Reconstitution and real-time quantification of membrane remodeling by single proteins and protein complexes

SARS-CoV-2 FP1 Destabilizes Lipid Membranes and Facilitates Pore Formation

SARS-CoV-2 viral entry requires membrane fusion, which is facilitated by the fusion peptides within its spike protein. These predominantly hydrophobic peptides insert into target membranes; however, their precise mechanistic role in membrane fusion remains incompletely understood. Here, we investigate how FP1 (SFIEDLLFNKVTLADAGFIK), the N-terminal fusion peptide, modulates membrane stability and barrier function across various model membrane systems. Through a complementary suite of biophysical techniques-including electrophysiology, fluorescence spectroscopy, and atomic force microscopy-we demonstrate that FP1 significantly promotes pore formation and alters the membrane's mechanical properties. Our findings reveal that FP1 reduces the energy barrier for membrane defect formation and stimulates the appearance of stable conducting pores, with effects modulated by membrane composition and mechanical stress. The observed membrane-destabilizing activity suggests that, beyond its anchoring function, FP1 may facilitate viral fusion by locally disrupting membrane integrity. These results provide mechanistic insights into SARS-CoV-2 membrane fusion mechanisms and highlight the complex interplay between fusion peptides and target membranes during viral entry.

Human Immunodeficiency Virus Type 1 Gag Polyprotein Modulates Membrane Physical Properties like a Surfactant: Potential Implications for Virus Assembly

Human immunodeficiency virus (HIV) assembly at an infected cell's plasma membrane requires membrane deformation to organize the near-spherical shape of an immature virus. While the cellular expression of HIV Gag is sufficient to initiate budding of virus-like particles, how Gag generates membrane curvature is not fully understood. Using highly curved lipid nanotubes, we have investigated the physicochemical basis of the membrane activity of recombinant nonmyristoylated Gag-Δp6. Gag protein, upon adsorption onto the membrane, resulted in the shape changes of both charged and uncharged nanotubes. This shape change was more pronounced in the presence of charged lipids, especially phosphatidylinositol bisphosphate (PI(4,5)P2). We found that Gag modified the interfacial tension of phospholipid bilayer membranes, as judged by comparison with the effects of amphipathic peptides and nonionic detergent. Bioinformatic analysis demonstrated that a region of the capsid and SP1 domains junction of Gag is structurally similar to the amphipathic peptide magainin-1. This region accounts for integral changes in the physical properties of the membrane upon Gag adsorption, as we showed with the synthetic CA-SP1 junction peptide. Phenomenologically, membrane-adsorbed Gag could diminish the energetic cost of increasing the membrane area in a way similar to foam formation. We propose that Gag acts as a surface-active substance at the HIV budding site that softens the membrane at the place of Gag adsorption, lowering the energy for membrane bending. Finally, our experimental data and theoretical considerations give a lipid-centric view and common mechanism by which proteins could bend membranes, despite not having intrinsic curvature in their molecular surfaces or assemblies.

Alteration of Average Thickness of Lipid Bilayer by Membrane-Deforming Inclusions

Thickness of lipid bilayer membranes is a key physical parameter determining membrane permeability and stability with respect to formation of through pores. Most membrane inclusions or impurities like amphipathic peptides, transmembrane peptides, lipid inclusions of a different molecular shape, lipid domains, and protein-lipid domains, locally deform the membrane. The detailed structure of the locally deformed region of the membrane is a kind of "fingerprint" for the inclusion type. However, most experimental methods allow determining only averaged parameters of membranes with incorporated inclusions, thus preventing the direct obtaining of the characteristics of the inclusion. Here we developed a model that allows the obtaining of characteristic parameters of three types of membrane inclusions (amphipathic peptides, transmembrane peptides, monolayer lipid patches) from experimentally observable dependencies of the average thickness of lipid bilayer on the surface concentration of the inclusions. In the case of amphipathic peptides, the model provided the peptide parameters that were in qualitative agreement with the available experimental data.

Molecular Sensing and Manipulation of Protein Oligomerization in Membrane Nanotubes with Bolaamphiphilic Foldamers

Adaptive and reversible self-assembly of supramolecular protein structures is a fundamental characteristic of dynamic living matter. However, the quantitative detection and assessment of the emergence of mesoscale protein complexes from small and dynamic oligomeric precursors remains highly challenging. Here, we present a novel approach utilizing a short membrane nanotube (sNT) pulled from a planar membrane reservoir as nanotemplates for molecular reconstruction, manipulation, and sensing of protein oligomerization and self-assembly at the mesoscale. The sNT reports changes in membrane shape and rigidity caused by membrane-bound proteins as variations of the ionic conductivity of the sNT lumen. To confine oligomerization to the sNT, we have designed and synthesized rigid oligoamide foldamer tapes (ROFTs). Charged ROFTs incorporate into the planar and sNT membranes, mediate protein binding to the membranes, and, driven by the luminal electric field, shuttle the bound proteins between the sNT and planar membranes. Using Annexin-V (AnV) as a prototype, we show that the sNT detects AnV oligomers shuttled into the nanotube by ROFTs. Accumulation of AnV on the sNT induces its self-assembly into a curved lattice, restricting the sNT geometry and inhibiting the material uptake from the reservoir during the sNT extension, leading to the sNT fission. By comparing the spontaneous and ROFT-mediated entry of AnV into the sNT, we reveal how intricate membrane curvature sensing by small AnV oligomers controls the lattice self-assembly. These results establish sNT-ROFT as a powerful tool for molecular reconstruction and functional analyses of protein oligomerization and self-assembly, with broad application to various membrane processes.

Membrane activity of viral proteins

COVID-19 infection, caused by the SARS-CoV-2 coronavirus, has led to the largest pandemic since the Spanish flu in 1918. In view of this, the development of vaccines and antiviral drugs that can stop the spread of this infection has become an acute issue. Currently, in the search for antiviral drugs against COVID-19, much attention is paid to the study of the structure of the receptor-binding domain of the surface protein S. However, the emergence of new SARS-CoV-2 coronavirus strains indicates its high variability, which reduces the effectiveness of vaccines and antiviral drugs. At the same time, the envelope protein E of this virus is membrane active and shows a rather high conservatism. Despite the critical importance of this protein in the coronavirus life cycle, the physicochemical mechanisms of its interaction with cell membranes still remain unclear. So, we investigated the membrane activity of protein E of the SARS-CoV-2 coronavirus on models of giant unilamellar vesicles and lipid nanotubes. As a result, it was found that the protein forms pores in the lipid bilayer, i.e., performs the main function of viroporin. In addition, protein E is able to deform lipid membranes and form double-membrane vesicles depending on the concentration.

Membrane Lipid Reshaping Underlies Oxidative Stress Sensing by the Mitochondrial Proteins UCP1 and ANT1

Oxidative stress and ROS are important players in the pathogenesis of numerous diseases. In addition to directly altering proteins, ROS also affects lipids with negative intrinsic curvature such as phosphatidylethanolamine (PE), producing PE adducts and lysolipids. The formation of PE adducts potentiates the protonophoric activity of mitochondrial uncoupling proteins, but the molecular mechanism remains unclear. Here, we linked the ROS-mediated change in lipid shape to the mechanical properties of the membrane and the function of uncoupling protein 1 (UCP1) and adenine nucleotide translocase 1 (ANT1). We show that the increase in the protonophoric activity of both proteins occurs due to the decrease in bending modulus in lipid bilayers in the presence of lysophosphatidylcholines (OPC and MPC) and PE adducts. Moreover, MD simulations showed that modified PEs and lysolipids change the lateral pressure profile of the membrane in the same direction and by the similar amplitude, indicating that modified PEs act as lipids with positive intrinsic curvature. Both results indicate that oxidative stress decreases stored curvature elastic stress (SCES) in the lipid bilayer membrane. We demonstrated that UCP1 and ANT1 sense SCES and proposed a novel regulatory mechanism for the function of these proteins. The new findings should draw the attention of the scientific community to this important and unexplored area of redox biochemistry.

Determination of Elastic Parameters of Lipid Membranes with Molecular Dynamics: A Review of Approaches and Theoretical Aspects

Lipid membranes are abundant in living organisms, where they constitute a surrounding shell for cells and their organelles. There are many circumstances in which the deformations of lipid membranes are involved in living cells: fusion and fission, membrane-mediated interaction between membrane inclusions, lipid-protein interaction, formation of pores, etc. In all of these cases, elastic parameters of lipid membranes are important for the description of membrane deformations, as these parameters determine energy barriers and characteristic times of membrane-involved phenomena. Since the development of molecular dynamics (MD), a variety of in silico methods have been proposed for the determination of elastic parameters of simulated lipid membranes. These MD methods allow for the consideration of details unattainable in experimental techniques and represent a distinct scientific field, which is rapidly developing. This work provides a review of these MD approaches with a focus on theoretical aspects. Two main challenges are identified: (i) the ambiguity in the transition from the continuum description of elastic theories to the discrete representation of MD simulations, and (ii) the determination of intrinsic elastic parameters of lipid mixtures, which is complicated due to the composition-curvature coupling effect.

Molecular Shape Solution for Mesoscopic Remodeling of Cellular Membranes

Cellular membranes self-assemble from and interact with various molecular species. Each molecule locally shapes the lipid bilayer, the soft elastic core of cellular membranes. The dynamic architecture of intracellular membrane systems is based on elastic transformations and lateral redistribution of these elementary shapes, driven by chemical and curvature stress gradients. The minimization of the total elastic stress by such redistribution composes the most basic, primordial mechanism of membrane curvature-composition coupling (CCC). Although CCC is generally considered in the context of dynamic compositional heterogeneity of cellular membrane systems, in this article we discuss a broader involvement of CCC in controlling membrane deformations. We focus specifically on the mesoscale membrane transformations in open, reservoir-governed systems, such as membrane budding, tubulation, and the emergence of highly curved sites of membrane fusion and fission. We reveal that the reshuffling of molecular shapes constitutes an independent deformation mode with complex rheological properties.This mode controls effective elasticity of local deformations as well as stationary elastic stress, thus emerging as a major regulator of intracellular membrane remodeling.

Nonlinear material and ionic transport through membrane nanotubes

Membrane nanotubes (NTs) and their networks play an important role in intracellular membrane transport and intercellular communications. The transport characteristics of the NT lumen resemble those of conventional solid-state nanopores. However, unlike the rigid pores, the soft membrane wall of the NT can be deformed by forces driving the transport through the NT lumen. This intrinsic coupling between the NT geometry and transport properties remains poorly explored. Using synchronized fluorescence microscopy and conductance measurements, we revealed that the NT shape was changed by both electric and hydrostatic forces driving the ionic and solute fluxes through the NT lumen. Far from the shape instability, the strength of the force effect is determined by the lateral membrane tension and is scaled with membrane elasticity so that the NT can be operated as a linear elastic sensor. Near shape instabilities, the transport forces triggered large-scale shape transformations, both stochastic and periodic. The periodic oscillations were coupled to a vesicle passage along the NT axis, resembling peristaltic transport. The oscillations were parametrically controlled by the electric field, making NT a highly nonlinear nanofluidic circuitry element with biological and technological implications.