Template-directed assembly of a de novo designed protein

Many naturally occurring biomaterials are composed of laminated structures in which layers of beta-sheet proteins alternate with layers of inorganic mineral. These ordered laminates often have structural and mechanical properties that differ significantly from those of nonbiological materials. An important step in the construction of novel biomaterials is the creation of composites wherein a de novo designed protein assembles into an ordered structure. To achieve this goal, we layered a de novo protein onto the surface of highly ordered pyrolytic graphite (HOPG). The protein was derived from a combinatorial library of novel sequences designed to fold into amphiphilic beta-sheet structures. Atomic force microscopy reveals that the protein assembles on the HOPG surface into ordered fibers aligned in three orientations at 120 degrees to each other. The symmetry and extent of the ordered regions indicate that the hexagonal lattice underlying the graphite surface templates assembly of millions of protein molecules into a highly ordered structure.     

应用纳米球刻蚀法在自组装膜修饰的硅表面生成中尺度的网状蛋白层

The patterning and immobilization of protein molecules onto functionalized silicon substrate through surface silane chemistry is of interest because protein patterning is an important prerequisite for the development of protein-based diagnostics in biological and medicinal fields. As a model system, mesoscale netty lysozyme arrays were assembled on oxidized undecyltrichlorosilane (UTSox) monolayer coated silicon surface through nanosphere lithography. The size of the arrays ranged from nanometer to micrometer can be easily adjusted by changing the size of nanospheres applied on the surface. By using nanosphere lithography, we are capable of fabricating a regular array of protein islands over centimeter sample regions. The created lysozyme protein patterns were characterized by atomic force microscopy (AFM) and fluorescence microscope, respectively. The analysis has demonstrated that this newly established approach offers a faster and more reliable process to fabricate netty protein arrays over large areas compared to conventional scanning-probe based fabrication methods. Furthermore, the carboxylic acid-terminated layer on surfaces is particularly effective for immobilizing protein molecules through either electrostatic interactions or covalent attachment via imine bonds. Therefore, the negative-toned protein structure on the surface with carboxylic acid groups coated on the bare areas makes it possible to fabricate two types of protein molecules on one surface.     

Thin film processing using S-layer proteins: biotemplated assembly of colloidal gold etch masks for fabrication of silicon nanopillar arrays

We explored the bionanofabrication of silicon nanopillar structures using ordered gold nanoparticle arrays generated from microbial surface layer (S-layer) protein templates. The S-layer template used for these thin film processing experiments was isolated from the Gram-positive bacterium Deinococcus radiodurans. In this preliminary work, S-layers preimmobilized onto chemically modified silicon substrates were initially used to template the fabrication of a nanolithographic hard mask pattern comprised of a hexagonally ordered array of 5-nm gold nanoparticles (lattice constant = 18 nm). Significantly, the use of the biotemplated gold nanoparticle mask patterns in an inductively coupled plasma (ICP) etching process successfully yielded silicon nanopillar structures. However, it was found that the resultant nanopillars (8–13 nm wide at the tip, 15–20 nm wide at half-height, 20–30 nm wide at the base, and 60–90 nm tall) appeared to lack any significant degree of translational ordering. The results suggest that further studies are needed in order to elucidate the optimal plasma processing parameters that will lead to the generation of long-range ordered arrays of silicon-based nanostructures using S-layer protein templates.     

Materials for the preparation of polymer pen lithography tip arrays and a comparison of their printing properties

Polymer Pen Lithography (PPL) uses an array of polymeric tips, typically composed of poly(dimethyl siloxane), to transfer ink onto a surface and create patterns of soft molecules with micrometer to nanometer feature dimensions. In this study, tip arrays were fabricated from poly(methyl methacrylate), poly([methyl methacrylate]‐co‐[butyl methacrylate]), and poly(3‐mercaptopropylmethylsiloxane), and used to pattern 1‐mercaptohexadecanoic acid onto Au surfaces to determine the fidelity of pattern transfer by PPL as a function of the mechanical properties of the materials. It was found that the dependence between the applied force and feature edge length correlates directly to the mechanical properties of each of the polymers used to fabricate the tip arrays, where stiffer polymers have a reduced dependence between the applied force and feature size. This study demonstrates that PPL tip arrays can be composed of a wide variety of materials whose choice is determined by the desired printing application. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2013     

On the Structure and Formation of Self-Assembled Lattices of Gold Nanoparticles

The structure and ordering of nanoparticles of gold functionalized with n-alkyl thiol molecules are studied both experimentally and theoretically. Samples where produced using n=6 to n=16 alkyl thiol molecules. High Resolution Electron Microscopy coupled with image processing was used to study the gold particle structure. The details of the particle structure are discussed. We found that when the gold surface is saturated with thiol molecules there is some tendency to produce molecules with a disulphide structure. We also show that ordered arrays of particles can be produced using Langmuir-Blodgett techniques. The crystal structure of the films produced is studied and found to be 3D hcp. We also report that thiol covered gold particles with a size of 5 nm present a rounded shape suggesting that thiol molecules might induce an isotropic surface energy. It is found in the theoretical calculations that a strong bond between gold and sulphur is required to stabilize the complex metal-n-alkyl thiol. It is predicted that otherwise a heavily distorted nanocore will be formed. This is contrary to the observed structure of the particles.     

Self-assembly of ionic liquid (BMI-PF6)-stabilized gold nanoparticles on a silicon surface: chemical and structural aspects

Ultrafine monodisperse gold nanoparticles (AuNPs) were synthesized by an elegant sputtering of gold onto 1- n-butyl-3-methylimidazolium hexafluorophosphate (BMI-PF(6)) ionic liquid. It was found that the BMI-PF(6) supramolecular aggregates were loosely coordinated to the gold nanoparticles and were replaceable with thiol molecules. The self-assembly of BMI-PF(6)-stabilized AuNPs onto a (3-mercaptopropyl)trimethoxysilane (MPS)-functionalized silicon surface in 2D arrays, followed by dodecanethiol (DDT) treatment, have been demonstrated using X-ray photoelectron spectroscopy, field emission scanning electron microscopy, and contact angle measurements. DDT treatment of tethered AuNPs revealed two types of interactions between AuNPs and the MPS-functionalized surface: (a) AuNPs anchor through Au-S chemisorption linkage resulting in strong immobilization and (b) some of the AuNPs are supported by physisorption, driven by BMI-PF(6). The attachment of these particles remains unchanged with sonication. The replacement of BMI-PF(6) aggregates from physisorbed AuNPs with DDT molecules advances the dilution of their interaction with the MPS-functionalized surface, and they subsequently detach from the silicon surface. The present finding is promising for the immobilization of ionic liquid-stabilized nanoparticles, which is very desirable for electronic and catalytic device fabrication. Additionally, these environmentally friendly AuNPs are expected to replace conventional citrate-stabilized AuNPs.     

Isolated heterometallic Cr7Ni rings grafted on Au(111) surface

A study of the deposition of heterometallic antiferromagnetically coupled rings onto gold surfaces is reported. Two new {Cr7Ni} rings, [NH2nPr2][Cr7NiF8(3-tpc)16] (1) (where 3-tpc=3-thiophenecarboxylate) and [nBuNH2CH2CH2SH] [Cr7NiF8(O2CtBu)16] (2) have been made and structurally characterized. They have been deposited from the liquid phase on Au(111) and the adsorbed molecules compared by means of scanning tunneling microscopy (STM) and X-ray photoemission spectroscopy (XPS). In both cases a two-dimensional distribution of individually accessible {Cr7Ni} heterometallic rings on the gold surface has been obtained, exploiting the direct grafting of sulfur-functionalized clusters. There is a competition between the chemisorption of the {Cr7Ni} clusters and a thiolic self-assembled monolayer (SAM) formed by free ligands. In 2, the presence of a single sulfur ligand should force the molecule to graft with the ring axis normal to the surface. The cluster stability in the STM images and the S-2p energy positions demonstrate, for both functionalizations, the strength of the grafting with the gold surface.     

Formation of a gold superlattice on an S-layer with square lattice symmetry

This work describes a new strategy in which a crystalline bacterial cell surface layer (S-layer) composed of a monolayer of a single protein species was used as periodic nanometric template in the nucleation of ordered arrays of gold nanoparticles. A square superlattice of uniform 4 to 5 nm sized gold particles with 12.8 nm repeat distance was fabricated by exposing the S-layer lattice of Bacillus sphaericus CCM2177, in which thiol groups had been introduced before, to a tetrachloroauric(III) acid solution. Transmission electron microscopical studies showed that the gold nanoparticles were formed in the pore region during electron irradiation of an initially grainy gold coating covering the whole S-layer lattice. The shape of the gold particles resembled the morphology of the pore region of the square S-layer lattice. By electron diffraction and energy dispersive X-ray analysis the crystallites were identified as gold (Au(0)). Electron diffraction patterns revealed that the gold nanoparticles were crystalline but in the long range order not crystallographically aligned. It is postulated that S-layers will allow the fabrication of a wide range of inorganic nanocrystal superlattice arrays.     

Pinning of size-selected Pd nanoclusters on graphite

The production of stable cluster arrays on smooth surfaces has several potential technological applications. We report a study of the pinning of size-selected palladium nanoclusters on the graphite surface. The clusters formed during gas aggregation in vacuum are projected with sufficient kinetic energy to create a defect in the graphite surface. The energy necessary to create such an immobilizing defect is investigated as a function of the palladium cluster size. The palladium pinning energy is found to deviate from the simple binary collision model as appropriate to previously reported silver and gold results. This finding is in agreement with the deviation of nickel clusters and points to the influence of the interatomic cluster bonding on the mechanics of the collision.     

Images of Azurin Protein Studied by AFM

Azurins, a wild type and a genetically mutant K27 altered one. were immobilized on annealed gold sur-face and investigated by means of atomic force microscopy. It was found that the surface coverage and height distribution of the adsorbed protein molecules are different from each other, which is possibly the result of the different orientation on the surface. It is believed that the wild type azurin is connected to gold surface by the disulphide bridge;while the mutant, K27C, might be through the thiol groups of the cysteine residues on their surface.     

Use of cellulose derivatives on gold surfaces for reduced nonspecific adsorption of immunoglobulin G

This study addresses the design of protein-repellent gold surfaces using hydroxyethyl- and ethyl(hydroxyethyl) cellulose (HEC and EHEC) and hydrophobically modified analogues of these polymers (HM-HEC and HM-EHEC). Adsorption behavior of the protein immunoglobulin G (IgG) onto pure gold and gold surfaces coated with cellulose polymers was investigated and described by quartz crystal microbalance with dissipation monitoring (QCM-D), atomic force microscopy (AFM) and contact angle measurements (CAM). Surfaces coated with the hydrophobically modified cellulose derivatives were found to significantly outperform a reference poly(ethylene glycol) (PEG) coating, which in turn prevented 90% of non-specific protein adsorption as compared to adsorption onto pure gold. HEC and EHEC prevented around 30% and 60% of the IgG adsorption observed on pure gold, while HM-HEC and HM-EHEC were both found to completely hinder biofouling when deposited on the gold substrates. Adsorption behavior of IgG has been discussed in terms of polymer surface coverage and roughness of the applied surfaces, together with hydrophobic interactions between protein and gold, and also polymer-protein interactions.     

Surface plasmon resonance imaging studies of protein-carbohydrate interactions

Carbohydrate arrays fabricated on gold films were used to study carbohydrate-protein interactions with surface plasmon resonance (SPR) imaging. An immobilization scheme consisting of the formation of a surface disulfide bond was used to attach thiol-modified carbohydrates onto gold films and to fabricate carbohydrate arrays. The carbohydrate attachment steps were characterized using polarization modulation Fourier transform infrared reflection absorption spectroscopy; and poly(dimethylsiloxane) microchannels were used to immobilize probe compounds at discrete locations on a gold film. The binding of the carbohydrate-binding proteins concanavalin A (ConA) and jacalin to arrays composed of the monosaccharides mannose and galactose was monitored with SPR imaging. SPR imaging measurements were employed to accomplish the following: (i) construct adsorption isotherms for the interactions of ConA and jacalin to the carbohydrate surfaces, (ii) monitor protein binding to surfaces presenting different compositions of the immobilized carbohydrates, and (iii) measure the solution equilibrium dissociation constants for ConA and jacalin toward mannose and galactose, respectively. Adsorption coefficients (K(ADS)) of 2.2 +/- 0.8 x 10(7) M(-)(1) and 5.6 +/- 1.7 x 10(6) M(-)(1) were obtained for jacalin adsorbing to a galactose surface and ConA adsorbing to a mannose surface, respectively. The solution equilibrium dissociation (K(D)) constant for the interaction of jacalin and galactose was found to be 16 +/- 5 microM, and for ConA and mannose was found to be 200 +/- 50 microM.     

Mechanism underlying bioinertness of self-assembled monolayers of oligo(ethyleneglycol)-terminated alkanethiols on gold: protein adsorption, platelet adhesion, and surface forces

The mechanism underlying the bioinertness of the self-assembled monolayers of oligo(ethylene glycol)-terminated alkanethiol (OEG-SAM) was investigated with protein adsorption experiments, platelet adhesion tests, and surface force measurements with an atomic force microscope (AFM). In this work, we performed systematic analysis with SAMs having various terminal groups (-OEG, -OH, -COOH, -NH(2), and -CH(3)). The results of the protein adsorption experiment by the quartz crystal microbalance (QCM) method suggested that having one EG unit and the neutrality of total charges of the terminal groups are essential for protein-resistance. In particular, QCM with energy dissipation analyses indicated that proteins absorb onto the OEG-SAM via a very weak interaction compared with other SAMs. Contrary to the protein resistance, at least three EG units as well as the charge neutrality of the SAM are found to be required for anti-platelet adhesion. When the identical SAMs were formed on both AFM probe and substrate, our force measurements revealed that only the OEG-SAMs possessing more than two EG units showed strong repulsion in the range of 4 to 6 nm. In addition, we found that the SAMs with other terminal groups did not exhibit such repulsion. The repulsion between OEG-SAMs was always observed independent of solution conditions [NaCl concentration (between 0 and 1 M) and pH (between 3 and 11)] and was not observed in solution mixed with ethanol, which disrupts the three-dimensional network of the water molecules. We therefore concluded that the repulsion originated from structured interfacial water molecules. Considering the correlation between the above results, we propose that the layer of the structured interfacial water with a thickness of 2 to 3 nm (half of the range of the repulsion observed in the surface force measurements) plays an important role in deterring proteins and platelets from adsorption or adhesion.     

Eluotropic strength in non-aqueous liquid chromatography with porous graphitic carbon

Protein adsorption can be either endothermic or exothermic depending upon the protein, the sorbent and process conditions. In the case of protein adsorption onto ion-exchange surfaces exothermic adsorption heats are usually characterized as representing the electrostatic interaction between two oppositely charged surfaces. Endothermic adsorption heats are typically characterized as representing protein reconfiguration and/or repulsive interactions between adsorbed molecules. In certain segments of the literature surface dehydration and solution non-idealities have been suggested as possible sources of endothermic heats of adsorption. Each of these phenomena was investigated during studies concerning the adsorption of bovine serum albumin and ovalbumin onto an anion-exchange sorbent. The results demonstrated that electrostatic repulsive interactions between adsorbed molecules appears to be a larger contributor to endothermic heats of adsorption than surface dehydration or solution non-idealities. The presence of mobile phase cations can reduce the magnitude of endothermic adsorption heats by screening repulsive interactions between adsorbed molecules. Although water release was not found to be a major contributor to endothermic adsorption heats, it is likely to be a contributor to the entropic driving force associated with the adsorption of bovine serum albumin.     

Fabrication and placement of a ring structure of nanoparticles by a laser-induced micronanobubble on a gold surface

We have developed a new fabrication method for a ring structure of assembled nanoparticles on a gold surface by the use of continuous Nd:YAG laser light. A micronanobubble on a gold surface, created by laser local heating, acts as a template for the formation of the ring structure. Both Marangoni convection flow and capillary flow around the micronanobubble are responsible for the driving force to assemble nanoparticles such as CdSe Q-dots into the ring structure from the solution. Because a single micronanobubble was generated by the Nd:YAG laser focusing point, the precise positioning of the ring structure was feasible directly on the gold surface, which makes it possible to fabricate various patterns of rings such as arrays and letters and even a double-ring structure without any photomasks or any templates.     

Influence of nanobubbles on the adsorption of nanoparticles

A quartz crystal microbalance was used to study the influence of nanobubbles on the adsorption of polystyrene nanoparticles onto surfaces coated with gold, or coated with dodecanethiol or mercaptoundecanoic acid self-assembled monolayers (SAMs). Adsorption of the nanoparticles onto the surface causes the resonant frequency of the quartz crystal to decrease. We found that particles were adsorbed onto the gold-coated quartz crystal in air-rich water, but not in degassed water. This finding supports the long-standing hypothesis that nanobubbles play a key role in the long-range attractive force between hydrophobic surfaces in aqueous solutions. When the experiments were conducted using quartz crystals coated with a hydrophobic dodecanethiol SAM, the nanoparticles were adsorbed onto the surface even in degassed water due to the short-range hydrophobic interactions between the nanoparticles and the dodecanethiol molecules. In contrast, the nanoparticles were adsorbed to a lesser degree onto the hydrophilic mercaptoundecanoic acid-coated crystals due to electrostatic repulsive forces.     

Surface grafted sulfobetaine polymers via atom transfer radical polymerization as superlow fouling coatings

One of the sulfobetaine methacrylate (SBMA) monomers, N-(3-sulfopropyl)-N-(methacryloxyethyl)-N,N-dimethylammonium betaine, was polymerized onto initiator-covered gold surfaces using atom transfer radical polymerization (ATRP) to form uniform polymer brushes. Self-assembled monolayers (SAMs) with ATRP initiators were characterized by X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). The thickness of grafted poly(SBMA) films was measured by ellipsometry. Fibrinogen adsorption on poly(SBMA) grafted surfaces was measured with a surface plasmon resonance (SPR) sensor. Two approaches were compared to graft ATRP initiators onto gold surfaces for surface polymerization and subsequent protein adsorption on these polymer grafted surfaces. The first was to prepare a SAM from omega-mercaptoundecyl bromoisobutyrate onto a gold surface. Superlow fouling surfaces with well-controlled poly(SBMA) brushes were achieved using this approach (e.g., fibrinogen adsorption <0.3 ng/cm2). The second approach was to react bromoisobutyryl bromide with a hydroxyl-terminated SAM on a gold surface. Although protein adsorption decreased as the density of surface initiators increased, the surface prepared using the second approach was not able to achieve as low protein adsorption as the first approach. Key parameters to achieve superlow fouling surfaces were studied and discussed.     

Direct structure determination using residual dipolar couplings: reaction-site conformation of methionine sulfoxide reductase in solution

Residual dipolar couplings (RDC) from partially aligned molecules provide long-range structural data and are thus particularly well adapted to rapid structure validation or protein fold recognition. Extensive measurements in two alignment media can also provide precise de novo structure from RDC alone. We have applied a novel combination of these approaches to the study of methionine sulfoxide reductase (MsrA) from Erwinia chrysanthemi, a 27 kDa enzyme essential for repairing oxidative stress damage. The tertiary fold was initially validated by comparing backbone RDC to expected values from the crystal structure of the homologous MsrA from Escherichia coli. Good agreement was found throughout the chain, verifying the overall topology of the molecule, with the exception of the catalytically important peptide P196-L202, where strong and systematic RDC violation was observed. No evidence for local differential mobility in this region was detected, implying that the structure of the strand differs in the two molecules. We have therefore applied the de novo approach meccano to determine the conformation of this peptide using only RDC. A single conformation is found that is in agreement with all measured data. The aligned peptide can be docked onto the expected covalence of the rest of the template molecule while respecting its strictly defined relative orientation. In contrast to the structure of MsrA from E. coli, the reactive side chain of Cys200 is oriented toward the interior of the molecule and therefore closer to the catalytic Cys53, obviating the need for previously proposed conformational reorganization prior to formation of this disulfide intermediate. This analysis requires only backbone assignment and uses unambiguously assigned and readily measurable structural data, thereby greatly economizing investigation time compared to established nuclear Overhauser effect- (nOe-) based structure calculation methods.     

Solvent induced aggregation of protoporphyrin and octacarboxylphthalocyanine of zinc deposited on gold surface

In this paper, we studied the influence of solvent on the morphology of zinc protoporphyrin and zinc octacarboxylphthalocyanine films transferred onto gold surface by dipping. In these films, carboxylic acid groups borne in periphery of macrocycles allow anchoring to gold via ionic interaction. First, we followed by UV-Visible absorption spectroscopy the solvation state of these conjugated macrocycles in pure DMF, in pure ethanol and in various ethanol/DMF mixtures. We show that the increase in ethanol proportion promotes interactions between macrocycles. Second, molecular layers of macrocycles spontaneously adsorbed from these various solutions onto gold surface were analyzed by ellipsometry, water contact angle measurements, UV-Visible absorption spectroscopy and atomic force microscopy. Results evidenced the layers were mainly composed of grains whose size of a few nanometers was directly related to the solvation conditions of molecules. In addition, Q band splitting was observed in the absorption spectrum of zinc octacarboxylphthalocyanine grain films which indicates specific organization of those molecules. Therefore solvent is shown to have a profound influence on the nanostructuration of as-prepared macrocycle layers on gold surface by promoting pre-organization in solution, and its composition enables to better control the morphology of those films by tuning the solubilization of macrocycles.