusion within the cytoplasm is fundamental to numerous biological processes. Fluorescence recovery after photobleaching (FRAP) is one of the most common method for quantifying molecular diffusivity in living cells using standard laser scanning confocal microscopy (LSCM). However, accurately measuring fast cytoplasmic diffusion (typically >10 m^2/s) is challenging due to rapid recovery kinetics, weak signal-to-noise ratios, post-bleach signal artifacts, and spatial restrictions affecting normalization. While individual challenges have been addressed in specific contexts, a simple and robust framework to quantify cytoplasmic diffusivity remains elusive. Here, we present a FRAP methodology specifically designed to overcome these obstacles. By utilizing the Gaussian function -- the impulse response (ImpRes) of the diffusion equation in an infinite medium -- our approach leverages the full spatiotemporal dataset through a single-equation three-parameter fitting procedure, thus releasing restrictions to small regions of interest and arbitrary initial time-points. The methodology was validated on three datasets of increasing complexity: in silico simulated recovery profiles, in vitro data from FITC-dextran in glycerol solution, and live-cell imaging of free cytoplasmic GFP. Systematic comparison with existing models demonstrates that the ImpRes approach significantly reduces sensitivity to noise and imperfect fluorescence normalization, while remaining robust against short-term biases, such as transient probe photo-activation. Given its robustness under realistic experimental conditions and its ease of implementation, the proposed FRAP methodology provides a reliable tool for quantitative cytoplasmic analysis.

ATP-driven myosin II activity remodels actin networks and drives cytoskeletal matter out of thermal equilibrium, but how ATP concentration controls these dynamics remains difficult to isolate in vivo. Here, we reconstitute minimal actomyosin networks from purified components and combine passive microrheology with mean back relaxation (MBR) analysis to quantify ATP-dependent nonequilibrium fluctuations. Nonequilibrium activity is strongest at intermediate ATP concentrations (0.2-0.5 mM) and decreases at higher ATP. While single-bead van Hove distributions are approximately Gaussian, pooled distributions display apparent tails caused mainly by bead-to-bead heterogeneity rather than frequent active bursts. MBR, however, reveals clear time-irreversible dynamics by distinguishing restoring relaxation from persistent active motion. Comparing activity with network stiffness suggests a trade-off between ATP-dependent stiffening and myosin-driven remodeling. A minimal active Langevin simulation reproduces the observed MBR phenomenology, supporting a picture in which rare myosin-driven cage rearrangements generate detectable nonequilibrium signatures. These results establish MBR as a sensitive probe of active matter behavior in actomyosin networks. Significance StatementCells operate out of equilibrium, yet the specific role of ATP concentration in driving cytoskeletal activity remains difficult to isolate in vivo. By reconstituting minimal actomyosin networks and applying passive microrheology, we directly quantify how ATP levels modulate out-of-equilibrium fluctuations. The application of mean back relaxation (MBR) analysis thereby provides a clear and broadly accessible measure of broken time-reversal symmetry that surpasses conventional analysis methods. Our results reveal an inverse relationship between ATP concentration and network dynamics, arising from different modes of myosin activity and ATP-dependent network stiffening. This work provides a quantitative framework for linking biochemical energy supply to mechanical activity in reconstituted cytoskeletal systems, offering new insights into cellular self-organization and energy-dependent regulation.

Biological membranes contain a diverse set of membrane proteins surrounded by many different lipids, and the lateral organization and function of these molecules are closely intertwined. Here, we use coarse-grained molecular dynamics (MD) simulations to explore how hydrophobic mismatch between the length of transmembrane (TM) proteins and the thickness of the surrounding lipid membrane impacts the spatial distribution of the lipids. We constructed idealized cylindrically symmetric proteins, inspired by the Mattress Model developed in the 1980s, and simulated these model proteins in different lipid compositions. We found that unsaturated lipids were attracted to short TM proteins that thinned the membrane, while fully saturated lipids were attracted to long TM proteins that induced membrane extension. A simple mechanical description of the membrane deformation energy coupled to a lipid mixing model accurately predicted the enrichment/depletion, which was up to 33% in some cases. Our simulations also highlight that lipid sorting behavior is sensitive to protein tilt and protein surface roughness. By teasing out the fundamental physical principles in these simple models, our results provide a foundational understanding of how proteins and lipids form complex and transient assemblies, which we believe will be important for interpreting lipid-protein interactions for a host of membrane proteins that regulate cellular membranes and cell function.

During the influenza viral life cycle, the viral glycoprotein hemagglutinin (HA) mediates binding, entry, and fusion. Densely packed clusters of HA trimers at the plasma membrane are required to produce infectious virions; however, the mechanism of HA clustering is still unknown. We have shown previously that HA co-clusters with and modulates phosphatidylinositol 4,5-bisphosphate (PIP2) in host cell plasma membranes (PM). Here, we further characterize the relationship between HA and PIP2 using molecular dynamics simulations (MD) and fluorescence photoactivation localization microscopy (FPALM) to elucidate a mechanism of HA-PIP2 interaction. We found that the interaction occurs largely between the PIP2 head group and the cytoplasmic tail domain (CTD) of HA. Mutations of the CTD were made to alter charge (HARE, HARREQ), palmitoylation sites (HAMAY), or a combination thereof (HAREMAY, RREQMAY). MD showed that HARREQ and RREQMAY had the strongest effect on HA-PIP2 interactions through a depletion in the radial distribution function of PIP2 around HA at distances [≤]2.5 nm. FPALM revealed that HA cluster density at the PM was significantly reduced by CTD mutations, with the largest reduction occurring in mutants where the CTD charge and acylation were both altered (HAREMAY). HAREMAY clusters were also found to have larger circularities and perimeters, implying a structural change to the clusters. Mutations in the HA transmembrane domain also caused modest changes to the cluster properties of HA and its co-clustering with PIP2. FPALM showed PIP2 co-clustering with HA was also affected by HA mutations with more free PIP2 localized under HAREMAY clusters. A chemical model of simultaneous HA-PIP2 and PH-PIP2 binding enables interpretation of HA-PIP2 interactions and reveals quantitative differences between PIP2 binding by HA CTD mutants. We conclude that the mechanism of HA-PIP2 interaction consists of at least electrostatic and hydrophobic components. Our insights into the mechanism of HA-PIP2 interaction, and the prevalence of putative PIP2-interacting domains in a number of viral spike proteins suggest it may be fruitful to identify methods of disrupting interactions between phosphoinositides and viral proteins.

In the active loop extrusion model, the cohesin protein complex creates chromatin loops in eukaryotic cells. Extrusion maintains topologically associated domains (TADs), which are contiguous segments of chromatin that preferentially colocalize in space and are typically bounded by CTCF proteins that pause cohesin translocation. Here, we model active loop extrusion with hybrid molecular dynamics - Monte Carlo simulations in entangled flexible linear polymer melts. Intra-chain contact probabilities of polymers with active loop extrusion are enhanced compared to their equilibrium, passive counterparts. Extrusion causes the size of chain segments to be much smaller than in passive melts. While the overlap parameter in passive melts without extrusion monotonically increases with segment length, it is nonmonotonic in active melts and on the order of unity within the parameters of this study. Active loop extrusion suppresses contacts between TADs in favor of intra-TAD contacts. Reduction of overlaps between chain segments dilutes entanglements in active melts. Depending on parameters, active extrusion without TADs may induce more compact conformations than with TADs, due in part to fractal loopy globule-like dynamics. This work suggests that active loop extrusion reduces overlaps between TADs, contributing to effective gene regulation by cis-regulatory elements.

The FoF1-ATP synthase drives cellular bioenergetics by translocating protons across the inner mitochondrial membrane. We recently demonstrated that the lipid cardiolipin acts as a 2D antenna, actively funnelling protons into the nanoconfined Fo motor and enforcing severe "dimensional squeezing". This 1D nanoconfinement forces protons into such close proximity that their hydration shells physically overlap, theoretically generating an infinite classical steric gridlock. Yet, empirical measurements show the Fo motor operates at ~90% efficiency and exhibits barrierless, Ohmic conductance, presenting a biophysical paradox. To resolve this contradiction between classical physics and biological reality, we employed a differentiable inverse-physics framework to blindly deduce the proton wires geometry based solely on macroscopic physiological constraints: ohmic linearity and a 1.7 Deuterium Kinetic Isotope Effect. By substituting classical diffusion frameworks with a Many-Body Overdamped Quantum Langevin Equation (QLE), the optimiser successfully converged. It deduced that physiological flux dictates a steric boundary of 0.137 nm (aligning with the effective crystal radius of oxygen) and a structural confinement scale of 0.974 nm. We demonstrate that when these discovered biological parameters are evaluated under classical, independent-particle assumptions, the 1/r12 steric repulsive forces diverge to infinity, causing a simulation collapse. In contrast, the quantum mechanical nature of the QLE allows protons to exist as spatially spread-out clouds rather than fixed point particles. This enables them to traverse tight steric boundaries via a coordinated chain reaction similar to a frictionless nanoscale Newtons cradle. These findings prove that classical, independent-particle models are incompatible with the spatial confinement of respiratory complexes. We conclude that physiological proton transport through the Fo motor mandates a continuous quantum percolation channel, redefining our theoretical understanding of biological energy transduction. Statement of significanceThe FoF1-ATP synthase sustains cellular life by translocating protons across membranes, driven by its membrane-bound Fo motor. Within this motor, protons navigate a 1-2 nm water wire. Under this extreme biological nanoconfinement, classical physics predicts a structural "traffic jam", i.e., protons should gridlock due to the repulsive overlap of their hydration shells. Yet, the motor operates with highly efficient, ohmic conductance. Using a differentiable inverse-physics framework and the Many-Body Quantum Langevin Equation, we prove classical physics cannot resolve this steric gridlock. Instead, we demonstrate that physiological proton transport inherently mandates many-body quantum percolation. Protons navigate extreme nanoconfinement via spatial quantum delocalisation, establishing that biological energy transduction operates as a nanoscale quantum percolation channel.

The assembly and budding of enveloped viruses requires thousands of membrane proteins to collectively remodel host-cell membranes into highly curved virions. In SARS-CoV-2, this process is driven by interactions between viral structural proteins and the endoplasmic reticulum-Golgi intermediate compartment (ERGIC) membrane. The membrane (M) protein, an embedded homodimer and the most abundant viral component, exists in two conformations: a compact ''short'' form and an elongated ''long'' form. Although M is essential for virion assembly, how its conformations contribute to the generation and organization of the membrane curvature required for budding has remained unknown. Here, we used all-atom and Martini coarse-grained molecular dynamics simulations to show that individual M proteins can induce distinct membrane curvatures, depending on their conformation. The long form bends the membrane around its C-terminal, forming a valley-like depression, while the short form predominantly bends the membrane away from the C-terminal producing an anisotropic ridge. The induced curvatures correspond to the bulb and neck regions of a budding virion, respectively. Coarse-grained simulations of M protein pairs further reveal that curvature modulates long-range, membrane-mediated M-M interactions, leading to repulsion between dissimilar conformations. Together, these results suggest that the long and short forms of M naturally segregate to shape the virion's bulb and neck, potentially facilitating genome encapsulation and membrane scission. This mechanism provides a physical basis for coronavirus budding and suggests that conformationally encoded curvature fields may represent a general principle underlying the formation of enveloped viruses.

Acetylcholine receptors (AChRs) expressed at the nerve-muscle synapses are prototypic allosteric receptors that shuttle between a resting Closed (C) and active Open (O) states. ACh binding at the neurotransmitter binding sites (TBS) leads to opening of the gate in the channel pore that regulates ion flow. How agonist binding to the TBS communicates the allosteric signal to the channel gate located [~]50 [A] away is not understood. In the absence of agonists, the wild-type and mutant AChRs, including those causing congenital myasthenia syndrome, show constitutive gating. However, whether allosteric activation pathways in the presence vs absence of agonists are identical, is debatable. Here, by using a combination of kinetic modelling, phi ({phi})- and activation energy ({Delta}{Delta}G[palclick]) estimation for >60 residues from single channel current recordings and molecular dynamics simulations, we show the existence of parallel gating pathways ( major and minor) in the unliganded AChRs and activation pathways are non-identical for the liganded vs unliganded AChRs. Kinetic analysis of the minor gating and correlation between the state residence probabilities vs C-loop conformations suggest, 1. the C-loop capping triggers allosteric communication independent of the presence of an agonist and, 2. the minor gating is a pre-existing allosteric pathway which is preferentially chosen in the presence of agonists. Further, we show the presence of a continuous live-wire like allosteric network in the liganded receptor between the TBS and the gate constituted by residues which lower the activation energy barrier by >-4 kcal/mol. In contrast, in the unliganded AChRs, the major gating seems to initiate from hub residues in the allosteric network. The results presented here provide novel insight into the mechanism of allosteric signal initiation and communication in AChRs.

Budding is a fundamental membrane-remodeling process central to many cellular functions and is exploited by numerous enveloped viruses to acquire their lipid envelopes. Despite extensive molecular characterization, the physical mechanisms that determine whether budding proceeds to completion or becomes stalled remain unclear. Here, we develop a theoretical model based on the Helfrich elastic formalism to investigate how membrane geometry and boundary conditions regulate the elastic energy of viral budding. We analyze two representative cases: budding from a flat membrane, characteristic of HIV-1 and alphaviruses, and budding from a vesicle, as observed for SARS-CoV-2 in the ER-Golgi intermediate compartment (ERGIC). Our results reveal distinct energetic pathways: vesicle-like geometries exhibit a stronger energetic bias toward closure, whereas flat membranes develop extended low-slope regions in the energy landscape that can hinder completion. Relaxing far-field boundary constraints reduces the energetic cost associated with membrane area conservation and renders the flat-membrane case energetically comparable to the vesicle case, providing a physical explanation for why viruses frequently bud adjacent to one another or within pre-curved membrane regions. Comparison with thin-section TEM images of alphavirus budding shows results consistent with the theoretical membrane profiles. Together, these findings establish how curvature coupling, boundary flexibility, and local membrane geometry cooperate to control the efficiency and completion of membrane budding.

We used simulations of short single stranded DNA (ssDNA) homopolymers, based on the sequence dependent Three Interaction Site (TIS) model, to calculate the persistence length (lp) in polyvalent cations. The TIS model accounts for stacking interactions and electrostatic interactions are treated using the Coulomb potential. We find that lp for dT30 (T is thymine) and dA30 (A is adenine) is quantitatively fit using [Formula] ([Formula] is the bare persistence length,{lambda} is a dimensionless constant, and{kappa} -1 is the inverse Debye length) in the divalent cations Mg2+ and Ca2+. The dependence of lp on{kappa} is surprising because it was derived for long flexible polyelectrolytes in which the charges interact via the Debye-Huckel potential. The [Formula] values are 0.4 nm and 1.1 nm for polyT and polyA, respectively. Strikingly, lp is almost independent of the tetravalent spermine concentration. There is no clear theoretical explanation although simulations suggest that the number of spermine molecules that bind to the ssDNA saturates at a small value. A qualitative picture, based on the restrictions of access to the phosphate groups due to volume exclusion of the anisotropic structure of Spm4+, rationalizes the simulation results. The predicted dependence of lp in spermine awaits experimental test.