Nanoscale protein assemblies from a circular permutant of the tobacco mosaic virus

Chemical technology principles for selective bioconjugation of proteins and antibodies

Proteins are multifunctional large organic compounds that constitute an essential component of a living system. Hence, control over their bioconjugation impacts science at the chemistry-biology-medicine interface. A chemical toolbox for their precision engineering can boost healthcare and open a gateway for directed or precision therapeutics. Such a chemical toolbox remained elusive for a long time due to the complexity presented by the large pool of functional groups. The precise single-site modification of a protein requires a method to address a combination of selectivity attributes. This review focuses on guiding principles that can segregate them to simplify the task for a chemical method. Such a disintegration systematically employs a multi-step chemical transformation to deconvolute the selectivity challenges. It constitutes a disintegrate (DIN) theory that offers additional control parameters for tuning precision in protein bioconjugation. This review outlines the selectivity hurdles faced by chemical methods. It elaborates on the developments in the perspective of DIN theory to demonstrate simultaneous regulation of reactivity, chemoselectivity, site-selectivity, modularity, residue specificity, and protein specificity. It discusses the progress of such methods to construct protein and antibody conjugates for biologics, including antibody-fluorophore and antibody-drug conjugates (AFCs and ADCs). It also briefs how this knowledge can assist in developing small molecule-based covalent inhibitors. In the process, it highlights an opportunity for hypothesis-driven routes to accelerate discoveries of selective methods and establish new targetome in the precision engineering of proteins and antibodies.

A Membrane-Associated Light-Harvesting Model is Enabled by Functionalized Assemblies of Gene-Doubled TMV Proteins

Photosynthetic light harvesting requires efficient energy transfer within dynamic networks of light-harvesting complexes embedded within phospholipid membranes. Artificial light-harvesting models are valuable tools for understanding the structural features underpinning energy absorption and transfer within chromophore arrays. Here, a method for attaching a protein-based light-harvesting model to a planar, fluid supported lipid bilayer (SLB) is developed.  The protein model consists of the tobacco mosaic viral capsid proteins that are gene-doubled to create a tandem dimer (dTMV). Assemblies of dTMV break the facial symmetry of the double disk to allow for differentiation between the disk faces. A single reactive lysine residue is incorporated into the dTMV assemblies for the site-selective attachment of chromophores for light absorption. On the opposing dTMV face, a cysteine residue is incorporated for the bioconjugation of a peptide containing a polyhistidine tag for association with SLBs. The dual-modified dTMV complexes show significant association with SLBs and exhibit mobility on the bilayer. The techniques used herein offer a new method for protein-surface attachment and provide a platform for evaluating excited state energy transfer events in a dynamic, fully synthetic artificial light-harvesting system.

Cascade Energy Transfer in Biopolymer-Templated Multi-Chromophoric Assemblies: Ratiometric Temperature Sensing

Natural light-harvesting complexes collect energy from sunlight and transfer it to the reaction center through a cascade of energy and electron transfer steps. Artificial light-harvesting systems functioning in aqueous media mimic natural photosynthetic systems. However, their design remains a challenging task as closely packed antenna chromophores often undergo severe self-quenching. Herein, we report luminescent co-assemblies between cationic pyrene-appended imidazolium amphiphiles and two anionic biopolymeric scaffolds, heparin and DNA in aqueous media. These co-assemblies served as excellent platforms for constructing artificial light-harvesting systems as upon co-embedding of multiple external dyes, highly efficient single-step and cascade energy transfer was observed from the pyrene donors to the acceptor dyes. Most notably, the efficiency of the energy transfer process was possible to modulate by employing multiple stimuli such as pH and temperature, and this resulted in the generation of multi-color luminescent materials in solution and film states, and they were also exploited in ratiometric temperature sensing. Their stimuli-responsive luminescence in the solid state was found to be advantageous for encryption studies.

Characterizing Heterogeneous Mixtures of Assembled States of the Tobacco Mosaic Virus Using Charge Detection Mass Spectrometry

The tobacco mosaic viral capsid protein (TMV) is a frequent target for derivatization for myriad applications, including drug delivery, biosensing, and light harvesting. However, solutions of the stacked disk assembly state of TMV are difficult to characterize quantitatively due to their large size and multiple assembled states. Charge detection mass spectrometry (CDMS) addresses the need to characterize heterogeneous populations of large protein complexes in solution quickly and accurately. Using CDMS, previously unobserved assembly states of TMV, including 16-monomer disks and odd-numbered disk stacks, have been characterized. We additionally employed a peptide-protein conjugation reaction in conjunction with CDMS to demonstrate that modified TMV proteins do not redistribute between disks. Finally, this technique was used to discriminate between protein complexes of near-identical mass but different configurations. We have gained a greater understanding of the behavior of TMV, a protein used across a broad variety of fields and applications, in the solution state.

Apodization Specific Fitting for Improved Resolution, Charge Measurement, and Data Analysis Speed in Charge Detection Mass Spectrometry

Short-time Fourier transforms with short segment lengths are typically used to analyze single ion charge detection mass spectrometry (CDMS) data either to overcome effects of frequency shifts that may occur during the trapping period or to more precisely determine the time at which an ion changes mass or charge, or enters an unstable orbit. The short segment lengths can lead to scalloping loss unless a large number of zero-fills are used, making computational time a significant factor in real-time analysis of data. Apodization specific fitting leads to a 9-fold reduction in computation time compared to zero-filling to a similar extent of accuracy. This makes possible real-time data analysis using a standard desktop computer. Rectangular apodization leads to higher resolution than the more commonly used Gaussian or Hann apodization and makes it possible to separate ions with similar frequencies, a significant advantage for experiments in which the masses of many individual ions are measured simultaneously. Equally important is a >20% increase in S/N obtained with rectangular apodization compared to Gaussian or Hann, which directly translates to a corresponding improvement in accuracy of both charge measurements and ion energy measurements that rely on the amplitudes of the fundamental and harmonic frequencies. Combined with computing the fast Fourier transform in a lower-level language, this fitting procedure eliminates computational barriers and should enable real-time processing of CDMS data on a laptop computer.

Effects of Molecular Size on Resolution in Charge Detection Mass Spectrometry

Instrumental resolution of Fourier transform-charge detection mass spectrometry instruments with electrostatic ion trap detection of individual ions depends on the precision with which ion energy is determined. Energy can be selected using ion optic filters or from harmonic amplitude ratios (HARs) that provide Fellgett's advantage and eliminate the necessity of ion transmission loss to improve resolution. Unlike the ion energy-filtering method, the resolution of the HAR method increases with charge (improved S/N) and thus with mass. An analysis of the HAR method with current instrumentation indicates that higher resolution can be obtained with the HAR method than the best resolution demonstrated for instruments with energy-selective optics for ions in the low MDa range and above. However, this gain is typically unrealized because the resolution obtainable with molecular systems in this mass range is limited by sample heterogeneity. This phenomenon is illustrated with both tobacco mosaic virus (0.6-2.7 MDa) and AAV9 (3.7-4.7 MDa) samples where mass spectral resolution is limited by the sample, including salt adducts, and not by instrument resolution. Nevertheless, the ratio of full to empty AAV9 capsids and the included genome mass can be accurately obtained in a few minutes from 1× PBS buffer solution and an elution buffer containing 300+ mM nonvolatile content despite extensive adduction and lower resolution. Empty and full capsids adduct similarly indicating that salts encrust the complexes during late stages of droplet evaporation and that mass shifts can be calibrated in order to obtain accurate analyte masses even from highly salty solutions.

Alcohol-perturbed self-assembly of the tobacco mosaic virus coat protein

The self-assembly of the tobacco mosaic virus coat protein is significantly altered in alcohol-water mixtures. Alcohol cosolvents stabilize the disk aggregate and prevent the formation of helical rods at low pH. A high alcohol content favours stacked disk assemblies and large rafts, while a low alcohol concentration favours individual disks and short stacks. These effects appear to be caused by the hydrophobicity of the alcohol additive, with isopropyl alcohol having the strongest effect and methanol the weakest. We discuss several effects that may contribute to preventing the protein-protein interactions between disks that are necessary to form helical rods.

Restricted valency (NPNA)n repeats and junctional epitope-based circumsporozoite protein vaccines against Plasmodium falciparum

The Circumsporozoite Protein (CSP) of Plasmodium falciparum contains an N-terminal region, a conserved Region I (RI), a junctional region, 25-42 copies of major (NPNA) and minor repeats followed by a C-terminal domain. The recently approved malaria vaccine, RTS,S/AS01 contains NPNAx19 and the C-terminal region of CSP. The efficacy of RTS,S against natural infection is low and short-lived, and mapping epitopes of inhibitory monoclonal antibodies may allow for rational improvement of CSP vaccines. Tobacco Mosaic Virus (TMV) was used here to display the junctional epitope (mAb CIS43), Region I (mAb 5D5), NPNAx5, and NPNAx20 epitope of CSP (mAbs 317 and 580). Protection studies in mice revealed that Region I did not elicit protective antibodies, and polyclonal antibodies against the junctional epitope showed equivalent protection to NPNAx5. Combining the junctional and NPNAx5 epitopes reduced immunogenicity and efficacy, and increasing the repeat valency to NPNAx20 did not improve upon NPNAx5. TMV was confirmed as a versatile vaccine platform for displaying small epitopes defined by neutralizing mAbs. We show that polyclonal antibodies against engineered VLPs can recapitulate the binding specificity of the mAbs and immune-focusing by reducing the structural complexity of an epitope may be superior to immune-broadening as a vaccine design approach. Most importantly the junctional and restricted valency NPNA epitopes can be the basis for developing highly effective second-generation malaria vaccine candidates.

Protein-Embedded Metalloporphyrin Arrays Templated by Circularly Permuted Tobacco Mosaic Virus Coat Proteins

Bioenergetic processes in nature have relied on networks of cofactors for harvesting, storing, and transforming the energy from sunlight into chemical bonds. Models mimicking the structural arrangement and functional crosstalk of the cofactor arrays are important tools to understand the basic science of natural systems and to provide guidance for non-natural functional biomaterials. Here, we report an artificial multiheme system based on a circular permutant of the tobacco mosaic virus coat protein (cpTMV). The double disk assembly of cpTMV presents a gap region sandwiched by the two C₂-symmetrically related disks. Non-native bis-his coordination sites formed by the mutation of the residues in this gap region were computationally screened and experimentally tested. A cpTMV mutant Q101H was identified to create a circular assembly of 17 protein-embedded hemes. Biophysical characterization using X-ray crystallography, cyclic voltammetry, and electron paramagnetic resonance (EPR) suggested both structural and functional similarity to natural multiheme cytochrome c proteins. This protein framework offers many further engineering opportunities for tuning the redox properties of the cofactors and incorporating non-native components bearing varied porphyrin structures and metal centers. Emulating the electron transfer pathways in nature using a tunable artificial system can contribute to the development of photocatalytic materials and bioelectronics.

Enzyme Activated Gold Nanoparticles for Versatile Site-Selective Bioconjugation

A new enzymatic method is reported for constructing protein- and DNA-AuNP conjugates. The strategy relies on the initial functionalization of AuNPs with phenols, followed by activation with the enzyme tyrosinase. Using an oxidative coupling reaction, the activated phenols are coupled to proteins bearing proline, thiol, or aniline functional groups. Activated phenol-AuNPs are also conjugated to a small molecule biotin and commercially available thiol-DNA. Advantages of this approach for AuNP bioconjugation include: (1) initial formation of highly stable AuNPs that can be selectively activated with an enzyme, (2) the ability to conjugate either proteins or DNA through a diverse set of functional handles, (3) site-specific immobilization, and (4) facile conjugation that is complete within 2 h at room temperature under aqueous conditions. The enzymatic oxidative coupling on AuNPs is applied to the construction of tobacco mosaic virus (TMV)-AuNP conjugates, and energy transfer between the AuNPs and fluorophores on TMV is demonstrated.

Reprogramming Virus Coat Protein Carboxylate Interactions for the Patterned Assembly of Hierarchical Nanorods

The self-assembly system of the rod-shaped tobacco mosaic virus (TMV) has been studied extensively for nanoscale applications. TMV coat protein assembly is modulated by intersubunit carboxylate groups whose electrostatic repulsion limits the assembly of virus rods without incorporating genomic RNA. To engineer assembly control into this system, we reprogrammed intersubunit carboxylate interactions to produce self-assembling coat proteins in the absence of RNA and in response to unique pH and ionic environmental conditions. Specifically, engineering a charge attraction at the intersubunit E50-D77 carboxylate group through a D77K substitution stabilized the coat proteins assembly into virus-like rods. In contrast, the reciprocal E50K modification alone did not confer virus-like rod assembly. However, a combination of R46G/E50K/E97G substitutions enabled virus-like rod assembly. Interestingly, the D77K substitution displays a unique pH-dependent assembly-disassembly profile, while the R46G/E50K/E97G substitutions confer a novel salt concentration dependency for assembly control. In addition, these unique environmentally controlled coat proteins allow for the directed assembly and disassembly of chimeric virus-like rods both in solution and on substrate-attached seed rods. Combined, these findings provide a controllable means to assemble functionally discrete virus-like rods for use in nanotechnology applications.

Hollow Tobacco Mosaic Virus Coat Protein Assisted Self-Assembly of One-Dimensional Nanoarchitectures

Herein, an efficient strategy to fabricate well-organized one-dimensional (1D) inorganic nanostructures is demonstrated by utilizing the hollow tobacco mosaic virus coat protein (TMVCP) as a restrictive template. Considering the advantages of the unique hollow structure and the dynamic self-assembly attribute of TMVCP, foreign nano-objects are successfully encapsulated and conveniently assembled into highly organized 1D chainlike structures in the cavity of the TMVCP multimer (TMV disk). Different kinds of functional nanoparticles, such as gold nanoparticles (AuNPs) and silver sulfide quantum dots (Ag₂S QDs), are used to demonstrate the successful construction of ordered 1D nanochains in high yields. Notably, binary nanochains of such different kinds of nanoparticles are also constructed through co-assembling the TMV disk-coated AuNPs and Ag₂S QDs. Further, the TMV-assisted AuNP nanochains are grown into the 1D nanowires through in situ Au deposition owing to the spatial confinement of the TMVCP cavity. Together, our findings indicate that the TMV-assisted self-assembly approach, resulting in higher yields and better controllability over the other reported studies based on directly mineralizing the metal architectures in the TMV nanorods, provides enormous potential toward the fabrication of highly complex hybrid-metal nanostructures.

Rationally Designed Protein Building Blocks for Programmable Hierarchical Architectures

Diverse natural/artificial proteins have been used as building blocks to construct a variety of well-ordered nanoscale structures over the past couple of decades. Sophisticated protein self-assemblies have attracted great scientific interests due to their potential applications in disease diagnosis, illness treatment, biomechanics, bio-optics and bio-electronics, etc. This review outlines recent efforts directed to the creation of structurally defined protein assemblies including one-dimensional (1D) strings/rings/tubules, two-dimensional (2D) planar sheets and three-dimensional (3D) polyhedral scaffolds. We elucidate various innovative strategies for manipulating proteins to self-assemble into desired architectures. The emergent applications of protein assemblies as versatile platforms in medicine and material science with improved performances have also been discussed.

Bifunctional pyridoxal derivatives as efficient bioorthogonal reagents for biomacromolecule modifications

Two types of pyridoxal analogs, azido pyridoxal (PL-N₃) and carboxyl pyridoxal (PL-COOH), were developed as novel bifunctional bioorthogonal molecules. These molecules showed fast imine formation with hydrazinyl groups and stable covalent linkages via azido/carboxyl groups, and thus were of great use for site-specific peptide and protein modifications.

Optimization of a Plasmodium falciparum circumsporozoite protein repeat vaccine using the tobacco mosaic virus platform

RTS,S/AS01 is a circumsporozoite protein (CSP)-based malaria vaccine that confers partial protection against malaria in endemic areas. Recent reports have elucidated structures of monoclonal antibodies that bind to the central (NPNA) repeat region of CSP and that inhibit parasite invasion. Antigen configuration and copy number of CSP repeats displayed on a tobacco mosaic virus (TMV) particle platform were studied. A TMV vaccine containing CSP repeats displayed as a loop induced 10× better antibody titer than a nearly full-length CSP in mice. In rhesus model, this translated to a 5× improvement in titer. Rhesus antibodies potently inhibited parasite invasion up to 11 mo after vaccination. An optimized epitope-focused, repeat-only CSP vaccine may be sufficient or better than the existing CSP vaccines.

Plasmodium falciparum vaccine RTS,S/AS01 is based on the major NPNA repeat and the C-terminal region of the circumsporozoite protein (CSP). RTS,S-induced NPNA-specific antibody titer and avidity have been associated with high-level protection in naïve subjects, but efficacy and longevity in target populations is relatively low. In an effort to improve upon RTS,S, a minimal repeat-only, epitope-focused, protective, malaria vaccine was designed. Repeat antigen copy number and flexibility was optimized using the tobacco mosaic virus (TMV) display platform. Comparing antigenicity of TMV displaying 3 to 20 copies of NPNA revealed that low copy number can reduce the abundance of low-affinity monoclonal antibody (mAb) epitopes while retaining high-affinity mAb epitopes. TMV presentation improved titer and avidity of repeat-specific Abs compared to a nearly full-length protein vaccine (FL-CSP). NPNAx5 antigen displayed as a loop on the TMV particle was found to be most optimal and its efficacy could be further augmented by combination with a human-use adjuvant ALFQ that contains immune-stimulators. These data were confirmed in rhesus macaques where a low dose of TMV-NPNAx5 elicited Abs that persisted at functional levels for up to 11 mo. We show here a complex association between NPNA copy number, flexibility, antigenicity, immunogenicity, and efficacy of CSP-based vaccines. We hypothesize that designing minimal epitope CSP vaccines could confer better and more durable protection against malaria. Preclinical data presented here supports the evaluation of TMV-NPNAx5/ALFQ in human trials.

Functionalized Tobacco Mosaic Virus Coat Protein Monomers and Oligomers as Nanocarriers for Anti-Cancer Peptides

Components with self-assembly properties derived from plant viruses provide the opportunity to design biological nanoscaffolds for the ordered display of agents of diverse nature and with complementing functions. With the aim of designing a functionalized nanoscaffold to target cancer, the coat protein (CP) of Tobacco mosaic virus (TMV) was tested as nanocarrier for an insoluble, highly hydrophobic peptide that targets the transmembrane domain of the Neuropilin-1 (NRP1) receptor in cancer cells. The resulting construct CPL-K (CP-linker-“Kill”) binds to NRP1 in cancer cells and disrupts NRP1 complex formation with PlexA1 as well as downstream Akt survival signaling. The application of CPL-K also inhibits angiogenesis and cell migration. CP was also fused to a peptide that targets the extracellular domain of NRP1 and this fusion protein (CPL-F, CP-Linker-“Find”) is shown to bind to cultured cancer cells and to inhibit NRP1-dependent angiogenesis as well. CPL-K and CPL-F maintain their anti-angiogenic properties upon co-assembly to oligomers/nanoparticles together with CPL. The observations show that the CP of TMV can be employed to generate a functionalized nanoparticle with biological activity. Remarkably, fusion to CPL allowed us to solubilize the highly insoluble transmembrane NRP1 peptide and to retain its anti-angiogenic effect.

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.

Plant virus-based materials for biomedical applications: Trends and prospects

Nanomaterials composed of plant viral components are finding their way into medical technology and health care, as they offer singular properties. Precisely shaped, tailored virus nanoparticles (VNPs) with multivalent protein surfaces are efficiently loaded with functional compounds such as contrast agents and drugs, and serve as carrier templates and targeting vehicles displaying e.g. peptides and synthetic molecules. Multiple modifications enable uses including vaccination, biosensing, tissue engineering, intravital delivery and theranostics. Novel concepts exploit self-organization capacities of viral building blocks into hierarchical 2D and 3D structures, and their conversion into biocompatible, biodegradable units. High yields of VNPs and proteins can be harvested from plants after a few days so that various products have reached or are close to commercialization. The article delineates potentials and limitations of biomedical plant VNP uses, integrating perspectives of chemistry, biomaterials sciences, molecular plant virology and process engineering.

Evaluation of Three Morphologically Distinct Virus-Like Particles as Nanocarriers for Convection-Enhanced Drug Delivery to Glioblastoma

Glioblastoma is a particularly challenging cancer, as there are currently limited options for treatment. New delivery routes are being explored, including direct intratumoral injection via convection-enhanced delivery (CED). While promising, convection-enhanced delivery of traditional chemotherapeutics such as doxorubicin (DOX) has seen limited success. Several studies have demonstrated that attaching a drug to polymeric nanoscale materials can improve drug delivery efficacy via CED. We therefore set out to evaluate a panel of morphologically distinct protein nanoparticles for their potential as CED drug delivery vehicles for glioblastoma treatment. The panel consisted of three different virus-like particles (VLPs), MS2 spheres, tobacco mosaic virus (TMV) disks and nanophage filamentous rods modified with DOX. While all three VLPs displayed adequate drug delivery and cell uptake in vitro, increased survival rates were only observed for glioma-bearing mice that were treated via CED with TMV disks and MS2 spheres conjugated to doxorubicin, with TMV-treated mice showing the best response. Importantly, these improved survival rates were observed after only a single VLP–DOX CED injection several orders of magnitude smaller than traditional IV doses. Overall, this study underscores the potential of nanoscale chemotherapeutic CED using virus-like particles and illustrates the need for further studies into how the overall morphology of VLPs influences their drug delivery properties.

Application of Plant Viruses as a Biotemplate for Nanomaterial Fabrication

Viruses are widely used to fabricate nanomaterials in the field of nanotechnology. Plant viruses are of great interest to the nanotechnology field because of their symmetry, polyvalency, homogeneous size distribution, and ability to self-assemble. This homogeneity can be used to obtain the high uniformity of the templated material and its related properties. In this paper, the variety of nanomaterials generated in rod-like and spherical plant viruses is highlighted for the cowpea chlorotic mottle virus (CCMV), cowpea mosaic virus (CPMV), brome mosaic virus (BMV), and tobacco mosaic virus (TMV). Their recent studies on developing nanomaterials in a wide range of applications from biomedicine and catalysts to biosensors are reviewed.

Protein cage assembly across multiple length scales

Within the materials science community, proteins with cage-like architectures are being developed as versatile nanoscale platforms for use in protein nanotechnology. Much effort has been focused on the functionalization of protein cages with biological and non-biological moieties to bring about new properties of not only individual protein cages, but collective bulk-scale assemblies of protein cages. In this review, we report on the current understanding of protein cage assembly, both of the cages themselves from individual subunits, and the assembly of the individual protein cages into higher order structures. We start by discussing the key properties of natural protein cages (for example: size, shape and structure) followed by a review of some of the mechanisms of protein cage assembly and the factors that influence it. We then explore the current approaches for functionalizing protein cages, on the interior or exterior surfaces of the capsids. Lastly, we explore the emerging area of higher order assemblies created from individual protein cages and their potential for new and exciting collective properties.

Sensing of heavy metal ions by intrinsic TMV coat protein fluorescence

We propose the use of a cysteine mutant of TMV coat protein as a signal transducer for the selective sensing and quantification of the heavy metal ions, Cd²⁺, Pb²⁺, Zn²⁺ and Ni²⁺ based on intrinsic tryptophan quenching. TMV coat protein is inexpensive, can be mass-produced since it is expressed and extracted from E-coli. It also displays several different functional groups, enabling a wide repertoire of bioconjugation chemistries; thus it can be easily integrated into functional devices. In addition, TMV-ion interactions have been widely reported and utilized for metallization to generate organic-inorganic hybrid composite novel materials. Building on these previous observations, we herein determine, for the first time, the TMV-ion binding constants assuming the static fluorescence quenching model. We also show that by comparing TMV-ion interactions between native and denatured coat protein, we can distinguish between chemically similar heavy metal ions such as cadmium and zinc ions.

Precision engineering of targeted nanocarriers

Since their introduction in 1980, the number of advanced targeted nanocarrier systems has grown considerably. Nanocarriers capable of targeting single receptors, multiple receptors, or multiple epitopes have all been used to enhance delivery efficiency and selectivity. Despite tremendous progress, preclinical studies and clinically translatable nanotechnology remain disconnected. The disconnect in targeting efficacy may stem from poorly-understood factors such as receptor clustering, spatial control of targeting ligands, ligand mobility, and ligand architecture. Further, the relationship between receptor distribution and ligand architecture remains elusive. Traditionally, targeted nanocarriers were engineered assuming a "static" target. However, it is becoming increasingly clear that receptor expression patterns change in response to external stimuli and disease progression. Here, we discuss how cutting-edge technologies will enable a better characterization of the spatiotemporal distribution of membrane receptors and their clustering. We further describe how this will enable the design of new nanocarriers that selectively target the site of disease. Ultimately, we explore how the precision engineering of targeted nanocarriers that adapt to receptor dynamics will have the potential to drive nanotechnology to the forefront of therapy and make targeted nanomedicine a clinical reality. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Biology-Inspired Nanomaterials > Lipid-Based Structures Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.

Viral-based nanomaterials for plasmonic and photonic materials and devices

Over the last decade, viruses have established themselves as a powerful tool in nanotechnology. Their proteinaceous capsids benefit from biocompatibility, chemical addressability, and a variety of sizes and geometries, while their ability to encapsulate, scaffold, and self-assemble enables their use for a wide array of purposes. Moreover, the scaling up of viral-based nanotechnologies is facilitated by high capsid production yield and speed, which is particularly advantageous when compared with slower and costlier lithographic techniques. These features enable the bottom-up fabrication of photonic and plasmonic materials, which relies on the precise arrangement of photoactive material at the nanoscale to control phenomena such as electromagnetic wave propagation and energy transfer. The interdisciplinary approach required for the fabrication of such materials combines techniques from the life sciences and device engineering, thus promoting innovative research. Materials with applications spanning the fields of sensing (biological, chemical, and physical sensors), nanomedicine (cellular imaging, drug delivery, phototherapy), energy transfer and conversion (solar cells, light harvesting, photocatalysis), metamaterials (negative refraction, artificial magnetism, near-field amplification), and nanoparticle synthesis are considered with exclusive emphasis on viral capsids and protein cages. This article is categorized under: Biology-Inspired Nanomaterials > Protein and Virus-Based Structures.

Diversification of Protein Cage Structure Using Circularly Permuted Subunits

Self-assembling protein cages are useful as nanoscale molecular containers for diverse applications in biotechnology and medicine. To expand the utility of such systems, there is considerable interest in customizing the structures of natural cage-forming proteins and designing new ones. Here we report that a circularly permuted variant of lumazine synthase, a cage-forming enzyme from Aquifex aeolicus (AaLS) affords versatile building blocks for the construction of nanocompartments that can be easily produced, tailored, and diversified. The topologically altered protein, cpAaLS, self-assembles into spherical and tubular cage structures with morphologies that can be controlled by the length of the linker connecting the native termini. Moreover, cpAaLS proteins integrate into wild-type and other engineered AaLS assemblies by coproduction in Escherichia coli to form patchwork cages. This coassembly strategy enables encapsulation of guest proteins in the lumen, modification of the exterior through genetic fusion, and tuning of the size and electrostatics of the compartments. This addition to the family of AaLS cages broadens the scope of this system for further applications and highlights the utility of circular permutation as a potentially general strategy for tailoring the properties of cage-forming proteins.

Tailoring lumazine synthase assemblies for bionanotechnology

The cage-forming protein lumazine synthase is readily modified, evolved and assembled with other components.

Bioinspired Silica Mineralization on Viral Templates

Plant virus capsids are attractive entities for nanotechnological applications because of their variation in shape and natural assembly ability. This chapter describes the production and modification of three differently shaped plant virus capsids for silica mineralization purposes. The chosen plant viruses exhibit either an icosahedral (cowpea mosaic virus, CPMV), or a flexuous rod-like structure (potato virus X, PVX), or a rigid rod-like shape (tobacco mosaic virus, TMV), and are well-known and frequently used plant viruses for biotechnological applications. We describe the production (including genetic or chemical modification) and purification of the plant viruses or of empty virus-like particles in the case of CPMV, as well as the characterization of these harvested templates. The mineralization procedures and differences in the protocols specific to the distinct viruses are described, and the analyses of the mineralization results are explained.

TMV Disk Scaffolds for Making sub-30 nm Silver Nanorings

Nanosized bioscaffolds can be utilized to tackle the challenge of size reduction of metallic rings owing to their miniature features as well as their well-known biomineralization capacity. The tobacco mosaic virus coat protein is used as a command surface to grow and assemble silver nanoparticles into sub-30 nm rings. The versatility of TMV allows the formation of both solid silver rings and rings consisting of discrete silver nanoparticles. The pH-dependent coulombic surface map along with the annular geometry of the protein aggregate allow the generation of rings with or without a central nanoparticle. Our silver rings are believed to be the smallest to date, and they can offer a test material for existing theories on metallic nanorings of this heretofore unreached size scale.

Fabrication of Tobacco Mosaic Virus-Like Nanorods for Peptide Display

Virus-like particles (VLPs) are genome-free protein shells assembled from virus coat proteins (CPs). The uniform and nanoscale structure of VLPs combined with their noninfectious nature have made them ideal candidates for the display of functional peptides. While the vast majority of VLPs are derived from spherical viruses, tobacco mosaic virus (TMV) produces a rod-shaped particle with a hollow central channel. However, under physiological conditions the TMV CP forms only disk-shaped macromolecules. Here, we describe the design, construction, purification, and processing of rod-shaped TMV-VLPs using a simple bacterial expression system. The robust nature of this system allows for the display of functional peptides and molecules on the outer surface of this novel VLP.

Ningnanmycin inhibits tobacco mosaic virus virulence by binding directly to its coat protein discs

Tobacco mosaic virus (TMV) causes severe plant diseases worldwide; however, effective antiviral agents for controlling TMV infections are not available. This lack of effective antiviral agents is mainly due to the poor understanding of potential targets associated with TMV infections. During infection, the coat protein (CP), which is delivered by viral particles into susceptible host cells, provides protection for viral RNA. Here, we found that Ningnanmycin (NNM), a commercially used plant antibacterial agent, inhibits the assembly of the CP by directly binding several residues. These interactions cause the disassembly of the CP from discs into monomers, leading to an almost complete loss of pathogenicity. Substitutions in the involved binding residues resulted in mutants that were significantly less sensitive to NNM. Thus, targeting the binding of viral CPs through small molecular agents offers an effective strategy to study the mechanism of NNM.

Targeting the N terminus for site-selective protein modification

The formation of well-defined protein bioconjugates is critical for many studies and technologies in chemical biology. Tried-and-true methods for accomplishing this typically involve the targeting of cysteine residues, but the rapid growth of contemporary bioconjugate applications has required an expanded repertoire of modification techniques. One very powerful set of strategies involves the modification of proteins at their N termini, as these positions are typically solvent exposed and provide chemically distinct sites for many protein targets. Several chemical techniques can be used to modify N-terminal amino acids directly or convert them into unique functional groups for further ligations. A growing number of N-terminus-specific enzymatic ligation strategies have provided additional possibilities. This Perspective provides an overview of N-terminal modification techniques and the chemical rationale governing each. Examples of specific N-terminal protein conjugates are provided, along with their uses in a number of diverse biological applications.

Nanoring formation via in situ photoreduction of silver on a virus scaffold

The fabrication of plasmonic nanorings remains of substantial interest by virtue of their enhanced electric and magnetic response to light fields which can be subsequently exploited in diverse applications. Scaling down the size of nanorings holds promise in creating artificial magnetism at wavelengths matching the solar spectrum. Nanosized bioscaffolds can be utilized to tackle the challenge of size reduction of metallic rings owing to their miniature features as well as their well-known biomineralization capacity. Herein, we use the tobacco mosaic virus coat protein as a command surface to grow and assemble silver nanoparticles into sub-30 nm rings. The versatility of TMV allows the formation of both solid rings and rings consisting of discrete nanoparticles that are characterized by UV-vis and TEM. The pH-dependent coulombic surface map along with the annular geometry of the protein aggregate allow the generation of rings with or without a central nanoparticle. Our silver rings are believed to be the smallest to date, and they can offer a test material for existing theories on metallic nanorings of this heretofore unreached size scale.

Stable Disk Assemblies of a Tobacco Mosaic Virus Mutant as Nanoscale Scaffolds for Applications in Drug Delivery

Current approaches to nanoscale therapeutic delivery rely on the attachment of a drug of interest to a nanomaterial scaffold that is capable of releasing the drug selectively in a tumor environment. One class of nanocarriers receiving significant attention is protein nanomaterials, which are biodegradable and homogeneous in morphology and can be equipped with multiple functional handles for drug attachment. Although most protein-based nanocarriers are spherical in morphology, recent research has revealed that nonspherical nanomaterials may have favorable tumor uptake in comparison to their spherical counterparts. It is therefore important to expand the number of nonspherical protein-based nanocarriers that are available. Herein, we report the development of a self-assembling nanoscale disk derived from a double arginine mutant of recombinantly expressed tobacco mosaic virus coat protein (RR-TMV). RR-TMV disks display highly stable double-disk assembly states. These RR-TMV disks were functionalized with the chemotherapy drug doxorubicin (DOX) and further modified with polyethylene glycol (PEG) for improved solubility. RR-TMV_DOX-PEG displayed cytotoxic properties similar to those of DOX alone when incubated with U87MG glioblastoma cells, but unmodified RR-TMV did not cause any cytotoxicity. The RR-TMV disk assembly represents a promising protein-based nanomaterial for applications in drug delivery.

Reversible and multi-cyclic protein-protein interaction in bacterial cellulosome-mimic system using rod-shaped viral nanostructure

The type II cohesin domain and type II dockerin of bacterial cellulosome were cloned from Clostridium thermocellum and expressed with the fusion of tobacco mosaic virus coat protein (TMVcp) and enhanced green fluorescent protein (EGFP), respectively, in Escherichia coli. The TMVcp-cohesin fusion protein was assembled to the stable and rod-shaped nanostructure (TMVcp-Coh rod) under a particular buffer condition, where many active cohesin proteins are biologically and densely displayed around the 3-dimensional surface of TMVcp-Coh rod. Using EGFP-dockerin as a fluorescent reporter, we confirmed that the Ca(2+)-dependent binding and dissociation between native cohesin and dockerin were reproduced with the two recombinant fusion proteins, TMVcp-cohesin and EGFP-dockerin. The multi-cyclic binding-dissociation operation of TMVcp-Coh rod and EGFP-dockerin was successfully performed with maintaining the reversible cohesin-dockerin interaction in every cycle. EGFP that was fused to dockerin as a proof-of-concept here can be switched to other functional proteins/peptides that need to be used in multi-cyclic operation.

New Strategies and Methods to Study Interactions between Tobacco Mosaic Virus Coat Protein and Its Inhibitors

Studies of the targets of anti-viral compounds are hot topics in the field of pesticide research. Various efficient anti-TMV (Tobacco Mosaic Virus) compounds, such as Ningnanmycin (NNM), Antofine (ATF), Dufulin (DFL) and Bingqingxiao (BQX) are available. However, the mechanisms of the action of these compounds on targets remain unclear. To further study the mechanism of the action of the anti-TMV inhibitors, the TMV coat protein (TMV CP) was expressed and self-assembled into four-layer aggregate disks in vitro, which could be reassembled into infectious virus particles with TMV RNA. The interactions between the anti-TMV compounds and the TMV CP disk were analyzed by size exclusion chromatography, isothermal titration calorimetry and native-polyacrylamide gel electrophoresis methods. The results revealed that assembly of the four-layer aggregate disk was inhibited by NNM; it changed the four-layer aggregate disk into trimers, and affected the regular assembly of TMV CP and TMV RNA. The four-layer aggregate disk of TMV CP was little inhibited by ATF, DFL and BQX. Our results provide original data, as well as new strategies and methods, for research on the mechanism of action of anti-viral drugs.

Micelle-Induced Self-Assembling Protein Nanowires: Versatile Supramolecular Scaffolds for Designing the Light-Harvesting System

Organic nanoparticle induced self-assembly of proteins with periodic nanostructures is a promising and burgeoning strategy to develop functional biomimetic nanomaterials. Cricoid proteins afford monodispersed and well-defined hollow centers, and can be used to multivalently interact with geometrically symmetric nanoparticles to form one-dimensional protein nanoarrays. Herein, we report that core-cross-linked micelles can direct cricoid stable protein one (SP1) to self-assembling nanowires through multiple electrostatic interactions. One micelle can act as an organic nanoparticle to interact with two central concaves of SP1 in an opposite orientation to form a sandwich structure, further controlling the assembly direction to supramolecular protein nanowires. The reported versatile supramolecular scaffolds can be optionally manipulated to develop multifunctional integrated or synergistic biomimetic nanomaterials. Artificial light-harvesting nanowires are further developed to mimic the energy transfer process of photosynthetic bacteria for their structural similarity, by means of labeling donor and acceptor chromophores to SP1 rings and spherical micelles, respectively. The absorbing energy can be transferred within the adjacent donors around the ring and shuttling the collected energy to the nearby acceptor chromophore. The artificial light-harvesting nanowires are designed by mimicking the structural characteristic of natural LH-2 complex, which are meaningful in exploring the photosynthesis process in vitro.

Metal induced self-assembly of designed V-shape protein into 2D wavy supramolecular nanostructure

In order to understand and imitate the more complex bio-processes and fascinating functions in nature, protein self-assembly has been studied and has attracted more and more interest in recent years. Artificial self-assemblies of proteins have been constructed through many strategies. However, the design of complicated protein self-assemblies utilizing the special profile of building blocks remains a challenge. We herein report linear and 2D nanostructures constructed from a V shape SMAC protein and induced by metal coordination. Zigzag nanowires and wavy 2D nanostructures have been demonstrated by AFM and TEM. The zigzag nanowires can translate to a 2D nanostructure with an excess of metal ions, which reveals the step by step assembly process. Fluorescence and UV/Vis spectra have also been obtained to further study the mechanism and process of self-assembly. Upon the protein nanostructure, fluorescence resonance energy transfer (FRET) could also be detected using fluorescein modified proteins as building blocks. This article provides an approach for designing and controlling self-assembled protein nanostructures with a distinctive topological morphology.

Structurally plastic peptide capsules for synthetic antimicrobial viruses

A conceptual design for artificial antimicrobial viruses is described. The design emulates viral assembly and function to create self-assembling peptide capsules that promote efficient gene delivery and silencing in mammalian cells. Unlike viruses, however, the capsules are antimicrobial, which allows them to exhibit a dual biological function: gene transport and antimicrobial activity. Unlike other antimicrobials, the capsules act as pre-concentrated antimicrobial agents that elicit rapid and localised membrane-disrupting responses by converting into individual pores at their precise landing positions on membranes. The concept holds promise for engineering virus-like scaffolds with biologically tuneable properties.

Viral nano-hybrids for innovative energy conversion and storage schemes

Typical rod-like viruses (the Tobacco Mosaic Virus (TMV) and the Bacteriophage M13) are biological nanostructures that couple a 1D mono-dispersed morphology with a precisely defined topology of surface spaced and orthogonal reactive domains. These biogenic scaffolds offer a unique alternative to synthetic nano-platforms for the assembly of functional molecules and materials. Spatially resolved 1D arrays of inorganic-organic hybrid domains can thus be obtained on viral nano-templates resulting in the functional arrangement of photo-triggers and catalytic sites with applications in light energy conversion and storage. Different synthetic strategies are herein highlighted depending on the building blocks and with a particular emphasis on the molecular design of viral-templated nano-interfaces holding great potential for the dream-goal of artificial photosynthesis.

Manipulating Excited-State Dynamics of Individual Light-Harvesting Chromophores through Restricted Motions in a Hydrated Nanoscale Protein Cavity

Manipulating the photophysical properties of light-absorbing units is a crucial element in the design of biomimetic light-harvesting systems. Using a highly tunable synthetic platform combined with transient absorption and time-resolved fluorescence measurements and molecular dynamics simulations, we interrogate isolated chromophores covalently linked to different positions in the interior of the hydrated nanoscale cavity of a supramolecular protein assembly. We find that, following photoexcitation, the time scales over which these chromophores are solvated, undergo conformational rearrangements, and return to the ground state are highly sensitive to their position within this cavity and are significantly slower than in a bulk aqueous solution. Molecular dynamics simulations reveal the hindered translations and rotations of water molecules within the protein cavity with spatial specificity. The results presented herein show that fully hydrated nanoscale protein cavities are a promising way to mimic the tight protein pockets found in natural light-harvesting complexes. We also show that the interplay between protein, solvent, and chromophores can be used to substantially tune the relaxation processes within artificial light-harvesting assemblies in order to significantly improve the yield of interchromophore energy transfer and extend the range of excitation transport. Our observations have implications for other important, similarly sized bioinspired materials, such as nanoreactors and biocompatible targeted delivery agents.

The near-symmetry of proteins

The majority of protein oligomers form clusters which are nearly symmetric. Understanding of that imperfection, its origins, and perhaps also its advantages requires the conversion of the currently used vague qualitative descriptive language of the near-symmetry into an accurate quantitative measure that will allow to answer questions such as: "What is the degree of symmetry deviation of the protein?," "how do these deviations compare within a family of proteins?," and so on. We developed quantitative methods to answer this type of questions, which are capable of analyzing the whole protein, its backbone or selected portions of it, down to comparison of symmetry-related specific amino-acids, and which are capable of visualizing the various levels of symmetry deviations in the form of symmetry maps. We have applied these methods on an extensive list of homomers and heteromers and found that apparently all proteins never reach perfect symmetry. Strikingly, even homomeric protein clusters are never ideally symmetric. We also found that the main burden of symmetry distortion is on the amino-acids near the symmetry axis; that it is mainly the more hydrophilic amino-acids that take place in symmetry-distortive interactions; and more. The remarkable ability of heteromers to preserve near-symmetry, despite the different sequences, was also shown and analyzed. The comprehensive literature on the suggested advantages symmetric oligomerizations raises a yet-unsolved key question: If symmetry is so advantageous, why do proteins stop shy of perfect symmetry? Some tentative answers to be tested in further studies are suggested in a concluding outlook.

RNA-controlled assembly of tobacco mosaic virus-derived complex structures: from nanoboomerangs to tetrapods

The in vitro assembly of artificial nanotubular nucleoprotein shapes based on tobacco mosaic virus-(TMV-)-derived building blocks yielded different spatial organizations of viral coat protein subunits on genetically engineered RNA molecules, containing two or multiple TMV origins of assembly (OAs). The growth of kinked nanoboomerangs as well as of branched multipods was determined by the encapsidated RNAs. A largely simultaneous initiation at two origins and subsequent bidirectional tube elongation could be visualized by transmission electron microscopy of intermediates and final products. Collision of the nascent tubes' ends produced angular particles with well-defined arm lengths. RNAs with three to five OAs generated branched multipods with a maximum of four arms. The potential of such an RNA-directed self-assembly of uncommon nanotubular architectures for the fabrication of complex multivalent nanotemplates used in functional hybrid materials is discussed.