Programmable assembly of nanoarchitectures using genetically engineered viruses

Effect of molecular conformations on the adsorption behavior of gold-binding peptides

Despite extensive recent reports on combinatorially selected inorganic-binding peptides and their bionanotechnological utility as synthesizers and molecular linkers, there is still only limited knowledge about the molecular mechanisms of peptide binding to solid surfaces. There is, therefore, much work that needs to be carried out in terms of both the fundamentals of solid-binding kinetics of peptides and the effects of peptide primary and secondary structures on their recognition and binding to solid materials. Here we discuss the effects of constraints imposed on FliTrx-selected gold-binding peptide molecular structures upon their quantitative gold-binding affinity. We first selected two novel gold-binding peptide (AuBP) sequences using a FliTrx random peptide display library. These were, then, synthesized in two different forms: cyclic (c), reproducing the original FliTrx gold-binding sequence as displayed on bacterial cells, and linear (l) dodecapeptide gold-binding sequences. All four gold-binding peptides were then analyzed for their adsorption behavior using surface plasmon resonance spectroscopy. The peptides exhibit a range of binding affinities to and adsorption kinetics on gold surfaces, with the equilibrium constant, Keq, varying from 2.5x10(6) to 13.5x10(6) M(-1). Both circular dichroism and molecular mechanics/energy minimization studies reveal that each of the four peptides has various degrees of random coil and polyproline type II molecular conformations in solution. We found that AuBP1 retained its molecular conformation in both the c- and l-forms, and this is reflected in having similar adsorption behavior. On the other hand, the c- and l-forms of AuBP2 have different molecular structures, leading to differences in their gold-binding affinities.

Structural analysis of a beta-helical protein motif stabilized by targeted replacements with conformationally constrained amino acids

Here we study conformational stabilization induced in a beta-helical nanostructure by position-specific mutations. The nanostructure is constructed through the self-assembly of the beta-helical building block excised from E. coli galactoside acetyltransferase (PDB code 1krr , chain A; residues 131-165). The mutations involve substitutions by cyclic, conformationally constrained amino acids. Specifically, a complete structural analysis of the Pro-Xaa-Val sequence [with Xaa being Gly, Ac 3c (1-aminocyclopropane-1-carboxylic acid) and Ac 5c (1-aminocyclopentane-1-carboxylic acid)], corresponding to the 148-150 loop region in the wild-type (Gly) and mutated (Ac 3c and Ac 5c) 1krr , has been performed using Molecular Dynamics simulations and X-ray crystallography. Simulations have been performed for the wild-type and mutants of three different systems, namely the building block, the nanoconstruct and the isolated Pro-Xaa-Val tripeptide. Furthermore, the crystalline structures of five peptides of Pro-Xaa-Val or Xaa-Val sequences have been solved by X-ray diffraction analysis and compared with theoretical predictions. Both the theoretical and crystallographic studies indicate that the Pro-Ac n c-Val sequences exhibit a high propensity to adopt turn-like conformations, and this propensity is little affected by the chemical environment. Overall, the results indicate that replacement of Gly149 by Ac 3c or Ac 5c significantly reduce the conformational flexibility of the target site enhancing the structural specificity of the building block and the nanoconstruct derived from the 1krr beta-helical motif.

Microtubule-based gold nanowires and nanowire arrays

Biological structures are attractive as templates to form nanoscale architectures for electronics because of their dimensions and the ability to interact with inorganic materials. In this study, we report the fabrication and electrical properties of microtubule (MT)-templated Au nanowires, and methods for assembling Au nanowire arrays based on these templates. The adsorption of MTs on silicon substrates is an effective means for preserving the conformation of the MT and provides a convenient platform for electrical measurements. To improve the metallization of MTs, a photochemical route for gold reduction is adapted, which leads to continuous coverage. The conductivity values measured on micrometer-long nanowires are similar to those reported for other biotemplated gold nanowires. A protocol for fabricating arrays of MT-templated gold nanowires is demonstrated.

Fabrication and characterization of a novel inclusion complex of chiral monomer derived from (+)-camphor with beta-cyclodextrins

In order to develop a highly ordered polymer dopant to improve the physical properties of polymer materials for microsystems, a novel supramolecular inclusion complex (IC) of chiral bornyl 4-(6-acryloyloxyhexyloxy) phenyl-4'-benzoate ( BAPB) threaded with beta-cyclodextrins (beta-CDs) was synthesized. The inclusion complex was identified using Fourier transform infrared (FTIR), UV, 13C cross-polarization/magic-angle spinning (CP/MAS) NMR, 1H NMR, and X-ray diffraction (XRD). The construction of the fibrous self-assembled inclusion complex was confirmed using scanning electron microscopy (SEM) and transmission electron microscopy (TEM) techniques. The highly ordered polymerized inclusion complex beta-CD-BAPB revealed significant birefringence and was confirmed using polarized optical microscopy (POM). Polymerization of self-assembled nanofibrous monomers with methyl methacrylate was carried out, and the distribution of the nanofibers in the polymer matrix was confirmed using POM. This investigation demonstrates a novel method for the fabrication of polymeric nanofibers with highly ordered, self-assembled functional monomers. The polymeric nanofibers are expected to improve the physical properties of polymer films in the field of microelectric and micromachine systems (MEMS).

Protein-templated semiconductor nanoparticle chains

Cadmium sulfide and lead sulfide semiconducting nanoparticle chains have been fabricated for the first time by exploiting a general property of proteins, amyloidogenicity. The diameter of the CdS and PbS nanowires was tuned in the range of ∼50 to ∼350 nm by changing the process parameters. The nanoparticle chains were characterized by field emission scanning electron microscopy, UV-visible spectroscopy, transmission electron microscopy, electron energy loss spectroscopy and high-resolution transmission electron microscopy.

Bottom-up assembly of hydrogels from bacteriophage and Au nanoparticles: the effect of cis- and trans-acting factors

Hydrogels have become a promising research focus because of their potential for biomedical application. Here we explore the long-range, electrostatic interactions by following the effect of trans-acting (pH) and cis-acting factors (peptide mutation) on the formation of Au-phage hydrogels. These bioinorganic hydrogels can be generated from the bottom-up assembly of Au nanoparticles (Au NP) with either native or mutant bacteriophage (phage) through electrostatic interaction of the phage pVIII major capsid proteins (pVIII). The cis-acting factor consists of a peptide extension displayed on the pVIII that mutates the phage. Our results show that pH can dictate the direct-assembly and stability of Au-phage hydrogels in spite of the differences between the native and the mutant pVIII. The first step in characterizing the interactions of Au NP with phage was to generate a molecular model that identified the charge distribution and structure of the native and mutant pVIII. This model indicated that the mutant peptide extension carried a higher positive charge relative to the native pVIII at all pHs. Next, by monitoring the Au-phage interaction by means of optical microscopy, elastic light scattering, fractal dimension analysis as well as Uv-vis and surface plasmon resonance spectroscopy, we show that the positive charge of the mutant peptide extension favors the opposite charge affinity between the phage and Au NP as the pH is decreased. These results show the versatility of this assembly method, where the stability of these hydrogels can be achieved by either adjusting the pH or by changing the composition of the phage pVIII without the need of phage display libraries.

Virus-mediated FCC iron nanoparticle induced synthesis of uranium dioxide nanocrystals

A reducing system involving M13 virus-mediated FCC Fe nanoparticles was employed to achieve uranium reduction and synthesize uranium dioxide nanocrystals. Here we show that metastable face-centered cubic (FCC) Fe nanoparticles were fabricated around the surface of the M13 virus during the specific adsorption of the virus towards Fe ions under a reduced environment. The FCC phase of these Fe nanoparticles was confirmed by careful TEM characterization. Moreover, this virus-mediated FCC Fe nanoparticle system successfully reduced contaminable U(VI) into UO(2) crystals with diameters of 2-5 nm by a green and convenient route.

In vitro self-assembly of tailorable nanotubes from a simple protein building block

We demonstrate a method for generating discretely structured protein nanotubes from the simple ring-shaped building block, homohexameric Hcp1 from Pseudomonas aeruginosa. Our design exploited the observation that the crystal lattice of Hcp1 contains rings stacked in a repeating head-to-tail pattern. High-resolution detail of the ring-ring interface allowed the selection of sites for specific cysteine mutations capable of engaging in disulfide bond formation across rings, thereby generating stable Hcp1 nanotubes. Protein nanotubes containing up to 25 subunits ( approximately 100 nm in length) were self-assembled under simple conditions. Furthermore, we demonstrate that the tube ends and interior can be independently and specifically functionalized to generate nanocapsules.

Self-assembly approaches to nanomaterial encapsulation in viral protein cages

A perspective on abiotic material encapsulation inside virus capsids is provided. The emphasis is on the physical principles of virus assembly relevant to packaging, strategies for encapsulation and capsid modification, and on emerging applications.

Principles of nanostructure design with protein building blocks

Currently there is increasing interest in nanostructures and their design. Nanostructure design involves the ability to predictably manipulate the properties of the self-assembly of autonomous units. Autonomous units have preferred conformational states. The units can be synthetic material science-based or derived from functional biological macromolecules. Autonomous biological building blocks with available structures provide an extremely rich and useful resource for design. For proteins, the structural databases contain large libraries of protein molecules and their building blocks with a range of shapes, surfaces, and chemical properties. The introduction of engineered synthetic residues or short peptides into these can expand the available chemical space and enhance the desired properties. Here we focus on the principles of nanostructure design with protein building blocks.

Conformational control of inorganic adhesion in a designer protein engineered for cuprous oxide binding

Combinatorial selection of peptides that bind technological materials has emerged as a valuable tool for room-temperature nucleation and assembly of complex nanostructured materials. At present, the parameters that control peptide-solid binding are poorly understood, but such knowledge is needed to build the next generation of hybrid materials. Here, we use a derivative of the DNA binding protein TraI engineered with a disulfide-bonded cuprous oxide binding sequence called CN225 to probe the influence of sequence composition and conformation on Cu2O binding affinity. We previously reported a statistically significant enrichment in paired arginines (RR) among a family of cuprous oxide binding peptides and hypothesized that this is a key motif for binding. However, systematic alanine (A) substitutions in the CN225 RR motif (creating RA, AR, and AA pairs) do not support the hypothesis that RR is critical for Cu2O binding by CN225. Instead, we find that the presentation of the peptide in a disulfide-constrained loop (i.e., the conformation present during combinatorial selection) is crucial for binding to the metal oxide. Our results suggest that caution should be exerted when extrapolating from statistical data and that, in some cases, conformation is more important than composition in determining peptide-inorganic adhesion.

Selection of biomolecules capable of mediating the formation of nanocrystals

Biopolymers in the biosphere are well known to mediate the formation of a wide array of inorganic materials, such as bone, shells, lenses, and magnetic particles to name a few. Recently, in vitro experiments with biopolymers such as peptides, RNA, and DNA have shown that templating by these macromolecules can yield a variety of materials under mild reaction conditions. The primary sequence of the biopolymer can be viewed as a proteomic or genomic signature for the templating of an inorganic material from defined metal precursors and reaction conditions. Together with the rapid advances in inorganic particle synthesis by other combinatorial methods, these bioinspired in vitro materials experiments may provide additional insights into possible inorganic materials yet to be discovered and subsequently synthesized by conventional methods. Some of the concepts important to understanding the crystallization phenomena occurring during biopolymer mediation are discussed. A simple kinetic model is provided in the context of known biopolymer-mediated inorganic crystallizations.

Viruses as building blocks for materials and devices

From the viewpoint of a materials scientist, viruses can be regarded as organic nanoparticles. They are composed of a small number of different (bio)polymers: proteins and nucleic acids. Many viruses are enveloped in a lipid membrane and all viruses do not have a metabolism of their own, but rather use the metabolic machinery of a living cell for their replication. Their surface carries specific tools designed to cross the barriers of their host cells. The size and shape of viruses, and the number and nature of the functional groups on their surface, is precisely defined. As such, viruses are commonly used in materials science as scaffolds for covalently linked surface modifications. A particular quality of viruses is that they can be tailored by directed evolution by taking advantage of their inbuilt colocalization of geno- and phenotypes. The powerful techniques developed by life sciences are becoming the basis of engineering approaches towards nanomaterials, opening a wide range of applications far beyond biology and medicine.

Selection and analysis of solid-binding peptides

Nature has long used peptide- and protein-based manufacturing to create structures whose remarkable mechanical, transport, optical, and even magnetic properties are determined by a fine control of composition and architecture extending from the nanoscale to the macroscale. Although there is much to learn from the tools and strategies that have been evolutionary selected for building biomaterials, accessing compositions and architectures of engineering interest is crucial to the development of the next generation of hybrid functional materials. In recent years, portable amino acid sequences selected from combinatorial libraries and supporting the assembly, nucleation, and geometrical organization of solid phases have emerged as attractive tools for bionanofabrication. Here, we review how these polypeptides are selected and progress in the understanding of their interaction with inorganic and synthetic materials.

Single M13 bacteriophage tethering and stretching

The ability to present biomolecules on the highly organized structure of M13 filamentous bacteriophage is a unique advantage. Where previously this viral template was shown to direct the orientation and nucleation of nanocrystals and materials, here we apply it in the context of single-molecule (SM) biophysics. Genetically engineered constructs were used to display different reactive species at each of the filament ends and along the major capsid, and the resulting hetero-functional particles were shown to consistently tether microscopic beads in solution. With this system, we report the development of a SM assay based on M13 bacteriophage. We also report the quantitative characterization of the biopolymer's elasticity by using an optical trap with nanometer-scale position resolution. Expanding the fluctuating rod limit of the wormlike chain to incorporate enthalpic polymer stretching yielded a model capable of accurately capturing the full range of extensions. Fits of the force-extension measurements gave a mean persistence length of approximately 1,265 nm, lending SM support for a shorter filamentous bacteriophage persistence length than previously thought. Furthermore, a predicted stretching modulus roughly two times that of dsDNA, coupled with the system's linkage versatility and load-bearing capability, makes the M13 template an attractive candidate for use in tethered bead architectures.

Biopolymer-based materials: the nanoscale components and their hierarchical assembly

Protein and nucleic acid biopolymers are well appreciated for their high-performance capabilities for molecular recognition, catalysis and information storage. Increasingly, these biopolymers are being examined for materials applications. Less tractable are polysaccharides and polymers of phenols, which, despite being nature's most abundant macromolecules, remain largely ignored for advanced materials applications. In our opinion, it seems certain that biology will contribute two major capabilities for materials biofabrication - the means to generate biopolymeric components with nanoscale precision, and the mechanisms for the hierarchical assembly of nanocomponents. These capabilities will enable unprecedented control of materials structure and provide exciting opportunities at the convergence of molecular biology and macromolecular science.

Manipulation of the growth of gold and silver nanomaterials on glass by seeding approach

This paper describes the growth of gold and silver nanomaterials from their corresponding colloidal seeds on glass substrates. The glass substrates were treated with 3-mercaptopropyltrimethoxysilane (MPTMS) and then with gold or silver nanoparticle seeds (AuNPSs or AgNPSs) at different concentrations. After separately immersing the thus-prepared MPTMS-AuNPS and MPTMS-AgNPS glass substrates in aqueous solutions containing cetyltrimethylammonium bromide, ascorbic acid, and gold or silver ions, we obtained Au and Ag nanomaterials of different sizes and shapes, which we characterized through scanning electron microscopy (SEM) and dark-field microscopy (DFM). At 0.001x concentrations AuNPSs and AgNPSs (i.e., 1000-fold-diluted solutions of the as-prepared samples), Au and Ag nanomaterials having 1.36 and 5.21 mum lengths and aspect ratios of 11 and 24 were prepared in yields of 27% and 54%, respectively. Scattering spectra of the thus-prepared single AuNRs and AgNRs revealed that the uniformity in the shape of the AuNRs was greater than that of the AgNRs. In addition, we demonstrate the preparation (using a laboratory-made synthesis system) and characterization (through DFM measurements) of Au nanomaterials, including AuNRs, from five AuNPS solutions of different concentrations on a single glass substrate.

Protein-mediated nanoscale biotemplating

Biomimetics--the concept of taking ideas from nature and implementing them in technology--has found particular use for the development of nanoscale materials. One such approach employs protein-mediated biotemplating for the nanostructuring of inorganic material. Recently, two key advances have been witnessed in this field. Firstly, the number of successfully employed biotemplates, including feasibility demonstrations of using three-dimensional crystalline structures, has been expanded. Secondly, the introduction of site-directed mutations on the protein template, or the display of peptides that exhibit effective biorecognition sequences for inorganic structures, has led to substantial improvements in our ability to control protein-mediated biotemplating. Taken together, these achievements will pave the way for the successful application of protein-mediated biotemplating in the future.

Virus-enabled synthesis and assembly of nanowires for lithium ion battery electrodes

The selection and assembly of materials are central issues in the development of smaller, more flexible batteries. Cobalt oxide has shown excellent electrochemical cycling properties and is thus under consideration as an electrode for advanced lithium batteries. We used viruses to synthesize and assemble nanowires of cobalt oxide at room temperature. By incorporating gold-binding peptides into the filament coat, we formed hybrid gold-cobalt oxide wires that improved battery capacity. Combining virus-templated synthesis at the peptide level and methods for controlling two-dimensional assembly of viruses on polyelectrolyte multilayers provides a systematic platform for integrating these nanomaterials to form thin, flexible lithium ion batteries.

Spontaneous assembly of viruses on multilayered polymer surfaces

The idea that randomly arranged supermolecular species incorporated in a network medium can ultimately create ordered structures at the surface may be counterintuitive. However, such order can be accommodated by regulating dynamic and equilibrium driving forces. Here, we present the ordering of M13 viruses, highly complex biomacromolecules, driven by competitive electrostatic binding, preferential macromolecular interactions and the rigid-rod nature of the virus systems during alternating electrostatic assembly. The steric constraints inherent to the competitive charge binding between M13 viruses and two oppositely charged weak polyelectrolytes leads to interdiffusion and the virtual 'floating' of viruses to the surface. The result is the spontaneous formation of a two-dimensional monolayer structure of viruses atop a cohesive polyelectrolyte multilayer. We demonstrate that this viral-assembled monolayer can be a biologically tunable scaffold to nucleate, grow and align nanoparticles or nanowires over multiple length scales. This system represents an interface that provides a general platform for the systematic incorporation and assembly of organic, biological and inorganic materials.

Characterization of silica-coated tobacco mosaic virus

The deposition of silica on the surface of tobacco mosaic virus (TMV) is achieved at a higher pH (>7) as a means to enhance its usefulness as a template for the synthesis of nanostructures. Electron energy loss spectroscopy definitively shows the presence of a silica shell on the surface of the TMV while small angle X-ray scattering differentiates successfully between silica-coated TMV and silica particles in the presence of uncoated TMV. Importantly, coating reactions done in a 50% w/v methanol/water solution produce smaller silica nanostructures during the condensation of the hydrolysis intermediates, possibly aiding in obtaining uniform coating. Furthermore, TMV-templated silica coatings are found to enhance the stability of the virus particle in methanol at conditions that would ordinarily disrupt the assembled particle. Combined these findings demonstrate that TMV can function as an efficient template for the controlled deposition of silica at neutral pH.

Assembly of multimeric phage nanostructures through leucine zipper interactions

One barrier to the construction of nanoscale devices is the ability to place materials into 2D- and 3D-ordered arrays by controlling the assembly and ordering of connections between nanomaterials. Ordered assembly of nanoscale materials may potentially be achieved using biological tools that direct specific connections between individual components. Recently, viruses were successfully employed as scaffolds for the nucleation of nanoparticles and nanowires (Mao et al., 2004); however, there is a paucity of methods for the higher order assembly of phage-templated materials. Here we describe a general strategy for the assembly of filamentous bacteriophages into long, wire-like or into tripod-like structures. To prepare the linear phage assemblies, dimeric leucine zipper protein domains, fused to the p3 and p9 proteins of M13 bacteriophage, were employed to direct the specific end-to-end self-association of the bacteriophage particles. Electron microscopy revealed that up to 90% of the phage displaying complementary leucine zipper domains formed linear multi-phage assemblies, composed of up to 30 phage in length. To prepare tripod-like assemblies, phage were engineered to express trimeric leucine zippers as p3 fusion proteins. This resulted in 3D assembly with three individual phages attached at a single point. These ordered phage structures should provide a foundation for self-assembly of virally templated nanomaterials into useful devices.