Biology subjects

Sodt, A. J.

Publications and source records attributed to Sodt, A. J..

16 recordsLinked to original sources

bioRxiv2026

So similar, yet so different: α-synuclein recognition of the isoform-specific VDAC protein-lipid interface

In mammals, VDAC exists as three isoforms--VDAC1, VDAC2, and VDAC3--each characterized by a distinct tissue-dependent distribution and physiologic role. Isoform-specific knockout studies in cells and mice demonstrate distinct physiological roles for each VDAC isoform. The isoforms share about 70% sequence homology and a conserved {beta}-barrel structure and, when reconstituted into planar lipid membranes, form similar highly conductive, anion-selective, voltage-gated channels. A natural question, then, is how relatively minor differences in isoform sequences lead to striking differences in their interactions with protein partners and, consequently, in their physiological functions. To address this question, we used a small, intrinsically disordered cytosolic protein -synuclein (Syn) as a sensitive molecular probe. A comparative study with recombinant VDACs reconstituted into planar lipid membranes shows that, depending on the isoform, the Syn-induced blockage exhibits up to 100-fold differences in on-rates and equilibrium constants. The isoforms also display distinct translocation regimes for Syn, as evidenced by altered dependences of the off-rates on the applied voltage. Deletion of cysteine residues has a significant effect on Syn binding. Combined with corresponding data obtained for VDAC2 substates--which show an order of magnitude variation in on-rates while maintaining the conserved equilibrium constants--and the results of molecular dynamics simulations, these findings point to a previously unrecognized step in VDAC inhibition by Syn: an isoform-specific Syn interaction with the VDAC protein-lipid interface. This finding opens a new paradigm for understanding VDAC isoform functions and developing isoform-specific therapeutics.

biophysics↗

bioRxiv2026

Inferring protein-induced spontaneous curvature of lipid bilayers from molecular simulation

Proteins and lipids of a biological cell work together to reshape the membranes in which they reside. Membrane reshaping is necessary for vesicular traffic and maintenance of organelle shape and structure. Curvature is the fundamental mathematical description of the local shape of a surface. Through the well-established Helfrich/Canham/Evans model of bilayer shape, curvature sensing and induction are both consequences of a protein's spontaneous curvature, the local curvature at which the Helfrich model energy is a minimum. This paper describes a straightforward approach for estimating the strength and sign of a bilayer-associated molecule's curvature induction from molecular simulation: Correlating the molecule's lateral position with curvature on thermally-fluctuating bilayer modes. Example demonstrations range from a large multi-pass coarse-grained transmembrane protein to an all-atom amphipathic helical segment. Quantification of these systems is placed in the context of experiments seeking the same strength and sign of curvature induction.

biophysics↗

bioRxiv2026

Fusion Peptide Insertion Configuration Determines the Mechanism of Membrane Curvature Induction in Human Parainfluenza Virus Type 3

Viral entry requires remodeling the host membrane with a short fusion peptide (FP) that anchors and deforms the target lipid bilayer. However, the contribution of the FP throughout the full fusion pathway remains unknown. Here, all-atom molecular dynamics simulations define the membrane- deformation mechanisms associated with two distinct insertion configurations of membrane-bound human parainfluenza virus type 3 (HPIV3) FP. Molecular simulations quantifying the linear response of curvature to the peptide are complemented with analyses of lipid organization and FP-lipid interactions to define the underlying membrane-deformation mechanisms. The surface-parallel FP configuration generates positive membrane curvature through deformation of the proximal leaflet, consistent with the classical hydrophobic insertion (wedging) mechanism. In contrast, the transmembrane FP configuration generates curvature through localized deformation of the distal leaflet, a distinct mechanism that would strongly influence later stages of fusion. Cryo-electron tomography shows that target membrane curvature at virus-host contact sites is consistent with the molecular dynamics prediction. In the absence of F-protein activation and FP insertion, the cryo-ET-determined curvature distribution shifts toward negative values, thereby isolating the role of the fusion protein in inducing early-stage curvature that enables the host and virus membranes to approach one another. Modeling key mutational changes isolates how aromatic and electrostatic interactions act together to promote curvature generation. Taken together, these findings establish FP insertion configuration as a determinant of productive membrane curvature across the full fusion pathway.

biophysics↗

bioRxiv2026

Ether linkages in phospholipids provide modular control of membrane mechanics

The structures of phospholipid headgroups and chains are well-established determinants of membrane elastic properties, but functions for different chemistries that join these moieties together are poorly understood. While common phospholipids feature ester linkages, alkyl ether- and plasmenyl-linked species emerged in prokaryotes, are highly abundant in metazoans, and have been implicated in neurodegeneration and aging. Multiple pathways for ether lipid synthesis evolved convergently, suggesting conserved functions for ether linkage chemistry in the structure of cell membranes. Here we combine experiments and molecular simulations to show that backbone linkage chemistry provides modular control of membrane mechanics and topology through a set of discrete drivers. Alkyl linkages provide the first of these by additively promoting negative intrinsic curvature, which destabilizes bilayers. Ethers also decouple membrane stiffness from viscosity, softening membranes while maintaining packing in the hydrophobic core. The plasmenyl C=C bond represents a second, distinct driver that stabilizes the inverted hexagonal phase by relieving interstitial packing frustration. These results explain the fusogenicity of ether lipids, show how they regulate membrane topology through multiple physical mechanisms, and provide a rationale for convergent evolution of the complex plasmenyl linkage moiety.

biophysics↗

bioRxiv2026

Photoreceptor outer segment disk rim curvature relies on a tetraspanin interaction web

Rod and cone photoreceptors are sensory neurons required for the first steps of image-forming vision. Mutations in PRPH2 damage photoreceptor viability and produce a broad range of inherited retinal degenerations (IRDs) for which no treatments are available. The gene product, PRPH2 (peripherin-2), is an integral membrane tetraspanin that is required for the biogenesis and normal structure of photoreceptor outer segment (OS) disks. Peripherin-2 and its homologous partner Rom1 (rom1) self-assemble into non-covalent dimers that organize into three parallel belts that encircle each disk, forming a supramolecular scaffold that imposes extreme curvature on the disk rim. The mechanism by which curvature is generated and maintained is not yet understood. Here, we report the development of blue native (BN)-PAGE and molecular dynamics (MD) simulation approaches that suggest these proteins form an interaction web characterized by multiple interaction modes. BN-PAGE reveals that disk rim belts consist of a mixture of free peripherin-2 dimers and variously-sized chains of disulfide-linked dimers. MD simulations find that although free dimers can generate spontaneous curvature in a model membrane, dimers that are disulfide-linked into linear chains generate highly anisotropic curvature - a key hallmark of normal disk rims. The MD findings further suggest that although individual belts likely provide sufficient thermodynamic driving force to generate extreme curvature, non-covalent inter-belt interactions may also constrain rim diameter. The new findings advance understanding of peripherin-2 and rom1 structure and function in health and disease, and simultaneously provide promising new strategies for molecular phenotyping these clinically important proteins.

neuroscience↗

bioRxiv2024

The PH domain in the ArfGAP ASAP1 drives catalytic activation through an unprecedented allosteric mechanism

ASAP1 is a multidomain Arf GTPase-activating protein (ArfGAP) that catalyzes GTP hydrolysis on the small GTPase Arf1 and is implicated in cancer progression. The PH domain of ASAP1 enhances its activity greater than 7 orders of magnitude but the underlying mechanisms remain poorly understood. Here, we combined Nuclear Magnetic Resonance (NMR), Molecular Dynamic (MD) simulations and mathematical modeling of functional data to build a comprehensive structural-mechanistic model of the complex of Arf1 and the ASAP1 PH domain on a membrane surface. Our results support a new conceptual model in which the PH domain contributes to efficient catalysis not only by membrane recruitment but by acting as a critical component of the catalytic interface, binding Arf{middle dot}GTP and allosterically driving it towards the catalytic transition state. We discuss the biological implications of these results and how they may apply more broadly to poorly understood membrane-dependent regulatory mechanisms controlling catalysis of the ArfGAP superfamily as well as other peripheral membrane enzymes.

biochemistry↗

bioRxiv2024

Magnesium Transporter MgtA revealed as a Dimeric P-type ATPase

Magnesium (Mg2+) uptake systems are present in all domains of life given the vital role of this ion. Bacteria acquire Mg2+ via conserved Mg2+ channels and transporters. The transporters are required for growth when Mg2+ is limiting or during bacterial pathogenesis, but, despite their significance, there are no known structures for these transporters. Here we report the first structure of the Mg2+ transporter MgtA solved by single particle cryo-electron microscopy (cryo-EM). Using mild membrane extraction, we obtained high resolution structures of both a homodimeric form (2.9 [A]), the first for a P-type ATPase, and a monomeric form (3.6 [A]). Each monomer unit of MgtA displays a structural architecture that is similar to other P-type ATPases with a transmembrane domain and two soluble domains. The dimer interface consists of contacts between residues in adjacent soluble nucleotide binding and phosphotransfer regions of the haloacid dehalogenase (HAD) domain. We suggest oligomerization is a conserved structural feature of the diverse family of P-type ATPase transporters. The ATP binding site and conformational dynamics upon nucleotide binding to MgtA were characterized using a combination of cryo-EM, molecular dynamics simulations, hydrogen-deuterium exchange mass spectrometry, and mutagenesis. Our structure also revealed a Mg2+ ion in the transmembrane segments, which, when combined with sequence conservation and mutagenesis studies, allowed us to propose a model for Mg2+ transport across the lipid bilayer. Finally, our work revealed the N-terminal domain structure and cytoplasmic Mg2+ binding sites, which have implications for related P-type ATPases defective in human disease.

biophysics↗

bioRxiv2024

Predicting how lipid composition controls protein curvature sensing with a continuum bilayer membrane model

Cytoplasmic proteins must recruit to membranes to function in processes such as endocytosis and cell division. Many of these proteins recognize not only the chemical structure of the membrane lipids, but the curvature of the surface, binding more strongly to more highly curved surfaces, or curvature sensing. Curvature sensing by amphipathic helices is known to vary with membrane bending rigidity, but changes to lipid composition can simultaneously alter membrane thickness, spontaneous curvature, and leaflet symmetry, thus far preventing a systematic characterization of lipid composition on such curvature sensing through either experiment or simulation. Here we develop and apply a bilayer continuum membrane model that can tractably address this gap, quantifying how controlled changes to each material property can favor or disfavor protein curvature sensing. We evaluate both energetic and structural changes to vesicles upon helix insertion, with strong agreement to new in vitro experiments and all-atom MD simulations, respectively. Our membrane model builds on previous work to include both monolayers of the bilayer via representation by continuous triangular meshes. We introduce a coupling energy that captures the incompressibility of the membrane and the established energetics of lipid tilt. In agreement with experiment, our model predicts stronger curvature sensing in membranes with distinct tail groups (POPC vs DOPC vs DLPC), despite having identical head-group chemistry; the model shows that the primary driving force for weaker curvature sensing in DLPC is that it is thinner, and more wedge shaped. Somewhat surprisingly, asymmetry in lipid shape composition between the two leaflets has a negligible contribution to membrane mechanics following insertion. Our multi-scale approach can be used to quantitatively and efficiently predict how changes to membrane composition in flat to highly curved surfaces alter membrane energetics driven by proteins, a mechanism that helps proteins target membranes at the correct time and place. SignificanceProteins must recruit to membranes for essential biological functions including endocytosis and cell division. In addition to recognizing specific lipid head-groups, many of these proteins also sense the curvature of the membrane, but the strength of sensing is known to vary with distinct membrane compositions. Predicting the dependence of sensing on changes to lipid composition cannot be done a priori due to the multiple material properties, including bilayer thickness, bending rigidity, tilt modulus, spontaneous curvature, and leaflet asymmetry that vary with lipid type. Here we use a multi-scale approach to systematically address this gap, developing a double-leaflet continuum model that is informed by structural deformations from all-atom MD and validated against in vitro experiments. This efficient approach can be applied and extended to quantify how proteins sense and drive membrane curvature across a wide range of membrane bilayers, including distinct leaflet compositions and membrane geometries.

biophysics↗

bioRxiv2024

Synaptotagmin 7 C2 domains induce membrane curvature stress via electrostatic interactions and the wedge mechanism

0.Synaptotagmin 7 (Syt-7) is part of the synaptotagmin protein family that regulates exocytotic lipid membrane fusion. Among the family, Syt-7 stands out by its membrane binding strength and stabilization of long-lived membrane fusion pores. Given that Syt-7 vesicles form long-lived fusion pores, we hypothesize that its interactions with the membrane stabilize the specific curvatures, thicknesses, and lipid compositions that support a metastable fusion pore. Using all-atom molecular dynamics simulations and FRET-based assays of Syt-7s membrane-binding C2 domains (C2A and C2B), we found that Syt-7 C2 domains sequester anionic lipids, are sensitive to cholesterol, thin membranes, and generate lipid membrane curvature by two competing, but related mechanisms. First, Syt-7 forms strong electrostatic contacts with the membrane, generating negative curvature stress. Second, Syt-7s calcium binding loops embed in the membrane surface, acting as a wedge to thin the membrane and induce positive curvature stress. These curvature mechanisms are linked by the protein insertion depth as well as the resulting protein tilt. Simplified quantitative models of the curvature-generating mechanisms link simulation observables to their membrane-reshaping effectiveness.

biophysics↗

bioRxiv2023

Softening in two-component lipid mixtures by spontaneous curvature variance

The bending modulus of a lipid bilayer quantifies its mechanical resistance to curvature. It is typically understood in terms of thickness, e.g., thicker bilayers are stiffer. Here, we describe an additional and powerful molecular determinant of stiffness -- the variance in the distribution of curvature sensitivity of lipids and lipid conformations. Zwitterionic choline and ethanolamine headgroups of glycero-phospholipids dynamically explore inter- and intra-species interactions, leading to transient clustering. We demonstrate that these clusters couple strongly to negative curvature, exciting undulatory membrane modes and reducing the apparent bending modulus. Three forcefields (Martini 2, Martini 3, and all-atom CHARMM C36) each show the effect to a different extent, with the coarse-grained Martini models showing the most clustering and thus the most softening. The theory is a guide to understanding the stiffness of biological membranes with their complex composition, as well as how choices of forcefield parameterization are translated into mechanical stiffness.

biophysics↗

bioRxiv2022

Kinetic relaxation of giant vesicles validates diffusional softening in a binary lipid mixture

The stiffness of biological membranes determines the work required by cellular machinery to form and dismantle vesicles and other lipidic shapes. Model membrane stiffness can be determined from the equilibrium distribution of giant unilamellar vesicle surface undulations observable by phase contrast microscopy. With two or more components, lateral fluctuations of composition will couple to surface undulations depending on the curvature sensitivity of the constituent lipids. The result is a broader distribution of undulations whose complete relaxation is partially determined by lipid diffusion. In this work, kinetic anaysis of the undulations of giant unilamellar vesicles made of phospatidylcholine-phosphatidylethanolamine mixtures validates the molecular mechanism by which the membrane is made 25% softer than a single-component one. The mechanism is relevant to biological membranes, which have diverse and curvature-sensitive lipids.

biophysics↗

bioRxiv2022

Dynamic cholesterol redistribution favors membrane fusion pore constriction

Previous experiments have shown that cholesterol strongly prefers concave leaflets (which have negative curvature and are typically thin), but cholesterol also orders and thickens bilayers (promoting liquid-ordered phases with positive curvature). Our all-atom molecular dynamics simulations resolve this discrepancy for highly curved fusion pores, similar to those found in the nascent fusion and terminal fission steps of endo-/exocytosis. We find that cholesterol is strongly excluded by bilayer thinning in the fusion pore neck, which is caused by the necks net negative Gaussian (saddle) curvature. Consistent with experiment and our fusion pore simulations, analysis of liquid-disordered planar bilayers indicates that cholesterol prefers overall thicker bilayers, but negative leaflet curvature. The exclusion of cholesterol from the neck because of saddle Gaussian curvature implies that it helps drive fusion pore closure, consistent with literature evidence that membrane reshaping is connected to lateral phase separation.

biophysics↗

bioRxiv2022

Molecular mechanisms of spontaneous curvature and softening in complex lipid bilayer mixtures

Membrane reshaping is an essential biological process. The chemical composition of lipid membranes determines their mechanical properties, and thus the energetics of their shape. Hundreds of distinct lipid species make up native bilayers, and this diversity complicates efforts to uncover what compositional factors drive membrane stability in cells. Simplifying assumptions, therefore, are used to generate quantitative predictions of bilayer dynamics based on lipid composition. One assumption commonly used is that "per lipid" mechanical properties are both additive and constant -- that they are an intrinsic property of lipids independent of the surrounding composition. Related to this, is the assumption that lipid bulkiness, or "shape" determines its curvature preference, independently of context. In this study, all-atom molecular dynamics simulations on three separate multi-lipid systems were used to explicitly test these assumptions, applying methodology recently developed to isolate properties of single lipids or nanometer-scale patches of lipids. The curvature preference of populations of lipid conformations were inferred from their redistribution on a dynamically fluctuating bilayer. Representative populations were extracted by both structural similarity and semi-automated hidden Markov model analysis. The curvature preferences of lipid dimers were then determined and compared to an additive model that combines the monomer curvature preference of both the individual lipids. In all three systems, we identified conformational subpopulations of lipid dimers that showed non-additive curvature preference, in each case mediated by a special chemical interaction (e.g., hydrogen bonding). Our study highlights the importance of specific chemical interactions between lipids in multicomponent bilayers and the impact of interactions on bilayer stiffness. We identify two mechanisms of bilayer softening: Diffusional softening, which is driven by the dynamic coupling between lipid distributions and membrane undulations, and conformational softening, which is driven by the inter-conversion between distinct dimeric conformations.

biophysics↗

bioRxiv2021

Nascent clathrin lattices spontaneously disassemble without sufficient adaptor proteins

Clathrin-coated structures must assemble on cell membranes to perform their primary function of receptor internalization. These structures show marked plasticity and instability, but what conditions are necessary to stabilize against disassembly have not been quantified. Recent in vitro fluorescence experiments have measured kinetics of stable clathrin assembly on membranes as controlled by key adaptor proteins like AP-2. Here, we combine this experimental data with microscopic reaction-diffusion simulations and theory to quantify mechanisms of stable vs unstable clathrin assembly on membranes. Both adaptor binding and dimensional reduction on the 2D surface are necessary to reproduce the cooperative kinetics of assembly. By applying our model to more physiologic-like conditions, where the stoichiometry and volume to area ratio are significantly lower than in vitro, we show that the critical nucleus contains ~25 clathrin, remarkably similar to sizes of abortive structures observed in vivo. Stable nucleation requires a stoichiometry of adaptor to clathrin that exceeds 1:1, meaning that AP-2 on its own has too few copies to nucleate lattices. Increasing adaptor concentration increases lattice sizes and nucleation speeds. For curved clathrin cages, we quantify both the cost of bending the membrane and the stabilization required to nucleate cages in solution. We find the energetics are comparable, suggesting that curving the lattice could offset the bending energy cost. Our model predicts how adaptor density controls stabilization of clathrin-coated structures against spontaneous disassembly, and shows remodeling and disassembly does not require ATPases, which is a critical advance towards predicting control of productive vesicle formation. Significance StatementStochastic self-assembly of clathrin-coated structures on the plasma membrane is essential for transport into cells. We show here that even with abundant clathrin available, robust nucleation and growth into stable structures on membranes is not possible without sufficient adaptor proteins. Our results thus provide quantitative justification for why structures observed to form in vivo can still spontaneously disassemble over many seconds. The ATPases that drive clathrin disassembly after productive vesicle formation are therefore not necessary to control remodeling during growth. With parameterization against in vitro kinetics of assembly on membranes, our reaction-diffusion model provides a powerful and extensible tool for establishing determinants of productive assembly in cells.

biophysics↗

bioRxiv2021

The spatial extent of a single lipid's influence on bilayer mechanics

To what spatial extent does a single lipid affect the mechanical properties of the membrane that surrounds it? The lipid composition of a membrane determines its mechanical properties. The shapes available to the membrane depend on its compositional material properties, and therefore, the lipid environment. Because each individual lipid species chemistry is different, it is important to know its range of influence on membrane mechanical properties. This is defined herein as the lipids mechanical extent. Here, a lipids mechanical extent is determined by quantifying lipid redistribution and the average curvature that lipid species experience on fluctuating membrane surfaces. A surprising finding is that, unlike unsaturated lipids, saturated lipids have a complicated, non-local effect on the surrounding surface, with the interaction strength maximal at a finite length-scale. The methodology provides the means to substantially enrich curvature-energy models of membrane structures, quantifying what was previously only conjecture.

biophysics↗

bioRxiv2019

An implicit lipid model for efficient reaction-diffusion simulations of protein binding to surfaces of arbitrary topology

Localization of proteins to a membrane is an essential step in a broad range of biological processes such as signaling, virion formation, and clathrin-mediated endocytosis. The strength and specificity of proteins binding to a membrane depend on the lipid composition. Single-particle reaction-diffusion methods offer a powerful tool for capturing lipid-specific binding to membrane surfaces by treating lipids explicitly as individual diffusible binding sites. However, modeling lipid particle populations is expensive. Here we present an algorithm for reversible binding of proteins to continuum surfaces with implicit lipids, providing dramatic speed-ups to many body simulations. Our algorithm can be readily integrated into most reaction-diffusion software packages. We characterize changes to kinetics that emerge from explicit versus implicit lipids as well as surface adsorption models, showing excellent agreement between our method and the full explicit lipid model. Compared to models of surface adsorption, which couple together binding affinity and lipid concentration, our implicit lipid model decouples them to provide more flexibility for controlling surface binding properties and lipid inhomogeneity, and thus reproducing binding kinetics and equilibria. Crucially, we demonstrate our methods application to membranes of arbitrary curvature and topology, modeled via a subdivision limit surface, again showing excellent agreement with explicit lipid simulations. Unlike adsorption models, our method retains the ability to bind lipids after proteins are localized to the surface (through e.g. a protein-protein interaction), which can greatly increase stability of multi-protein complexes on the surface. Our method will enable efficient cell-scale simulations involving proteins localizing to realistic membrane models, which is a critical step for predictive modeling and quantification of in vitro and in vivo dynamics.

biophysics↗