Functional enzyme-polymer complexes.

SignificanceThe use of biological enzyme catalysts could have huge ramifications for chemical industries. However, these enzymes are often inactive in nonbiological conditions, such as high temperatures, present in industrial settings. Here, we show that the enzyme PETase (polyethylene terephthalate [PET]), with potential application in plastic recycling, is stabilized at elevated temperature through complexation with random copolymers. We demonstrate this through simulations and experiments on different types of substrates. Our simulations also provide strategies for designing more enzymatically active complexes by altering polymer composition and enzyme charge distribution.

Tailoring Interactions of Random Copolymer Polyelectrolyte Complexes to Remove Nanoplastic Contaminants from Water.

We investigate the usage of polyelectrolyte complex materials for water remediation purposes, specifically their ability to remove nanoplastics from water, on which there is currently little to no prior research. We demonstrate that oppositely charged random copolymers are effective at quantitatively removing nanoplastic contamination from aqueous solution. The mechanisms underlying this remediation ability are explored through computational simulations, with corroborating quartz crystal microbalance adsorption experiments. We find that hydrophobic nanostructures and interactions likely play an important role.

Many Body Effects and Icosahedral Order in Superlattice Self-Assembly.

We elucidate how nanocrystals "bond" to form ordered structures. For that purpose we consider nanocrystal configurations consisting of regular polygons and polyhedra, which are the motifs that constitute single component and binary nanocrystal superlattices, and simulate them using united atom models. We compute the free energy and quantify many body effects, i.e., those that cannot be accounted for by pair potential (two-body) interactions, further showing that they arise from coalescing vortices of capping ligands. We find that such vortex textures exist for configurations with local coordination number ≤6. For higher coordination numbers, vortices are expelled and nanocrystals arrange in configurations with tetrahedral or icosahedral order. We provide explicit formulas for the optimal separations between nanocrystals, which correspond to the minima of the free energies. Our results quantitatively explain the structure of superlattice nanocrystals as reported in experiments and reveal how packing arguments, extended to include soft components, predict ordered nanocrystal aggregation.

Potential of mean force for two nanocrystals: Core geometry and size, hydrocarbon unsaturation, and universality with respect to the force field.

We present a detailed analysis of the interaction between two nanocrystals capped with ligands consisting of hydrocarbon chains by united atom molecular dynamics simulations. We analyze large cores (up to 10 nm in diameter) and ligands with unsaturated carbon bonds (oleic acid) and we investigate the accuracy of the computed potential of mean force by comparing different force fields. We also analyze the vortices that determine the bonding, including the case of asymmetric nanocrystals, and discuss effects related to the intrinsic anisotropy of the core. Overall our results are in agreement with the predictions of the recently proposed orbifold topological model.

Patterning of multicomponent elastic shells by gaussian curvature.

Recent findings suggest that shell protein distribution and the morphology of bacterial microcompartments regulate the chemical fluxes facilitating reactions which dictate their biological function. We explore how the morphology and component patterning are coupled through the competition of mean and gaussian bending energies in multicomponent elastic shells that form three-component irregular polyhedra. We observe two softer components with lower bending rigidities allocated on the edges and vertices while the harder component occupies the faces. When subjected to a nonzero interfacial line tension, the two softer components further separate and pattern into subdomains that are mediated by the gaussian curvature. We find that this degree of fractionation is maximized when there is a weaker line tension and when the ratio of bending rigidities between the two softer domains ≈2. Our results reveal a patterning mechanism in multicomponent shells that can capture the observed morphologies of bacterial microcompartments, and moreover, can be realized in synthetic vesicles.

Kinetic Growth of Multicomponent Microcompartment Shells.

An important goal of systems and synthetic biology is to produce high value chemical species in large quantities. Microcompartments, which are protein nanoshells encapsulating catalytic enzyme cargo, could potentially function as tunable nanobioreactors inside and outside cells to generate these high value species. Modifying the morphology of microcompartments through genetic engineering of shell proteins is one viable strategy to tune cofactor and metabolite access to encapsulated enzymes. However, this is a difficult task without understanding how changing interactions between the many different types of shell proteins and enzymes affect microcompartment assembly and shape. Here, we use multiscale molecular dynamics and experimental data to describe assembly pathways available to microcompartments composed of multiple types of shell proteins with varied interactions. As the average interaction between the enzyme cargo and the multiple types of shell proteins is weakened, the shell assembly pathway transitions from (i) nucleating on the enzyme cargo to (ii) nucleating in the bulk and then binding the cargo as it grows to (iii) an empty shell. Atomistic simulations and experiments using the 1,2-propanediol utilization microcompartment system demonstrate that shell protein interactions are highly varied and consistent with our multicomponent, coarse-grained model. Furthermore, our results suggest that intrinsic bending angles control the size of these microcompartments. Overall, our simulations and experiments provide guidance to control microcomparmtent size and assembly by modulating the interactions between shell proteins.

Vertex protein PduN tunes encapsulated pathway performance by dictating bacterial metabolosome morphology.

Engineering subcellular organization in microbes shows great promise in addressing bottlenecks in metabolic engineering efforts; however, rules guiding selection of an organization strategy or platform are lacking. Here, we study compartment morphology as a factor in mediating encapsulated pathway performance. Using the 1,2-propanediol utilization microcompartment (Pdu MCP) system from Salmonella enterica serovar Typhimurium LT2, we find that we can shift the morphology of this protein nanoreactor from polyhedral to tubular by removing vertex protein PduN. Analysis of the metabolic function between these Pdu microtubes (MTs) shows that they provide a diffusional barrier capable of shielding the cytosol from a toxic pathway intermediate, similar to native MCPs. However, kinetic modeling suggests that the different surface area to volume ratios of MCP and MT structures alters encapsulated pathway performance. Finally, we report a microscopy-based assay that permits rapid assessment of Pdu MT formation to enable future engineering efforts on these structures.

Heterogeneous Charged Complexes of Random Copolymers for the Segregation of Organic Molecules.

Nature harnesses the disorder of intrinsically disordered proteins to organize enzymes and biopolymers into membraneless organelles. The heterogeneous nature of synthetic random copolymers with charged, polar, and hydrophobic groups has been exploited to mimic intrinsically disordered proteins, forming complexes with enzymatically active proteins and delivering them into nonbiological environments. Here, the properties of polyelectrolyte complexes composed of two random copolymer polyelectrolytes are studied experimentally and via simulation with the aim of exploiting such complexes for segregating organic molecules from water. The anionic polyelectrolyte contains hydrophilic and hydrophobic side chains and forms self-assembled hydrophobic domains. The cationic polymer is a high-molecular-weight copolymer of hydrophilic and charged side groups and acts as a flocculant. We find that the polyelectrolyte complexes obtained with this anionic and cationic random copolymer system are capable of absorbing small cationic, anionic, and hydrophobic organic molecules, including perfluorooctanoic acid, a compound of great environmental and toxicologic concern. Importantly, these macroscopic complexes can be easily removed from water, thereby providing a simple approach for organic contaminant removal in aqueous media. MARTINI and coarse-grained molecular dynamics simulations explore how the microscale heterogeneity of these random copolymer complexes relates to their segregation functionality.

Assembly and Stability of Simian Virus 40 Polymorphs.

Understanding viral assembly pathways is of critical importance to biology, medicine, and nanotechology. Here, we study the assembly path of a system with various structures, the simian vacuolating virus 40 (SV40) polymorphs. We simulate the templated assembly process of VP1 pentamers, which are the constituents of SV40, into icosahedal shells made of N = 12 pentamers (T = 1). The simulations include connections formed between pentamers by C-terminal flexible lateral units, termed here "C-terminal ligands", which are shown to control assembly behavior and shell dynamics. The model also incorporates electrostatic attractions between the N-terminal peptide strands (ligands) and the negatively charged cargo, allowing for agreement with experiments of RNA templated assembly at various pH and ionic conditions. During viral assembly, pentamers bound to any template increase its effective size due to the length and flexibility of the C-terminal ligands, which can connect to other VP1 pentamers and recruit them to a partially completed capsid. All closed shells formed other than the T = 1 feature the ability to dynamically rearrange and are thus termed "pseudo-closed". The N = 13 shell can even spontaneously "self-correct" by losing a pentamer and become a T = 1 capsid when the template size fluctuates. Bound pentamers recruiting additional pentamers to dynamically rearranging capsids allow closed shells to continue growing via the pseudo-closed growth mechanism, for which experimental evidence already exists. Overall, we show that the C-terminal ligands control the dynamic assembly paths of SV40 polymorphs.

Capping Ligand Vortices as "Atomic Orbitals" in Nanocrystal Self-Assembly.

We present a detailed analysis of the interaction between two nanocrystals capped with ligands consisting of hydrocarbon chains by united atom molecular dynamics simulations. We show that the bonding of two nanocrystals is characterized by ligand textures in the form of vortices. These results are generalized to nanocrystals of different types (differing core and ligand sizes) where the structure of the vortices depends on the softness asymmetry. We provide rigorous calculations for the binding free energy, show that these energies are independent of the chemical composition of the cores, and derive analytical formulas for the equilibrium separation. We discuss the implications of our results for the self-assembly of single-component and binary nanoparticle superlattices. Overall, our results show that the structure of the ligands completely determines the bonding of nanocrystals, fully supporting the predictions of the recently proposed Orbifold topological model.