Shape control of deformable charge-patterned nanoparticles.

Deformable nanoparticles (NPs) offer unprecedented opportunities as dynamic building blocks that can spontaneously reconfigure during assembly in response to environmental cues. Designing reconfigurable materials based on deformable NPs hinges on an understanding of the shapes that can be engineered in these NPs. We solve for the low-energy shapes of charge-patterned deformable NPs by using molecular dynamics-based simulated annealing to minimize a coarse-grained model Hamiltonian characterized with NP elastic and electrostatic energies subject to a volume constraint. We show that deformable spherical NPs of radius 50 nm whose surface is tailored with octahedrally distributed charged patches and double-cap charged patches adapt their shape differently in response to changes in surface charge coverage and ionic strength. We find shape transitions to rounded octahedra, faceted octahedra, faceted bowls, oblate spheroids, spherocylinders, dented beans, and dimpled rounded bowls. We demonstrate that similar shape transitions can be achieved in deformable NPs of different sizes. The effects of counterion condensation on the free-energetic drive associated with the observed deformations are examined via Manning model calculations that utilize simulation-derived estimates for the NP Coulomb energy under salt-free conditions. The charge-pattern-based shape control of deformable NPs has implications for the design of responsive nanocontainers and for assembling reconfigurable materials whose functionality hinges on the shape-shifting properties of their nanoscale building blocks.

Multilayered Ordered Protein Arrays Self-Assembled from a Mixed Population of Virus-like Particles.

Biology shows many examples of spatially controlled assembly of cells and biomacromolecules into hierarchically organized structures, to which many of the complex biological functions are attributed. While such biological structures have inspired the design of synthetic materials, it is still a great challenge to control the spatial arrangement of individual building blocks when assembling multiple types of components into bulk materials. Here, we report self-assembly of multilayered, ordered protein arrays from mixed populations of virus-like particles (VLPs). We systematically tuned the magnitude of the surface charge of the VLPs via mutagenesis to prepare four different types of VLPs for mixing. A mixture of up to four types of VLPs selectively assembled into higher-order structures in the presence of oppositely charged dendrimers during a gradual lowering of the ionic strength of the solution. The assembly resulted in the formation of three-dimensional ordered VLP arrays with up to four distinct layers including a central core, with each layer comprising a single type of VLP. A coarse-grained computational model was developed and simulated using molecular dynamics to probe the formation of the multilayered, core-shell structure. Our findings establish a simple and versatile bottom-up strategy to synthesize multilayered, ordered materials by controlling the spatial arrangement of multiple types of nanoscale building blocks in a one-pot fabrication.

In Silico Development of Combinatorial Therapeutic Approaches Targeting Key Signaling Pathways in Metabolic Syndrome.

PURPOSE: Dysregulations of key signaling pathways in metabolic syndrome are multifactorial, eventually leading to cardiovascular events. Hyperglycemia in conjunction with dyslipidemia induces insulin resistance and provokes release of proinflammatory cytokines resulting in chronic inflammation, accelerated lipid peroxidation with further development of atherosclerotic alterations and diabetes. We have proposed a novel combinatorial approach using FDA approved compounds targeting IL-17a and DPP4 to ameliorate a significant portion of the clustered clinical risks in patients with metabolic syndrome. In our current research we have modeled the outcomes of metabolic syndrome treatment using two distinct drug classes. METHODS: Targets were chosen based on the clustered clinical risks in metabolic syndrome: dyslipidemia, insulin resistance, impaired glucose control, and chronic inflammation. Drug development platform, BIOiSIM™, was used to narrow down two different drug classes with distinct modes of action and modalities. Pharmacokinetic and pharmacodynamic profiles of the most promising drugs were modeling showing predicted outcomes of combinatorial therapeutic interventions. RESULTS: Preliminary studies demonstrated that the most promising drugs belong to DPP-4 inhibitors and IL-17A inhibitors. Evogliptin was chosen to be a candidate for regulating glucose control with long term collateral benefit of weight loss and improved lipid profiles. Secukinumab, an IL-17A sequestering agent used in treating psoriasis, was selected as a repurposed candidate to address the sequential inflammatory disorders that follow the first metabolic insult. CONCLUSIONS: Our analysis suggests this novel combinatorial therapeutic approach inducing DPP4 and Il-17a suppression has a high likelihood of ameliorating a significant portion of the clustered clinical risk in metabolic syndrome.

Percolation Theory Reveals Biophysical Properties of Virus-like Particles.

The viral protein containers that encapsulate a virus' genetic material are repurposed as virus-like particles in a host of nanotechnology applications, including cargo delivery, storage, catalysis, and vaccination. These viral architectures have evolved to sit on the knife's edge between stability, to provide adequate protection for their genetic cargoes, and instability, to enable their efficient and timely release in the host cell environment upon environmental cues. By introducing a percolation theory for viral capsids, we demonstrate that the geometric characteristics of a viral capsid in terms of its subunit layout and intersubunit interaction network are key for its disassembly behavior. A comparative analysis of all alternative homogeneously tiled capsid structures of the same stoichiometry identifies evolutionary drivers favoring specific viral geometries in nature and offers a guide for virus-like particle design in nanotechnology.

Designing Surface Charge Patterns for Shape Control of Deformable Nanoparticles.

Designing reconfigurable materials based on deformable nanoparticles (NPs) hinges on an understanding of the energetically favored shapes these NPs can adopt. Using simulations, we show that hollow, deformable, patchy NPs tailored with surface charge patterns such as Janus patches, stripes, and polyhedrally distributed patches differently adapt their shape in response to changes in patterns and ionic strength, transforming into capsules, hemispheres, variably dimpled bowls, and polyhedra. The links between anisotropy in NP surface charge, shape, and the elastic energy density are discussed.

Computational studies of shape control of charged deformable nanocontainers.

Biological matter is often compartmentalized by soft membranes that dynamically change their shape in response to chemical and mechanical cues. Deformable soft-matter-based nanoscale membranes or nanocontainers that mimic this behavior can be used as drug-delivery carriers that can adapt to evolving physiological conditions, or as dynamic building blocks for the design of novel hierarchical materials via assembly engineering. Here, we connect the intrinsic features of charged deformable nanocontainers such as their size, charge, surface tension, and elasticity with their equilibrium shapes for a wide range of solution conditions using molecular dynamics simulations. These links identify the fundamental mechanisms that establish the chemical and materials design control strategies for modulating the equilibrium shape of these nanocontainers. We show that flexible nanocontainers of radii ranging from 10-20 nm exhibit sphere-to-rod-to-disc shape transitions yielding rods and discs over a wide range of aspect ratio λ (0.3 < λ < 5). The shape transitions can be controlled by tuning salt and/or surfactant concentration as well as material elastic parameters. The shape changes are driven by reduction in the global electrostatic energy and are associated with dramatic changes in local surface elastic energy distributions. To illustrate the shape transition mechanisms, exact analytical calculations for idealized spheroidal nanocontainers in salt-free conditions are performed. Explicit counterion simulations near nanocontainers and associated Manning model calculations provide an assessment of the stability of observed shape deformations in the event of ion condensation.

Linker-Mediated Assembly of Virus-Like Particles into Ordered Arrays via Electrostatic Control.

Nanoscale virus-like particles (VLPs), which are self-assembled from protein subunits, offer the possibility of generating hierarchically assembled functional materials such as biomimetic catalytic systems and optical metamaterials. We explore the capacity to control and tune a higher-order assembly of VLPs into ordered array materials over a wide range of ionic conditions using a combination of experimental and computational methods. The integrated methodology demonstrates that P22 VLP variants, genetically engineered to exhibit different surface charges, self-assemble into ordered arrays in the presence of PAMAM dendrimers acting as oppositely charged, macromolecular linkers. Ordered assembly occurs at an optimal ionic strength that strongly correlates with the VLP surface charge. The ordered VLP arrays exhibit the same long-range order and a similar configuration of VLP-bound dendrimers, regardless of the VLP surface charge. The experimentally validated model identifies key electrostatic and kinetic mechanisms underlying the self-assembly process and guides the modulation of dendrimer concentration as a control parameter to tune the assembly of VLPs. The integrated approach opens new design and control strategies to fabricate active functional materials via the self-assembly of engineered VLPs.

Competition between Normative and Drug-Induced Virus Self-Assembly Observed with Single-Particle Methods.

Disruption of virus capsid assembly has compelling antiviral potential that has been applied to hepatitis B virus (HBV). HBV core protein assembly can be modulated by heteroaryldihydropyrimidines (HAPs), and such molecules are collectively termed core protein allosteric modulators (CpAMs). Although the antiviral effects of CpAMs are acknowledged, the mechanism of action remains an open question. Challenging aspects of characterizing misdirected assembly are the large size and nonuniform nature of the final particles. In this study of HBV assembly, we observed a competition between normative and CpAM-induced aberrant assembly with electron microscopy and resistive-pulse sensing on nanofluidic devices. This competition was a function of the strength of the association energy between individual core proteins, which is proportional to ionic strength. At strong association energy, assembly reactions primarily yielded morphologically normal HBV capsids, despite the presence of HAP-TAMRA. At weak association energy, HAP-TAMRA led to increased assembly product size and disrupted morphology. The smallest particles were T = 4 icosahedra, whereas the larger particles were defective spheres, ellipsoids, and bacilliform cylinders, with regions of T = 4 geometry interspersed with flat regions. Deviation from spherical geometry progressively increased with particle size, which is consistent with the interpretation of a competition between two alternative assembly pathways.

Molecular jenga: the percolation phase transition (collapse) in virus capsids.

Virus capsids are polymeric protein shells that protect the viral cargo. About half of known virus families have icosahedral capsids that self-assemble from tens to thousands of subunits. Capsid disassembly is critical to the lifecycles of many viruses yet is poorly understood. Here, we apply a graph and percolation theory to examine the effect of removing capsid subunits on capsid stability and fragmentation. Based on the structure of the icosahedral capsid of hepatitis B virus (HBV), we constructed a graph of rhombic subunits arranged with icosahedral symmetry. Though our approach neglects dependence on energetics, time, and molecular detail, it quantitatively predicts a percolation phase transition consistent with recent in vitro studies of HBV capsid dissociation. While the stability of the capsid graph followed a gradual quadratic decay, the rhombic tiling abruptly fragmented when we removed more than 25% of the 120 subunits, near the percolation threshold observed experimentally. This threshold may also affect results of capsid assembly, which also experimentally produces a preponderance of 90 mer intermediates, as the intermediate steps in these reactions are reversible and can thus resemble dissociation. Application of percolation theory to understanding capsid association and dissociation may prove a general approach to relating virus biology to the underlying biophysics of the virus particle.

A molecular breadboard: Removal and replacement of subunits in a hepatitis B virus capsid.

Hepatitis B virus (HBV) core protein is a model system for studying assembly and disassembly of icosahedral structures. Controlling disassembly will allow re-engineering the 120 subunit HBV capsid, making it a molecular breadboard. We examined removal of subunits from partially crosslinked capsids to form stable incomplete particles. To characterize incomplete capsids, we used two single molecule techniques, resistive-pulse sensing and charge detection mass spectrometry. We expected to find a binomial distribution of capsid fragments. Instead, we found a preponderance of 3 MDa complexes (90 subunits) and no fragments smaller than 3 MDa. We also found 90-mers in the disassembly of uncrosslinked HBV capsids. 90-mers seem to be a common pause point in disassembly reactions. Partly explaining this result, graph theory simulations have showed a threshold for capsid stability between 80 and 90 subunits. To test a molecular breadboard concept, we showed that missing subunits could be refilled resulting in chimeric, 120 subunit particles. This result may be a means of assembling unique capsids with functional decorations.