Virus capsid assembly across different length scales inspire the development of virus-based biomaterials

Advancements in Functional Nanomaterials Inspired by Viral Particles

Virus-like particles (VLPs) are nanostructures composed of one or more structural proteins, exhibiting stable and symmetrical structures. Their precise compositions and dimensions provide versatile opportunities for modifications, enhancing their functionality. Consequently, VLP-based nanomaterials have gained widespread adoption across diverse domains. This review focuses on three key aspects: the mechanisms of viral capsid protein self-assembly into VLPs, design methods for constructing multifunctional VLPs, and strategies for synthesizing multidimensional nanomaterials using VLPs. It provides a comprehensive overview of the advancements in virus-inspired functional nanomaterials, encompassing VLP assembly, functionalization, and the synthesis of multidimensional nanomaterials. Additionally, this review explores future directions, opportunities, and challenges in the field of VLP-based nanomaterials, aiming to shed light on potential advancements and prospects in this exciting area of research.

Modeling reveals the strength of weak interactions in stacked-ring assembly

Cells employ many large macromolecular machines for the execution and regulation of processes that are vital for cell and organismal viability. Interestingly, cells cannot synthesize these machines as functioning units. Instead, cells synthesize the molecular parts that must then assemble into the functional complex. Many important machines, including chaperones such as GroEL and proteases such as the proteasome, comprise protein rings that are stacked on top of one another. While there is some experimental data regarding how stacked-ring complexes such as the proteasome self-assemble, a comprehensive understanding of the dynamics of stacked-ring assembly is currently lacking. Here, we developed a mathematical model of stacked-trimer assembly and performed an analysis of the assembly of the stacked homomeric trimer, which is the simplest stacked-ring architecture. We found that stacked rings are particularly susceptible to a form of kinetic trapping that we term "deadlock," in which the system gets stuck in a state where there are many large intermediates that are not the fully assembled structure but that cannot productively react. When interaction affinities are uniformly strong, deadlock severely limits assembly yield. We thus predicted that stacked rings would avoid situations where all interfaces in the structure have high affinity. Analysis of available crystal structures indicated that indeed the majority-if not all-of stacked trimers do not contain uniformly strong interactions. Finally, to better understand the origins of deadlock, we developed a formal pathway analysis and showed that, when all the binding affinities are strong, many of the possible pathways are utilized. In contrast, optimal assembly strategies utilize only a small number of pathways. Our work suggests that deadlock is a critical factor influencing the evolution of macromolecular machines and provides general principles for understanding the self-assembly efficiency of existing machines.

Structural Studies of Bacteriophage Φ6 and Its Transformations during Its Life Cycle

From the first isolation of the cystovirus bacteriophage Φ6 from Pseudomonas syringae 50 years ago, we have progressed to a better understanding of the structure and transformations of many parts of the virion. The three-layered virion, encapsulating the tripartite double-stranded RNA (dsRNA) genome, breaches the cell envelope upon infection, generates its own transcripts, and coopts the bacterial machinery to produce its proteins. The generation of a new virion starts with a procapsid with a contracted shape, followed by the packaging of single-stranded RNA segments with concurrent expansion of the capsid, and finally replication to reconstitute the dsRNA genome. The outer two layers are then added, and the fully formed virion released by cell lysis. Most of the procapsid structure, composed of the proteins P1, P2, P4, and P7 is now known, as well as its transformations to the mature, packaged nucleocapsid. The outer two layers are less well-studied. One additional study investigated the binding of the host protein YajQ to the infecting nucleocapsid, where it enhances the transcription of the large RNA segment that codes for the capsid proteins. Finally, I relate the structural aspects of bacteriophage Φ6 to those of other dsRNA viruses, noting the similarities and differences.

Higher-Order VLP-Based Protein Macromolecular Framework Structures Assembled via Coiled-Coil Interactions

Hierarchical organization is one of the fundamental features observed in biological systems that allows for efficient and effective functioning. Virus-like particles (VLPs) are elegant examples of a hierarchically organized supramolecular structure, where many subunits are self-assembled to generate the functional cage-like architecture. Utilizing VLPs as building blocks to construct two- and three-dimensional (3D) higher-order structures is an emerging research area in developing functional biomimetic materials. VLPs derived from P22 bacteriophages can be repurposed as nanoreactors by encapsulating enzymes and modular units to build higher-order catalytic materials via several techniques. In this study, we have used coiled-coil peptide interactions to mediate the P22 interparticle assembly into a highly stable, amorphous protein macromolecular framework (PMF) material, where the assembly does not depend on the VLP morphology, a limitation observed in previously reported P22 PMF assemblies. Many encapsulated enzymes lose their optimum functionalities under the harsh conditions that are required for the P22 VLP morphology transitions. Therefore, the coiled-coil-based PMF provides a fitting and versatile platform for constructing functional higher-order catalytic materials compatible with sensitive enzymes. We have characterized the material properties of the PMF and utilized the disordered PMF to construct a biocatalytic 3D material performing single- and multistep catalysis.

Characterization and genome analysis of G1 sub-cluster mycobacteriophage Lang

Phage therapy is revitalized as an alternative to antibiotics therapy against antimicrobials resistant pathogens. Mycobacteriophages are genetically diverse viruses that can specifically infect Mycobacterium genus including Mycobacterium tuberculosis and Mycobacterium smegmatis. Here, we isolated and annotated the genome of a mycobacteriophage Lang, a temperate mycobacteriophage isolated from the soil of Hohhot, Inner Mongolia, China, by using Mycolicibacterium smegmatis mc² 155 as the host. It belongs to the Siphoviridae family of Caudovirales as determined by transmission electron microscopy. The morphological characteristics and certain biological properties of the phage were considered in detail. Phage Lang genomes is 41,487 bp in length with 66.85% GC content and encodes 60 putative open reading frames and belongs to the G1 sub-cluster. Genome annotation indicated that genes for structure proteins, assembly proteins, replications/transcription and lysis of the host are present in function clucters. The genome sequence of phage Lang is more than 95% similar to that of mycobacteriophage Grizzly and Sweets, differing in substitutions, insertions and deletions in Lang. One-step growth curve revealed that Lang has a latent period of 30 min and a outbreak period of 90 min. The short latent period and rapid outbreak mark the unique properties of phage Lang, which can be another potential source for combating M. tuberculosis.

Fabrication of Protein Macromolecular Frameworks (PMFs) and Their Application in Catalytic Materials

The construction of three-dimensional (3D) array materials from nanoscale building blocks has drawn significant interest because of their potential to exhibit collective properties and functions arising from the interactions between individual building blocks. Protein cages such as virus-like particles (VLPs) have distinct advantages as building blocks for higher-order assemblies because they are extremely homogeneous in size and can be engineered with new functionalities by chemical and/or genetic modification. In this chapter, we describe a protocol for constructing a new class of protein-based superlattices, called protein macromolecular frameworks (PMFs). We also describe an exemplary method to evaluate the catalytic activity of enzyme-enclosed PMFs, which exhibit enhanced catalytic activity due to the preferential partitioning of charged substrates into the PMF.

Rapid Assembly and Prototyping of Biocatalytic Virus-like Particle Nanoreactors

Protein cages are attractive as molecular scaffolds for the fundamental study of enzymes and metabolons and for the creation of biocatalytic nanoreactors for in vitro and in vivo use. Virus-like particles (VLPs) such as those derived from the P22 bacteriophage capsid protein make versatile self-assembling protein cages and can be used to encapsulate a broad range of protein cargos. In vivo encapsulation of enzymes within VLPs requires fusion to the coat protein or a scaffold protein. However, the expression level, stability, and activity of cargo proteins can vary upon fusion. Moreover, it has been shown that molecular crowding of enzymes inside VLPs can affect their catalytic properties. Consequently, testing of numerous parameters is required for production of the most efficient nanoreactor for a given cargo enzyme. Here, we present a set of acceptor vectors that provide a quick and efficient way to build, test, and optimize cargo loading inside P22 VLPs. We prototyped the system using a yellow fluorescent protein and then applied it to mevalonate kinases (MKs), a key enzyme class in the industrially important terpene (isoprenoid) synthesis pathway. Different MKs required considerably different approaches to deliver maximal encapsulation as well as optimal kinetic parameters, demonstrating the value of being able to rapidly access a variety of encapsulation strategies. The vector system described here provides an approach to optimize cargo enzyme behavior in bespoke P22 nanoreactors. This will facilitate industrial applications as well as basic research on nanoreactor-cargo behavior.

Bioinspired Approaches to Self-Assembly of Virus-like Particles: From Molecules to Materials

ConspectusWhen viewed through the lens of materials science, nature provides a vast library of hierarchically organized structures that serve as inspiration and raw materials for new synthetic materials. The structural organization of complex bioarchitectures with advanced functions arises from the association of building blocks and is strongly supported by ubiquitous mechanisms of self-assembly, where interactions among components result in spontaneous assembly into defined structures. Viruses are exemplary, where a capsid structure, often formed from the self-assembly of many individual protein subunits, serves as a vehicle for the transport and protection of the viral genome. Higher-order assemblies of viral particles are also found in nature with unexpected collective behaviors. When the infectious aspect of viruses is removed, the self-assembly of viral particles and their potential for hierarchical assembly become an inspiration for the design and construction of a new class of functional materials at a range of different length scales.Salmonella typhimurium bacteriophage P22 is a well-studied model for understanding viral self-assembly and the construction of virus-like particle (VLP)-based materials. The formation of cage-like P22 VLP structures results from scaffold protein (SP)-directed self-assembly of coat protein (CP) subunits into icosahedral capsids with encapsulation of SP inside the capsid. Employing the CP-SP interaction during self-assembly, the encapsulation of guest protein cargos inside P22 VLPs can be achieved with control over the composition and the number of guest cargos. The morphology of cargo-loaded VLPs can be altered, along with changes in both the physical properties of the capsid and the cargo-capsid interactions, by mimicking aspects of the infectious P22 viral maturation. The structure of the capsid differentiates the inside cavity from the outside environment and serves as a protecting layer for the encapsulated cargos. Pores in the capsid shell regulate molecular exchange between inside and outside, where small molecules can traverse the capsid freely while the diffusion of larger molecules is limited by the pores. The interior cavity of the P22 capsid can be packed with hundreds of copies of cargo proteins (especially enzymes), enforcing intermolecular proximity, making this an ideal model system in which to study enzymatic catalysis in crowded and confined environments. These aspects highlight the development of functional nanomaterials from individual P22 VLPs, through biomimetic design and self-assembly, resulting in fabrication of nanoreactors with controlled catalytic behaviors.Individual P22 VLPs have been used as building blocks for the self-assembly of higher-order structures. This relies on a balance between the intrinsic interparticle repulsion and a tunable interparticle attraction. The ordering of VLPs within three-dimensional assemblies is dependent on the balance between repulsive and attractive interactions: too strong an attraction results in kinetically trapped disordered structures, while decreasing the attraction can lead to more ordered arrays. These higher-order assemblies display collective behavior of high charge density beyond those of the individual VLPs.The development of synthetic nanomaterials based on P22 VLPs demonstrates how the potential for hierarchical self-assembly can be applied to other self-assembling capsid structures across multiple length scales toward future bioinspired functional materials.

Nano-biotechnology, an applicable approach for sustainable future

Nanotechnology is one of the most emerging fields of research within recent decades and is based upon the exploitation of nano-sized materials (e.g., nanoparticles, nanotubes, nanomembranes, nanowires, nanofibers and so on) in various operational fields. Nanomaterials have multiple advantages, including high stability, target selectivity, and plasticity. Diverse biotic (e.g., Capsid of viruses and algae) and abiotic (e.g., Carbon, silver, gold and etc.) materials can be utilized in the synthesis process of nanomaterials. "Nanobiotechnology" is the combination of nanotechnology and biotechnology disciplines. Nano-based approaches are developed to improve the traditional biotechnological methods and overcome their limitations, such as the side effects caused by conventional therapies. Several studies have reported that nanobiotechnology has remarkably enhanced the efficiency of various techniques, including drug delivery, water and soil remediation, and enzymatic processes. In this review, techniques that benefit the most from nano-biotechnological approaches, are categorized into four major fields: medical, industrial, agricultural, and environmental.

Substrate Partitioning into Protein Macromolecular Frameworks for Enhanced Catalytic Turnover

Spatial partitioning of chemical processes is an important attribute of many biological systems, the effect of which is reflected in the high efficiency of enzymes found within otherwise chaotic cellular environments. Barriers, often provided through the formation of compartments or phase segregation, gate the access of macromolecules and small molecules within the cell and provide an added level of metabolic control. Taking inspiration from nature, we have designed virus-like particles (VLPs) as nanoreactor compartments that sequester enzyme catalysts and have used these as building blocks to construct 3D protein macromolecular framework (PMF) materials, which are structurally characterized using small-angle X-ray scattering (SAXS). The highly charged PMFs form a separate phase in suspension, and by tuning the ionic strength, we show positively charged molecules preferentially partition into the PMF, while negatively charged molecules are excluded. This molecular partitioning was exploited to tune the catalytic activity of enzymes enclosed within the individual particles in the PMF, the results of which showed that positively charged substrates had turnover rates that were 8500× faster than their negatively charged counterparts. Moreover, the catalytic PMF led to cooperative behavior resulting in charge dependent trends opposite to those observed with individual P22 nanoreactor particles.

Biophysical approaches to understand and re-purpose bacterial microcompartments

Bacterial microcompartments represent a modular class of prokaryotic organelles associated with metabolic processes. They harbor a congregation of enzymes that work in cascade within a small, confined volume. These sophisticated nano-engineered crafts of nature offer a tempting paradigm for the fabrication of biosynthetic nanoreactors. Repurposing bacterial microcompartments to develop nanostructures with desired functions requires a careful manipulation in their structural makeup and composition. This calls for a comprehensive understanding of all the interactions of the physical components which frame such molecular architectures. Over recent years, several biophysical techniques have been essential in illuminating the role played by bacterial microcompartments within cells, and have revealed crucial details regarding the morphology, physical properties and functions of their constituent proteins. This has promoted contemplation of ideas for engineering microcompartments inspired biomaterials with novel features and functions.

Protein cages as building blocks for superstructures

Proteins naturally self-assemble to function. Protein cages result from the self-assembly of multiple protein subunits that interact to form hollow symmetrical structures with functions that range from cargo storage to catalysis. Driven by self-assembly, building elegant higher-order superstructures with protein cages as building blocks has been an increasingly attractive field in recent years. It presents an engineering challenge not only at the molecular level but also at the supramolecular level. The higher-order constructs are proposed to provide access to diverse functional materials. Focussing on design strategy as a perspective, current work on protein cage supramolecular self-assembly are reviewed from three principles that are electrostatic, metal-ligand coordination and inherent symmetry. The review also summarises possible applications of the superstructure architecture built using modified protein cages.

Supramolecular virus-like particles by co-assembly of triblock polypolypeptide and PAMAM dendrimers

Virus-like particles are of special interest as functional delivery vehicles in a variety of fields ranging from nanomedicine to materials science. Controlled formation of virus-like particles relies on manipulating the assembly of the viral coat proteins. Herein, we report a new assembly system based on a triblock polypolypeptide C4-S10-BK12 and -COONa terminated PAMAM dendrimers. The polypolypeptide has a cationic BK12 block with 12 lysines; its binding with anionic PAMAM triggers the folding of the peptide's middle silk-like block and leads to formation of virus-like nanorods, stabilized against aggregation by the long hydrophilic "C" block of the polypeptide. Varying the dendrimer/polypeptide mixing ratio hardly influences the structure and size of the nanorod. However, increasing the dendrimer generation, that is, increasing the dendrimer size results in increased particle length and height, without affecting the width of the nanorod. The branched structure and well-defined size of the dendrimers allows delicate control of the particle size; it is impossible to achieve similar control over assembly of the polypeptide with linear polyelectrolyte as template. In conclusion, we report a novel protein assembling system with properties resembling a viral coat; the findings may therefore be helpful for designing functional virus-like particles like vaccines.

Polymer Coatings on Virus-like Particle Nanoreactors at Low Ionic Strength-Charge Reversal and Substrate Access

Virus-like particles (VLPs) are a class of biomaterials which serve as platforms for achieving the desired functionality through interior and exterior modifications. Through ionic strength-mediated electrostatic interactions, VLPs have been assembled into hierarchically ordered materials. This work builds on predictive models to prepare polymer-coated VLP clusters at very low ionic strength. Zeta potential measurements showed that the clusters carried a strongly positive charge, a complete charge reversal from the VLP building block. SAXS analysis confirmed polymer adsorption onto the VLP exterior. We then studied the activity of an encapsulated enzyme toward small molecular and macromolecular substrates to determine the effect of each component of the hierarchically assembled material. We found that while encapsulation and polymer coating did not have a large effect on access to the enzyme by its native, small molecular substrate, substrate modification with a macromolecule caused the polymer coating and encapsulation to affect the access to the enzyme.

Enzyme encapsulation by protein cages

Protein cages are hollow protein shells with a nanometric cavity that can be filled with useful materials. The encapsulating nature of the cages means that they are particularly attractive for loading with biological macromolecules, affording the guests protection in conditions where they may be degraded. Given the importance of proteins in both industrial and all cellular processes, encapsulation of functional protein cargoes, particularly enzymes, are of high interest both for in vivo diagnostic and therapeutic use as well as for ex vivo applications. Increasing knowledge of protein cage structures at high resolution along with recent advances in producing artificial protein cages means that they can now be designed with various attachment chemistries on their internal surfaces - a useful tool for cargo capture. Here we review the different available attachment strategies that have recently been successfully demonstrated for enzyme encapsulation in protein cages and consider their future potential.

Tuning the catalytic properties of P22 nanoreactors through compositional control

Enzymes are biomacromolecular protein catalysts that are widely used in a plethora of industrial-scale applications due to their high selectivity, efficiency and ability to work under mild conditions. Many industrial processes require the immobilization of enzymes to enhance their performance and stability. Encapsulation of enzymes in protein cages provides an excellent immobilization platform to create nanoreactors with enhanced enzymatic stability and desired catalytic activities. Here we show that the catalytic activity of nanoreactors, derived from the bacteriophage P22 viral capsids, can be finely-tuned by controlling the packaging stoichiometry and packing density of encapsulated enzymes. The packaging stoichiometry of the enzyme alcohol dehydrogenase (AdhD) was controlled by co-encapsulating it with wild-type scaffold protein (wtSP) at different stoichiometric ratios using an in vitro assembly approach and the packing density was controlled by selectively removing wtSP from the assembled nanoreactors. An inverse relationship was observed between the catalytic activity (k_cat) of AdhD enzyme and the concentration of co-encapsulated wtSP. Selective removal of the wtSP resulted in the similar activity of AdhD in all nanoreactors despite the difference in the volume occupied by enzymes inside nanoreactors, indicating that the AdhD enzymes do not experience self-crowding even under high molarity of confinement (M_conf) conditions. The approach demonstrated here not only allowed us to tailor the activity of encapsulated AdhD catalysts but also the overall functional output of nanoreactors (enzyme-VLP complex). The approach also allowed us to differentiate the effects of crowding and confinement on the functional properties of enzymes encapsulated in an enclosed system, which could pave the way for designing more efficient nanoreactors.

From stars to stripes: RNA-directed shaping of plant viral protein templates-structural synthetic virology for smart biohybrid nanostructures

The self-assembly of viral building blocks bears exciting prospects for fabricating new types of bionanoparticles with multivalent protein shells. These enable a spatially controlled immobilization of functionalities at highest surface densities-an increasing demand worldwide for applications from vaccination to tissue engineering, biocatalysis, and sensing. Certain plant viruses hold particular promise because they are sustainably available, biodegradable, nonpathogenic for mammals, and amenable to in vitro self-organization of virus-like particles. This offers great opportunities for their redesign into novel "green" carrier systems by spatial and structural synthetic biology approaches, as worked out here for the robust nanotubular tobacco mosaic virus (TMV) as prime example. Natural TMV of 300 x 18 nm is built from more than 2,100 identical coat proteins (CPs) helically arranged around a 6,395 nucleotides ssRNA. In vitro, TMV-like particles (TLPs) may self-assemble also from modified CPs and RNAs if the latter contain an Origin of Assembly structure, which initiates a bidirectional encapsidation. By way of tailored RNA, the process can be reprogrammed to yield uncommon shapes such as branched nanoobjects. The nonsymmetric mechanism also proceeds on 3'-terminally immobilized RNA and can integrate distinct CP types in blends or serially. Other emerging plant virus-deduced systems include the usually isometric cowpea chlorotic mottle virus (CCMV) with further strikingly altered structures up to "cherrybombs" with protruding nucleic acids. Cartoon strips and pictorial descriptions of major RNA-based strategies induct the reader into a rare field of nanoconstruction that can give rise to utile soft-matter architectures for complex tasks. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures.