Biology subjects

Hagan, M. F.

Publications and source records attributed to Hagan, M. F..

9 recordsLinked to original sources

bioRxiv2026

Modeling Reveals How Direct-Acting Antivirals Redirect HBV Capsid Assembly Pathways to Noninfectious Products

Hepatitis B virus (HBV) infections cause chronic liver disease, resulting in about one million deaths per year, and there is currently no cure. Recent work has shown that a class of small molecules called capsid assembly modulators (CAMs) is promising for treating HBV. CAMs bind to HBV capsid protein subunits and alter their assembly, leading to non-functional and malformed structures rather than functional, closed shells. However, the mechanisms by which CAMs alter capsid assembly pathways remain unclear. Here, we extend a recently-developed kinetic Monte Carlo (KMC) model for HBV capsid assembly to simulate how CAMs affect assembly. In the model, CAMs alter assembly by preferentially binding to interfaces between certain quasi-equivalent subunit conformations. Simulations of the model reproduce experimental assembly product distributions. By analyzing assembly trajectories, we clarify the roles of thermodynamics and kinetics in determining assembly products, identify assembly mechanisms, and predict the key intermediates that lead to either capsids or malformed structures. Our findings enhance our fundamental understanding of capsid assembly, help advance the development of CAMs as a treatment for HBV and, more broadly, inform efforts to direct self-assembly pathways toward specific products.

biophysics↗

bioRxiv2023

Active membrane deformations of a minimal synthetic cell

Biological cells exhibit the remarkable ability to adapt their shape in response to their environment, a phenomenon that hinges on the intricate interplay between their deformable membrane and the underlying activity of their cytoskeleton. Yet, the precise physical mechanisms of this coupling remain mostly elusive. Here, we introduce a synthetic cell model, comprised of an active cytoskeletal network of microtubules, crosslinkers and molecular motors encapsulated inside giant vesicles. Remarkably, these active vesicles exhibit large shape fluctuations and life-like morphing abilities. Active forces from the encapsulated cytoskeleton give rise to large-scale traveling membrane deformations. Quantitative analysis of membrane and microtubule fluctuations shows how the intricate coupling of confinement, membrane material properties and cytoskeletal forces yields fluctuation spectra whose characteristic scales in space and time are distinctly different from passive vesicles. We demonstrate how activity leads to uneven probability fluxes between fluctuation modes and hence sets the temporal scale of membrane fluctuations. Using simulations and theoretical modelling, we extend the classical approach to membrane fluctuations to active cytoskeleton-driven vesicles, highlighting the effect of correlated activity on the dynamics of membrane deformations and paving the way for quantitative descriptions of the shape-morphing ability typical of living systems.

biophysics↗

bioRxiv2022

Self-Assembly Coupled to Liquid-Liquid Phase Separation

Liquid condensate droplets with distinct compositions of proteins and nucleic acids are widespread in biological cells. While it is known that such droplets can regulate irreversible protein aggregation, their effect on reversible self-assembly remains largely unexplored. In this article, we use kinetic theory and solution thermodynamics to investigate the effect of liquid-liquid phase separation on the reversible self-assembly of structures with well-defined sizes and architectures. We find that when assembling subunits preferentially partition into liquid domains, robustness against kinetic traps and maximum achievable assembly rates can be significantly increased. In particular, the range of solution conditions over which productive assembly and the corresponding assembly rates can increase by orders of magnitude. We analyze the rate equation predictions using simple scaling estimates to identify effect of liquid-liquid phase separation as a function of relevant control parameters. These results may elucidate self-assembly processes that underlie normal cellular functions or pathogenesis, and suggest strategies for designing efficient bottom-up assembly for nanomaterials applications.

biophysics↗

bioRxiv2022

Effect of Ionic Strength on the Assembly of Simian Vacuolating Virus Capsid Protein Around Poly(Styrene Sulfonate)

Virus-like particles (VLPs) are noninfectious nanocapsules that can be used for drug delivery or vaccine applications. VLPs can be assembled from virus capsid proteins around a condensing agent like RNA, DNA, or a charged polymer. Electrostatic interactions play an important role in the assembly reaction. VLPs assemble from many copies of capsid protein, with combinatorial intermediates, and therefore the mechanism of the reaction is poorly understood. In this paper, we determined the effect of ionic strength on the assembly of Simian Vacuolating Virus 40 (SV40)-like particles. We mixed poly(styrene sulfonate) with SV40 capsid protein pentamers at different ionic strengths. We then characterized the assembly product by solution small-angle X-ray scattering (SAXS) and cryo-TEM. To analyze the data, we performed Brownian dynamics simulations using a coarse-grained model that revealed incomplete, asymmetric VLP structures that were consistent with the experimental data. We found that close to physiological ionic strength, T=1 VLPs coexisted with VP1 pentamers. At lower or higher ionic strengths, incomplete particles coexisted with pentamers and T=1 particles. Including the simulation, structures were essential to explaining the SAXS data.

biophysics↗

bioRxiv2022

Microcompartment assembly around multicomponent fluid cargoes

This article describes dynamical simulations of the assembly of an icosahedral protein shell around a bicomponent fluid cargo. Our simulations are motivated by bacterial microcompartments, which are protein shells found in bacteria that assemble around a complex of enzymes and other components involved in certain metabolic processes. The simulations demonstrate that the relative interaction strengths among the different cargo species play a key role in determining the amount of each species that is encapsulated, their spatial organization, and the nature of the shell assembly pathways. However, the shell protein-shell protein and shell protein-cargo component interactions that help drive assembly and encapsulation also influence cargo composition within certain parameter regimes. These behaviors are governed by a combination of thermodynamic and kinetic effects. In addition to elucidating how natural microcompartments encapsulate multiple components involved within reaction cascades, these results have implications for efforts in synthetic biology to colocalize alternative sets of molecules within microcompartments to accelerate specific reactions. More broadly, the results suggest that coupling between self-assembly and multicomponent liquid-liquid phase separation may play a role in the organization of the cellular cytoplasm.

biophysics↗

bioRxiv2022

Multiscale Modeling of Hepatitis B Virus Capsid Assembly and its Dimorphism

Hepatitis B Virus (HBV) is an endemic, chronic virus that leads to 800,000 deaths per year. Central to the HBV lifecycle, the viral core has a protein capsid assembled from many copies of a single protein. The capsid protein adopts different (quasi-equivalent) conformations to form icosahedral capsids containing 180 or 240 proteins, T=3 or T=4 respectively in Caspar-Klug nomenclature. HBV capsid assembly has become an important target for new antivirals; nonetheless the assembly pathways and mechanisms that control HBV dimorphism remain unclear. We describe computer simulations of HBV assembly, using a coarse-grained model that has parameters learned from all-atom molecular dynamics simulations of a complete HBV capsid, and yet is computationally tractable. Dynamical simulations with the resulting model reproduce experimental observations of HBV assembly pathways and products. By constructing Markov state models and employing transition path theory, we identify pathways leading to T=3, T=4, and other experimentally observed capsid morphologies. The analysis identifies factors that control this polymorphism, in particular, the conformational free energy landscape of the capsid proteins and their interactions.

biophysics↗

bioRxiv2020

Mechanisms of scaffold-mediated microcompartment assembly and size-control

This article describes a theoretical and computational study of the dynamical assembly of a protein shell around a complex consisting of many cargo molecules and long flexible scaffold molecules. Our study is motivated by bacterial microcompartments, which are proteinaceous organelles that assemble around a condensed droplet of enzymes and reactants. As in many examples of cytoplasmic liquid-liquid phase separation, condensation of the microcompartment interior cargo is driven by long flexible scaffold proteins that have weak multivalent interactions with the cargo. We describe a minimal model for the thermodynamics and dynamics of assembly of a protein shell around cargo and scaffold molecules, with scaffold-mediated cargo coalescence and encapsulation. Our results predict that the shell size, amount of encapsulated cargo, and assembly pathways depend sensitively on properties of the scaffold, including its length and valency of scaffold-cargo interactions. Moreover, the ability of self-assembling protein shells to change their size to accommodate scaffold molecules of different lengths depends crucially on whether the spontaneous curvature radius of the protein shell is smaller or larger than a characteristic elastic length scale of the shell. Beyond natural microcompartments, these results have important implications for synthetic biology efforts to target new molecules for encapsulation by microcompartments or viral shells. More broadly, the results elucidate how cells exploit coupling between self-assembly and liquid-liquid phase separation to organize their interiors.

biophysics↗

bioRxiv2020

Synchronized oscillations, metachronal waves, and jammed clusters in sterically interacting active filament arrays

Autonomous active, elastic filaments that interact with each other to achieve cooperation and synchrony underlie many critical functions in biology. A striking example is ciliary arrays in the mammalian respiratory tract; here individual filaments communicate through direct interactions and through the surrounding fluid to generate metachronal traveling waves crucial for mucociliary clearance. The mechanisms underlying this collective response and the essential ingredients for stable synchronization remain a mystery. In this article, we describe Brownian dynamics simulations of multi-filament arrays, demonstrating that short-range steric inter-filament interactions and surface-roughness are sufficient to generate a rich variety of collective spatiotemporal oscillatory, traveling and static patterns. Starting from results for the collective dynamics of two- and three-filament systems, we identify parameter ranges in which inter-filament interactions lead to synchronized oscillations. We then study how these results generalize to large one-dimensional arrays of many interacting filaments. The phase space characterizing the multi-filament array dynamics and deformations exhibits rich behaviors, including oscillations and traveling metachronal waves, depending on the interplay between geometric spacing between filaments, activity, and elasticity of the filaments. Interestingly, the existence of metachronal waves is nonmonotonic with respect to the inter-filament spacing. We also find that the degree of filament surface roughness significantly affects the dynamics -- roughness on scales comparable to the filament thickness generates a locking-mechanism that transforms traveling wave patterns into statically stuck and jammed configurations. Our simulations suggest that short-ranged steric inter-filament interactions are sufficient and perhaps even critical for the development, stability and regulation of collective patterns.

biophysics↗

bioRxiv2018

Gaussian curvature and the budding kinetics of enveloped viruses

The formation of a membrane-enveloped virus such as HIV-1 starts with the assembly of a curved layer of capsid proteins lining the interior of the plasma membrane (PM) of the host cell. This layer grows into a spherical shell enveloped by a lipid membrane that is connected to the PM via a curved neck (\"budding\"). For many enveloped viruses the scission of this neck is not spontaneous. Instead, the elaborate \"ESCRT\" cell machinery needs to be recruited to carry out that task. It is not clear why this is necessary since scission is spontaneous for much simpler systems, such as vesiculation driven by phase-separation inside lipid bilayers. Recently, Brownian dynamics simulations of enveloped virus budding reproduced protracted pausing and stalling after formation of the neck [1], which suggest that the origin of pausing/stalling is to be found in the physics of the budding process. Here, we show that the pausing/stalling observed in the simulations can be understood as a purely kinetic phenomenon associated with a \"geometrical\" energy barrier that must be overcome by capsid proteins diffusing along the membrane prior to incorporation into the viral capsid. This geometrical energy barrier is generated by the conflict between the positive Gauss curvature of the capsid and the large negative Gauss curvature of the neck region. The theory is compared with the Brownian simulations of the budding of enveloped viruses.\n\nAuthor summaryDespite intense study, the life-cycle of the HIV-1 virus continues to pose mysteries. One of these concerns the assembly of the HIV-1 virus inside infected host cells: it is interrupted at the very last moment. During the subsequent pause, HIV-1 recruits a complex cell machinery, the so-called \"ESCRT pathway\". The ESCRT proteins pinch-off the \"viral bud\" from the host cell. In this paper, we propose that the reason for the stalling emerges from the fundamental physics of the lipid membrane that surrounds the virus. The membrane mostly follows the spherical geometry of the virus, but in the pinch-off region the geometry is radically different: it resembles a neck. By combining numerical and analytical methods, we demonstrate that a neck geometry creates a barrier to protein entry, thus blocking proteins required to complete viral assembly. This \"geometrical barrier\" mechanism is general: such a barrier should form during assembly of all membrane-enveloped viruses - including the Ebola and Herpes viruses. Indeed many families of enveloped viruses also recruit the ESCRT machinery for pinch-off. A fundamental understanding of the budding process could enable a new strategy to combat enveloped viruses, based on selective stabilization of membrane neck geometries.

biophysics↗