Self-assembled synthetic viral capsids from a 24-mer viral peptide fragment

DNA Origami Inside-Out Viruses

A synthetic topology for everted viruses is reported. The topology is a single-stranded virion DNA assembled into a hollow cube with exterior decorated with HIV-Tat transduction domains. The cube incorporates a pH-responsive lid allowing for the controlled encapsulation of functional proteins and their transfer and release into live cells. Unlike viruses, which are protein shells with a [3,5]-fold rotational symmetry that encase nucleic acids, these cubes are [3, 4]-fold DNA boxes encapsulating proteins. Like viruses, such everted DNA-built viruses are monodisperse nanoscale assemblies that infect human cells with a specialist cargo. The design offers a bespoke bottom-up platform for engineering nonpolyhedral, nonprotein synthetic viruses.

Self-assembled artificial viral capsids bearing coiled-coils at the surface

In order to construct artificial viral capsids bearing complementary dimeric coiled-coils on the surface, a β-annulus peptide bearing a coiled-coil forming sequence at the C-terminus (β-annulus-coiled-coil-B) was synthesized by a native chemical ligation of a β-annulus-SBn peptide with a Cys-containing coiled-coil-B peptide. Dynamic light scattering (DLS) measurements and transmission electron microscopy (TEM) images revealed that the β-annulus-coiled-coil-B peptide self-assembled into spherical structures of about 50 nm in 10 mM Tris-HCl buffer. Circular dichroism (CD) spectra indicated the formation of the complementary coiled-coil structure on the spherical assemblies. Addition of 0.25 equivalent of the complementary coiled-coil-A peptide to the β-annulus-coiled-coil-B peptide showed the formation of spherical assemblies of 46 ± 14 nm with grains of 5 nm at the surface, whereas addition of 1 equivalent of the complementary coiled-coil-A peptide generated fibrous assemblies.

Self-assembly of Ni-NTA-modified β-annulus peptides into artificial viral capsids and encapsulation of His-tagged proteins

β-Annulus peptides bearing Cys at the N-terminal from tomato bushy stunt virus were synthesised using a standard Fmoc-protected solid-phase method, and the peptide was modified with Ni-NTA at the N-terminal. The Ni-NTA-modified β-annulus peptide self-assembled into virus-like nanocapsules of approximately 40 nm in diameter. The critical aggregation concentration of these nanocapsules in 10 mM Tris-HCl buffer (pH 7.3) at 25 °C was 0.053 μM, which is 470 times lower than that of unmodified β-annulus peptides. Moreover, size exclusion chromatography of the peptide assembly indicated encapsulation of His-tagged green fluorescent protein in the Ni-NTA-modified artificial viral capsid.

Synthetic approaches to construct viral capsid-like spherical nanomaterials

This feature article describes recent progress in synthetic strategies to construct viral capsid-like spherical nanomaterials using the self-assembly of peptides and/or proteins.

Protein Complexes and Virus-Like Particle Technology

Virus-like particle (VLP) technologies are based on virus-inspired artificial structures and the intrinsic ability of viral proteins to self-assemble at controlled conditions. Therefore, the basic knowledge about the mechanisms of viral particle formation is highly important for designing of industrial applications. As an alternative to genetic and chemical processes, different physical methods are frequently used for VLP construction, including well characterized protein complexes for introduction of foreign molecules in VLP structures.This chapter shortly discusses the mechanisms how the viruses form their perfectly ordered structures as well as the principles and most interesting application examples, how to exploit the structural and assembly/disassembly properties of viral structures for creation of new nanomaterials.

Antimicrobial peptide capsids of de novo design

The spread of bacterial resistance to antibiotics poses the need for antimicrobial discovery. With traditional search paradigms being exhausted, approaches that are altogether different from antibiotics may offer promising and creative solutions. Here, we introduce a de novo peptide topology that—by emulating the virus architecture—assembles into discrete antimicrobial capsids. Using the combination of high-resolution and real-time imaging, we demonstrate that these artificial capsids assemble as 20-nm hollow shells that attack bacterial membranes and upon landing on phospholipid bilayers instantaneously (seconds) convert into rapidly expanding pores causing membrane lysis (minutes). The designed capsids show broad antimicrobial activities, thus executing one primary function—they destroy bacteria on contact.

With the growing threat of antibiotic resistance, unconventional approaches to antimicrobial discovery are needed. Here, the authors present a peptide topology that mimics virus architecture and assembles into antimicrobial capsids that disrupt bacterial membranes upon contact.

Preparation and Formation Process of Zn(II)-Coordinated Nanovesicles

Mixing a glycylglycine lipid and zinc acetate has been reported to form novel supramolecular Zn(II)-coordinated nanovesicles in ethanol. In this study, we investigate in detail the formation of nanovesicles by using three lipids at different temperatures and discuss their formation process. The original lipids show extremely low solubilities and appear as plate structures in ethanol. Within a small window of lipid solubility, the formation of lipid-Zn(II) complexes occurs mainly on the solid surfaces of plate structures. Controlling of the lipid solubility by temperature affects the kinetics of complex formation and the subsequent transformation of the complexes into nanovesicles and nanotubes. An improved method of two-step control of temperature is developed for preparing all the three kinds of nanovesicles. We provide new insights into the formation process of nanovesicles based on several control experiments. A tetrahedral lipid-cobalt(II) complex similarly produces nanovesicles, whereas an octahedral complex gives sheet structures. Mixing of zinc acetate with a β-alanyl-β-alanine lipid can only give sheet structures, which lack a polyglycine II hydrogen-bond network and induce no morphological changes. We conclude that the formation of the lipid-Zn(II) complexes on solid plate structures, tetrahedral geometry, and polyglycine II hydrogen-bond network in the complexes shall work cooperatively for the formation of Zn(II)-coordinated nanovesicles.

Synthetic Approach to biomolecular science by cyborg supramolecular chemistry

BACKGROUND

To imitate the essence of living systems via synthetic chemistry approaches has been attempted. With the progress in supramolecular chemistry, it has become possible to synthesize molecules of a size and complexity close to those of biomacromolecules. Recently, the combination of precisely designed supramolecules with biomolecules has generated structural platforms for designing and creating unique molecular systems. Bridging between synthetic chemistry and biomolecular science is also developing methodologies for the creation of artificial cellular systems.

SCOPE OF REVIEW

This paper provides an overview of the recently expanding interdisciplinary research to fuse artificial molecules with biomolecules, that can deepen our understanding of the dynamical ordering of biomolecules.

MAJOR CONCLUSIONS AND GENERAL SIGNIFICANCE

Using bottom-up approaches based on the precise chemical design, synthesis and hybridization of artificial molecules with biological materials have been realizing the construction of sophisticated platforms having the fundamental functions of living systems. The effective hybrid, molecular cyborg, approaches enable not only the establishment of dynamic systems mimicking nature and thus well-defined models for biophysical understanding, but also the creation of those with highly advanced, integrated functions. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato.

Branched Amphipathic Peptide Capsules: Different Ratios of the Two Constituent Peptides Direct Distinct Bilayer Structures, Sizes, and DNA Transfection Efficiency

Branched amphipathic peptide capsules (BAPCs) are biologically derived, bilayer delimited, nanovesicles capable of being coated by or encapsulating a wide variety of solutes. The vesicles and their cargos are readily taken up by cells and become localized in the perinuclear region of cells. When BAPCs are mixed with DNA, the BAPCs act as cationic nucleation centers around which DNA winds. The BAPCs-DNA nanoparticles are capable of delivering plasmid DNA in vivo and in vitro yielding high transfection rates and minimal cytotoxicity. BAPCs share several biophysical properties with lipid vesicles. They are however considerably more stable-resisting disruption in the presence of chaotropes such as urea and guanidinium chloride, anionic detergents, proteases, and elevated temperature (∼95 °C). To date, all of our published results have utilized BAPCs that are composed of equimolar concentrations of the two branched sequences (Ac-FLIVI)₂-K-K₄-CO-NH₂ and (Ac-FLIVIGSII)₂-K-K₄-CO-NH₂. The mixture of sizes was utilized to relieve potential curvature strain in the spherical capsule. In this article, different molar ratios of the two peptides were studied to test whether alternate ratios produced BAPCs with different biological and biophysical properties. Additionally, preparation (annealing) temperature was included as a second variable.

DNA-modified artificial viral capsids self-assembled from DNA-conjugated β-annulus peptide

β-Annulus peptides from tomato bushy stunt virus conjugated with DNAs (dA₂₀ and dT₂₀ ) at the C-terminal were synthesized. The DNA-modified β-annulus peptides self-assembled into artificial viral capsids with sizes of 45-160 nm. ζ-Potential measurements revealed that the DNAs were coated on the surface of artificial viral capsids. Fluorescence assays indicated that the DNAs on the artificial viral capsids were partially hybridized with the complementary DNAs. Moreover, the DNA-modified artificial viral capsids formed aggregates by adding complementary polynucleotides. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

A De Novo Virus-Like Topology for Synthetic Virions

A de novo topology of virus-like assembly is reported. The design is a trifaceted coiled-coil peptide helix, which self-assembles into ultrasmall, monodisperse, anionic virus-like shells that encapsulate and transfer both RNA and DNA into human cells. Unlike existing artificial systems, these shells share the same physical characteristics of viruses being anionic, nonaggregating, abundant, hollow, and uniform in size, while effectively mediating gene silencing and transgene expression. These are the smallest virus-like structures reported to date, both synthetic and native, with the ability to adapt and transfer small and large nucleic acids. The design thus offers a promising solution for engineering bespoke artificial viruses with desired functions.

Protein Assembly: Versatile Approaches to Construct Highly Ordered Nanostructures

Nature endows life with a wide variety of sophisticated, synergistic, and highly functional protein assemblies. Following Nature's inspiration to assemble protein building blocks into exquisite nanostructures is emerging as a fascinating research field. Dictating protein assembly to obtain highly ordered nanostructures and sophisticated functions not only provides a powerful tool to understand the natural protein assembly process but also offers access to advanced biomaterials. Over the past couple of decades, the field of protein assembly has undergone unexpected and rapid developments, and various innovative strategies have been proposed. This Review outlines recent advances in the field of protein assembly and summarizes several strategies, including biotechnological strategies, chemical strategies, and combinations of these approaches, for manipulating proteins to self-assemble into desired nanostructures. The emergent applications of protein assemblies as versatile platforms to design a wide variety of attractive functional materials with improved performances have also been discussed. The goal of this Review is to highlight the importance of this highly interdisciplinary field and to promote its growth in a diverse variety of research fields ranging from nanoscience and material science to synthetic biology.

Peptide self-assembly for nanomaterials: the old new kid on the block

Peptide self-assembly is an increasingly attractive tool for nanomaterials. Perfected in biology peptide self-assembling systems have impacted on nearly any conceivable nanomaterial type. However, with all the information available to us commercialisation of peptide materials remains in its infancy. In an attempt to better understand the reasons behind this shortcoming we categorise peptide self-assembled materials in relation to their non-peptide counterparts. A particular emphasis is placed on the versatility of peptide self-assembly in terms of modularity, responsiveness and functional diversity, which enables direct comparisons with more traditional material chemistries.

A photoinduced growth system of peptide nanofibres addressed by DNA hybridization

Spatiotemporal control of peptide nanofibre growth was achieved by photocleavage of a DNA-conjugated β-sheet-forming peptide with a photoresponsive amino acid.

Interlocked dimerization of C3-Symmetrical boron difluoride complex: designing non-cooperative supramolecular materials for luminescent thin films

Radially integrated, luminescent boron difluoride complexes form inter-locked dimers in chloroform. The inter-locked dimers show anti-cooperative features and give homogeneous thin-films on solid surfaces.

Inclusion of Zinc Oxide Nanoparticles into Virus-Like Peptide Nanocapsules Self-Assembled from Viral β-Annulus Peptide

A viral β-annulus peptide connected with a zinc oxide (ZnO)-binding sequence (HCVAHR) at its N-terminal was synthesized, and the inclusion behavior of quantum-sized ZnO nanoparticles into the peptide nanocapsules formed by self-assembly of the peptide in water was investigated. Dynamic light scattering (DLS) measurements showed that ZnO nanoparticles (approximately 10 nm) in the presence of the peptide (0.1 mM) formed assemblies with an average size of 48 ± 24 nm, whereas ZnO nanoparticles in the absence of the peptide formed large aggregates. Transmission electron microscopy (TEM) observations of the ZnO nanoparticles in the presence of the peptide revealed that ZnO nanoparticles were encapsulated into the peptide nanocapsules with a size of approximately 50 nm. Fluorescence spectra of a mixture of the peptide and ZnO nanoparticles suggested that the ZnO surface and the peptide interact. Template synthesis of ZnO nanoparticles with the peptide nanocapsules afforded larger nanoparticles (approximately 40 nm), which are not quantum-sized ZnO.

CO2-Switchable Supramolecular Block Glycopolypeptide Assemblies

A novel supramolecular block glycopolypeptide, designed to have the viral building blocks and be sensitive to CO₂, a physiological stimulus, was prepared via the orthogonal coupling of two end-functionalized biopolymers, dextran with β-cyclodextrin terminal (Dex-CD) and poly(l-valine) with a benzimidazole tail (BzI-PVal), respectively, driven by the end-to-end host-guest interactions. Due to the CO₂-cleavable CD/BzI connection, both the vesicular and fibrous aggregates of this supramolecular block copolymer self-assembled in aqueous solution can undergo a reversible process of disassembly upon "breathing in" CO₂ and assembly upon "breathing out" CO₂, which mimics, to some extent, the disintegration and construction of viral capsid nanostructures.

Hemoprotein-based supramolecular assembling systems

Hemoproteins are metalloproteins which include iron porphyrin as a cofactor. These proteins have received much attention as promising building blocks for development of new types of biomaterials. This review summarizes recent efforts in the rational design of supramolecular hemoprotein assemblies using myoglobin, horseradish peroxidase, cytochrome b562 and cytochrome c as a monomer unit. The processes of coordination bond-mediated assembly or domain swapping-mediated assembly provide defined oligomers, while hemoprotein reconstitution with synthetic heme derivatives provides submicrometer-sized structures such as fibrils, vesicles/micelles, or networks. Interestingly, several of these assembled structures maintain the intrinsic functions of monomer units. The chemical and/or biological strategies described in this review will lead to the creation of unique hemoprotein-based functional biomaterials.

Molecular tools for the construction of peptide-based materials

Proteins and peptides are fundamental components of living systems where they play crucial roles at both functional and structural level. The versatile biological properties of these molecules make them interesting building blocks for the construction of bio-active and biocompatible materials. A variety of molecular tools can be used to fashion the peptides necessary for the assembly of these materials. In this tutorial review we shall describe five of the main techniques, namely solid phase peptide synthesis, native chemical ligation, Staudinger ligation, NCA polymerisation, and genetic engineering, that have been used to great effect for the construction of a host of peptide-based materials.

Simultaneous dual protein labeling using a triorthogonal reagent

Construction of heterofunctional proteins is a rapidly emerging area of biotherapeutics. Combining a protein with other moieties, such as a targeting element, a toxic protein or small molecule, and a fluorophore or polyethylene glycol (PEG) group, can improve the specificity, functionality, potency, and pharmacokinetic profile of a protein. Protein farnesyl transferase (PFTase) is able to site-specifically and quantitatively prenylate proteins containing a C-terminal CaaX-box amino acid sequence with various modified isoprenoids. Here, we describe the design, synthesis, and application of a triorthogonal reagent, 1, that can be used to site-specifically incorporate an alkyne and aldehyde group simultaneously into a protein. To illustrate the capabilities of this approach, a protein was enzymatically modified with compound 1 followed by oxime ligation and click reaction to simultaneously incorporate an azido-tetramethylrhodamine (TAMRA) fluorophore and an aminooxy-PEG moiety. This was performed with both a model protein [green fluorescent protein (GFP)] as well as a therapeutically useful protein [ciliary neurotrophic factor (CNTF)]. Next, a protein was enzymatically modified with compound 1 followed by coupling to an azido-bis-methotrexate dimerizer and aminooxy-TAMRA. Incubation of that construct with a dihydrofolate reductase (DHFR)-DHFR-anti-CD3 fusion protein resulted in the self-assembly of nanoring structures that were endocytosed into T-leukemia cells and visualized therein. These results highlight how complex multifunctional protein assemblies can be prepared using this facile triorthogonal approach.

Supramolecular self-assemblies as functional nanomaterials

In this review, we survey the diversity of structures and functions which are encountered in advanced self-assembled nanomaterials. We highlight their flourishing implementations in three active domains of applications: biomedical sciences, information technologies, and environmental sciences. Our main objective is to provide the reader with a concise and straightforward entry to this broad field by selecting the most recent and important research articles, supported by some more comprehensive reviews to introduce each topic. Overall, this compilation illustrates how, based on the rules of supramolecular chemistry, the bottom-up approach to design functional objects at the nanoscale is currently producing highly sophisticated materials oriented towards a growing number of applications with high societal impact.

Multicompartment micelle-structured peptide nanoparticles: a new biocompatible gene- and drug-delivery tool

Self-assembled, biodegradable materials that embed fragile, soluble, or insoluble compounds of therapeutic interest have potential use as drug delivery systems. The bead-forming peptide Ac-X3-gT can embed hydrophobic and hydrophilic payloads. Loaded peptide beads were internalized by human acute monocytic leukemia cell line (THP-1) macrophages, THP-1 monocytes, and hepatocellular carcinoma cells (Huh7). Furthermore, paclitaxel and doxorubicin coencapsulated in the peptide beads were delivered to THP-1 monocytes, causing a decrease in cell viability due to the activity of the anticancer drugs. In addition to the bead-forming peptide Ac-X3-gT, the use of a positively charged peptide analogue increased the RNA/DNA embedding efficiency to 99% by charge compensation and micellar complexation. Internalization of the resulting gene delivery systems by Huh7 cells led to specific gene silencing either by embedded small interfering RNA or by plasmid-encoding small hairpin RNA delivered in cells. The new class of purely peptidic material caused no measurable toxicity during in vitro experiments, thereby indicating potential use as a drug delivery system for multidrug delivery and gene therapy.

Supramolecular assembling systems formed by heme-heme pocket interactions in hemoproteins

A native protein in a biological system spontaneously produces large and elegant assemblies via self-assembly or assembly with various biomolecules which provide non-covalent interactions. In this context, the protein plays a key role in construction of a unique supramolecular structure operating as a functional system. Our group has recently highlighted the structure and function of hemoproteins reconstituted with artificially created heme analogs. The heme molecule is a replaceable cofactor of several hemoproteins. Here, we focus on the successive supramolecular protein assemblies driven by heme-heme pocket interactions to afford various examples of protein fibers, networks and three-dimensional clusters in which an artificial heme moiety is introduced onto the surface of a hemoprotein via covalent linkage and the native heme cofactor is removed from the heme pocket. This strategy is found to be useful for constructing hybrid materials with an electrode or with nanoparticles. The new systems described herein are expected to lead to the generation of various biomaterials with functions and characteristic physicochemical properties similar to those of hemoproteins.

Chemically programmed supramolecular assembly of hemoprotein and streptavidin with alternating alignment

Alternating: a cofactor dyad consisting of a heme group (red in picture) and a bis(biotin) unit (blue) was synthesized and shown to specifically bind to both apomyoglobin and streptavidin. In the presence of the dyad, the 1:1 association of a disulfide-bridged myoglobin dimer (green) with streptavidin (gray) afforded a submicrometer-sized fibrous alternating copolymer.

Syntheses and self-assembling behaviors of pentagonal conjugates of tryptophane zipper-forming peptide

Pentagonal conjugates of tryptophane zipper-forming peptide (CKTWTWTE) with a pentaazacyclopentadecane core (Pentagonal-Gly-Trpzip and Pentagonal-Ala-Trpzip) were synthesized and their self-assembling behaviors were investigated in water. Pentagonal-Gly-Trpzip self-assembled into nanofibers with the width of about 5 nm in neutral water (pH 7) via formation of tryptophane zipper, which irreversibly converted to nanoribbons by heating. In contrast, Pentagonal-Ala-Trpzip formed irregular aggregates in water.