Biology subjects

Zandi, R.

Publications and source records attributed to Zandi, R..

15 recordsLinked to original sources

bioRxiv2026

SARS-CoV-2 membrane protein conformations induce distinct membrane curvatures

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 virions 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. Significance StatementEnveloped viruses must bend host cell membranes to form new viral particles, but the driving force for membrane bending has been unclear. Using molecular dynamics simulations, we show that the SARS-CoV-2 membrane protein, the most abundant structural protein of the virus, drives membrane bending, and that its two natural conformations generate opposite signs of curvature which match the geometry of distinct regions of a budding virus. Moreover, these induced curvatures cause proteins in different conformations to repel one another providing a physical basis for their spatial segregation. Our results suggest that the membrane proteins conformations can contribute significantly to the membrane remodeling needed for virus assembly and release, revealing a simple mechanism that may apply to other enveloped viruses.

biophysics↗

bioRxiv2026

Mechanisms of viral budding through cellular membranes

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.

biophysics↗

bioRxiv2025

Multiple protein-protein interactions drive the assembly and budding of the Chikungunya virion

The assembly of enveloped viruses is a highly orchestrated process that depends on the coupling of multiple protein-protein interactions within a membrane environment. To gain mechanistic insight into this process, we use Chikungunya virus as a model system to study Alphavirus assembly, focusing on the interplay between core-spike and spike-spike interactions. We begin with coarse-grained molecular dynamics simulations to systematically explore how the symmetry of the nucleocapsid core, together with the relative strengths of spike-core and spike- spike interactions, influences budding efficiency and the emergence of icosahedral particle symmetry. Building on these computational predictions, we perform site-directed mutagenesis on Chikungunya virus 181/25 and examine the consequences for particle assembly and budding in cultured cells, as well as the impact of these mutations during in-cellulo assembly. Our results reveal that canonical core-spike interactions, while necessary, are not sufficient for successful assembly. Instead, lateral interactions among glycoproteins emerge as critical determinants of efficient budding, particle stability, and the maintenance of icosahedral symmetry. Together, these findings provide an integrated computational and experimental framework for understanding the molecular principles governing Alphavirus assembly.

biophysics↗

bioRxiv2025

Clustering of SARS-CoV-2 membrane proteins in lipid bilayer membranes

The accumulation of viral structural proteins along the ER-Golgi intermediate compartment (ERGIC) membrane leads to SARS-CoV-2 self-assembly and budding, driven by the interactions between these proteins, RNA and the ERGIC membrane. The membrane protein (M) is believed to interact with other structural proteins and form clusters needed for the induction of membrane curvature that facilitates virion formation. However, the role played by direct and membrane-mediated interactions between M proteins and their interactions with other proteins in the clustering process remains unclear. Here, we utilize a combination of all-atom molecular dynamics (MD) simulations, continuum modeling and experiments to show that M-M interactions are sufficient to drive clustering in ERGIC-like lipid bilayers in the absence of other proteins or RNA. Using all-atom MD simulations we were able to estimate the membrane thinning induced by M proteins and the resulting membrane-mediated M-M interaction. Combining this with a continuum model that describes the evolution of M protein density in a planar lipid membrane, we identified the existence of a critical, direct M-M interaction energy needed for cluster assembly at a given density. By comparing the model predictions with analysis of atomic force microscopy images of M protein clusters in supported lipid bilayers, we were able to estimate the direct M-M interaction energy and found it to be significantly larger than the membrane mediated interaction energy. Our work therefore establishes that M protein interactions are sufficient to drive clustering and provides a quantitative understanding of the role played by direct and membrane-mediated interactions of M proteins in viral assembly and budding.

biophysics↗

bioRxiv2025

Highly Conserved Core Residues Define Old-World Alphaviruses and Trace Early Evolutionary Divergence

Alphaviruses are positive-sense, single-stranded RNA viruses that assemble into striking double-icosahedral particles. During budding, their nucleocapsid core forms in the cytoplasm and adopts a T=4 icosahedral symmetry, a hallmark of Alphaviruses. Here, we combine structural and phylogenetic analyses to identify the amino acids most likely to govern capsomer formation (pentamers and hexamers) and core organization. We find that these residues are highly conserved in present-day Old-World alphaviruses but are divergent in New-World lineages. This suggests that the common ancestor of both groups likely assembled cores using the same molecular interactions seen in present-day Old-World viruses. We propose that early divergence in these interactions weakened core assembly efficiency, potentially contributing to the attenuation observed in encephalitic New-World alphaviruses. This attenuation may reflect an adaptive trade-off, in which reduced assembly efficiency lowers viral replication and virulence, supporting long-term persistence in enzootic cycles. Revealing how specific residues control capsid architecture and tracing their evolutionary history, this study provides key insights into alphavirus assembly mechanisms, opening new avenues for antiviral strategies and rational vaccine design.

evolutionary biology↗

bioRxiv2025

Competitive binding and geometric changes allow fast, complete translocation of intact HIV-1 capsids through the nuclear pore complex

Recent experiments on HIV-1 capsid translocation through the nuclear pore complex (NPC) have demonstrated the docking of intact or nearly intact capsids at the pore, followed by translocation, with capsid disassembly occurring only within the nucleus near the site of integration. Given that the size of the capsid is comparable to the pore dimensions, these new findings raise questions regarding the energetics and dynamics of capsid passage across the significant entropic barrier created by the disordered FG nucleoporins (FG nups) in the NPC central channel. Here, we develop an analytical model for the transport of the HIV-1 capsid that considers the geometry of the capsid and pore, the free energy barrier due to the FG nups, and capsid-nup interactions. Our results show that capsid entry into the pore is favorable if the narrow end enters first, consistent with experimental observations, and that increasing the capsid-nup interaction strength enhances inward capsid flux. However, capsid-nup interaction alone is insufficient for complete capsid nuclear import and competitive binding by the nuclear factor CPSF6 to FG-binding sites on the capsid can serve as a ratcheting mechanism for full nuclear import. We show that nuclear import is arrested below a minimum CPSF6 concentration, consistent with experimental observations, and that pore dilation or capsid deformation can accelerate the translocation process. Our work explores the physics underlying a new perspective on HIV-1 viral genome nuclear import and provides quantitative explanations for experimentally observed phenomena while making testable predictions. Significance statementHIV-1 remains a devastating global health threat, with millions of new infections each year. However, the mechanism by which the viral genome enters the host nucleus is still not fully understood. Recent experiments show that the HIV-1 capsid can remain intact - or nearly so - during nuclear import, challenging long-held assumptions about the limits on size for transport through the nuclear pore. Here, we present a biophysical model that explains the directional transport of the capsid, the role of capsid and pore geometry and host factors such as CPSF6, and elucidates a ratcheting mechanism that allows entry of intact capsids within physiological timescales. This work provides a mechanistic framework for a critical step in the early stages of HIV-1 infection.

biophysics↗

bioRxiv2025

Dynamics and Regulation of mRNA Cap Recognition by Human eIF4F

Efficient eukaryotic messenger RNA translation requires dynamic collaboration between the three subunits of initiation factor 4F (eIF4F, eIF4E*G*A), which recognises and activates mRNA at its 5' cap structure for ribosome recruitment. Despite its high biological and pharmacological importance, the dynamics of full human eIF4F-mRNA engagement remain largely uncharacterised, hindering mechanistic understanding of translation initiation and its regulation. Here we observed human eIF4F activity with single-molecule fluorescence assays that directly visualise mRNA cap recognition by its eIF4E subunit. Unexpectedly, we find that inherently transient eIF4E-cap binding is repressed by full-length human eIF4G, predominantly through its C-terminus, representing an unanticipated role for eIF4G as a central rate-limiting factor in the eIF4F complex. This repression is relieved by nucleotide-bound eIF4A in the eIF4F heterotrimer, placing eIF4A as a crucial determinant of efficient cap recognition for translation. Molecular dynamics simulations reveal that electrostatic modulation of eIF4E-mRNA interaction allows eIF4G to control the cap-recognition frequency. Our findings also indicate that intrinsic eIF4F- mRNA dynamics are insufficient to support cap-tethered ribosomal scanning to locate translation start sites. They illuminate fundamental design-principle differences for the overall mechanism and division of labour among eIF4F subunits during mRNA recognition in humans and yeast.

biophysics↗

bioRxiv2025

Human Stress Response Specificity through Bioresonance Selectivity

Bold First ParagraphIn eukaryotes, the mitogen activated protein kinase (MAPK) cascade, a multilayered interconnected network of enzymes, connects external stimuli to gene regulation, determining cellular fate 1. Environmental stress sensed by a cell starts a complex chain of reactions between MAPK enzymes that ultimately activates the master stress response regulator protein p38 MAPK 2,3. Thus activated, p38 must then selectively activate targets from a pool of hundreds to initiate appropriate cellular responses 3. Mechanisms for how p38 performs this selection remain unclear 4,5. Here we show that human p38 target selectivity is based on the same principles as modern electronic telecommunications systems, except using waves of chemicals rather than electromagnetic fields or electric currents. p38 encodes information about stimuli as different frequency oscillations of its activation state, and targets are selected through frequency-dependent resonance of oscillating biochemical reactions between p38 and its targets. We demonstrate this mechanism by activating various genetic responses in human cells by applying only sugar at different frequencies. These results unify observations of oscillating signaling components and altered responses 6-19 into a coherent framework to understand and control human gene expression. As failures of this mechanism may contribute to some p38-associated diseases 2,20-28, these findings may have implications for pharmaceutical development and therapeutic strategies.

biophysics↗

bioRxiv2024

Switchable Conformation in Protein Subunits: Unveiling Assembly Dynamics of Icosahedral Viruses

The packaging of genetic material within a protein shell, called the capsid, marks a pivotal step in the life cycle of numerous single-stranded RNA viruses. Understanding how hundreds, or even thousands, of proteins assemble around the genome to form highly symmetrical structures remains an unresolved puzzle. In this paper, we design novel subunits and develop a model that enables us to explore the assembly pathways and genome packaging mechanism of icosahedral viruses, which were previously inaccessible. Using molecular dynamics (MD) simulations, we observe capsid fragments, varying in protein number and morphology, assembling at different locations along the genome. Initially, these fragments create a disordered structure that later merges to form a perfect symmetric capsid. The model demonstrates remarkable strength in addressing numerous unresolved issues surrounding virus assembly. For instance, it enables us to explore the advantages of RNA packaging by capsid proteins over linear polymers. Our MD simulations are in excellent agreement with our experimental findings from small-angle X-ray scattering and cryo-transmission electron microscopy, carefully analyzing the assembly products of viral capsid proteins around RNAs with distinct topologies.

biophysics↗

bioRxiv2024

Study of Impacts of Two Types of Cellular Aging on the Yeast Bud Morphogenesis

Understanding the mechanisms of cellular aging processes is crucial for attempting to extend organismal lifespan and for studying age-related degenerative diseases. Yeast cells divide through budding, providing a classical biological model for studying cellular aging. With their powerful genetics, relatively short lifespan and well-established signaling pathways also found in animals, yeast cells offer valuable insights into the aging process. Recent experiments suggested the existence of two aging modes in yeast characterized by nucleolar and mitochondrial declines, respectively. In this study, by analyzing experimental data it was shown that cells evolving into those two aging modes behave differently when they are young. While buds grow linearly in both modes, cells that consistently generate spherical buds throughout their lifespan demonstrate greater efficacy in controlling bud size and growth rate at young ages. A three-dimensional chemical-mechanical model was developed and used to suggest and test hypothesized mechanisms of bud morphogenesis during aging. Experimentally calibrated simulations showed that tubular bud shape in one aging mode could be generated by locally inserting new materials at the bud tip guided by the polarized Cdc42 signal during the early stage of budding. Furthermore, the aspect ratio of the tubular bud could be stabilized during the late stage, as observed in experiments, through a reduction on the new cell surface material insertion or an expansion of the polarization site. Thus model simulations suggest the maintenance of new cell surface material insertion or chemical signal polarization could be weakened due to cellular aging in yeast and other cell types. Significance StatementAging yeast exhibits two modes with different bud shapes. Experimental data analysis reveals that control of growth rate and bud size is more robust in cells aging in a spherical budding mode than in cells aging in a tubular budding mode. A computational model was developed and used in combination with experiments to test the hypothesized mechanisms underlying different types of budding in aging cells. Model simulations suggest that localized growth is sufficient to generate tubular budding and its aspect ratio can be stabilized through the regulation of chemical signals with an expanding polarization site or a decline on the new cell surface material insertion. Proposed mechanisms of morphological changes in aging yeast can be present in other cell types.

biophysics↗

bioRxiv2023

Synthesis, Insertion and Characterization of SARS-CoV-2 Membrane Protein Within Lipid Bilayers

SUMMARY/ABSTRACTThe membrane protein (M) is the most abundant structural protein in the SARS-CoV-2 virus and functions exclusively as a membrane-embedded homodimer. M protein is required for the formation of the SARS-CoV-2 virus particle and has been shown to interact with the Spike and Envelope proteins, as well as the RNA-packaging Nucleocapsid protein. Our knowledge of M protein is very limited due to its small size and challenges in expressing enough protein for use in structural and biophysical experiments. We report the successful development of a SUMO tag-based expression system to produce and purify significant quantities of M protein, and a method to insert the synthesized dimers into a suspended lipid membrane in a homogeneous orientation. We used AFM and Cryo-EM to image individual membrane-bound M protein dimers and characterize the configurations that they can assume. Our experimental results are in agreement with our molecular dynamics simulations which predict thinning of the membrane around the M protein and a propensity to induce local membrane curvature. Taken together, our results shed new light on M protein properties within the lipid bilayer and suggest mechanisms that could contribute to viral assembly and budding.

biophysics↗

bioRxiv2022

A Chemical-mechanical Coupled Model Predicts Roles of Spatial Distribution of Morphogen in Maintaining Tissue Growth

The exact mechanism controlling cell growth remains a grand challenge in developmental biology and regenerative medicine. The Drosophila wing disc tissue serves as an ideal biological model to study growth regulation due to similar features observed in other developmental systems. The mechanism of growth regulation in the wing disc remains a subject of intense debate. Most existing models to study tissue growth focus on either chemical signals or mechanical forces only. Here we developed a multiscale chemical-mechanical coupled model to test a growth regulation mechanism depending on the spatial range of the morphogen gradient. By comparing the spatial distribution of cell division and the overall shape of tissue obtained in the coupled model with experimental data, our results show that the distribution of the Dpp morphogen can be critical in resulting tissue size and shape. A larger tissue size with a faster growth rate and more symmetric shape can be achieved if the Dpp gradient spreads in a larger domain. Together with the absorbing boundary conditions, the feedback regulation that downregulates Dpp receptors on the cell membrane allows the further spread of the morphogen away from its source region, resulting in prolonged tissue growth at a more spatially homogeneous growth rate. Summary StatementA multiscale chemical-mechanical model was developed by coupling submodels representing dynamics of a morphogen gradient at the tissue level, intracellular chemical signals, and mechanical properties at the subcellular level. By applying this model to study the Drosophila wing disc, it was found that the spatial range of the morphogen gradient affected tissue growth in terms of the growth rate and the overall shape.

developmental biology↗

bioRxiv2022

Endocytosis at Extremes: Formation and Internalization of Giant Clathrin-coated Pits Under Elevated Membrane Tension

Internalization of clathrin-coated vesicles from the plasma membrane constitutes the major endocytic route for receptors and their ligands. Dynamic and structural properties of endocytic clathrin coats are regulated by the mechanical properties of the plasma membrane. Here, we used conventional fluorescence imaging and multiple modes of structured illumination microscopy (SIM) to image formation of endocytic clathrin coats within live cells and tissues of developing fruit fly embryos. High resolution in both spatial and temporal domains allowed us to detect and characterize distinct classes of clathrin-coated structures. For the first time, we show that membrane tension induces formation of giant coated pits (GCPs) that can be up to two orders of magnitude larger than the canonical clathrin-coated pits. GCPs take longer to form but their mechanism of curvature generation is the same as the canonical pits. We also demonstrate that GCPs can split into smaller fragments during internalization. Considering the supporting roles played by actin filament dynamics in clathrin-mediated endocytosis under mechanically stringent conditions, we suggest that local changes in the coat curvature driven by actin machinery can drive splitting and internalization of GCPs.

biophysics↗

bioRxiv2020

Role of combined cell membrane and wall mechanicalproperties regulated by polarity signals in cell budding

The budding yeast, Saccharomyces cerevisiae, is a prime biological model to study mechanisms underlying asymmetric growth. Previous studies have shown that, prior to yeast bud emergence, polarization of a conserved small GTPase, Cdc42, must be established. Additionally, hydrolase changes the mechanical properties of the cell wall and plasma membrane with the periplasm between them (cell surface). However, how the surface mechanical properties in the emerging bud are different from the properties of the mother cell and their role in bud formation are not well understood. We hypothesize that the polarized chemical signal alters the local dimensionless ratio of stretching to bending stiffness of the cell surface of the emerging yeast bud. To test this hypothesis, a novel three-dimensional coarse-grained particle-based model has been developed which describes inhomogeneous mechanical properties of the cell surface. Model simulations suggest that regulation of the dimensionless ratio of stretching to bending stiffness of the cell surface is necessary to initiate bud formation. Furthermore, model simulations predict that bud shape depends strongly on the experimentally observed molecular distribution of the polarized signaling molecule Cdc42, while the neck shape of the emerging bud is strongly impacted by the properties of the chitin and septin ring. This 3D model of asymmetric cell growth can also be used for studying viral budding and other vegetative reproduction processes performed via budding.

biophysics↗

bioRxiv2019

Endocytic Clathrin Coats Develop Curvature at Early Stages of Their Formation

Sculpting a flat patch of membrane into an endocytic vesicle requires curvature generation on the cell surface, which is the primary function of endocytic protein complexes. The mechanism through which membrane curvature is imposed during formation of clathrin-coated vesicles is an ongoing controversy. Using super-resolved live cell fluorescence imaging, we demonstrate that curvature generation by clathrin-coated pits can be detected in real time within cultured cells and tissues of developing metazoan organisms. We found that the footprint of clathrin coats increase monotonically during formation of curved pits at different levels of plasma membrane tension. Our findings are only compatible with models that predict curvature generation at early stages of endocytic clathrin-coated pit formation. Therefore, clathrin-coated vesicle formation does not necessitate a dynamically unstable clathrin lattice that would allow an abrupt flat-to-curved transition. SummaryEndocytic clathrin coats acquire curvature without a flat-to-curved transition that requires an extensive reorganization of the clathrin lattice.

biophysics↗