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.     

Dielectrophoretic immobilization of proteins: Quantification by atomic force microscopy

The combination of alternating electric fields with nanometer‐sized electrodes allows the permanent immobilization of proteins by dielectrophoretic force. Here, atomic force microscopy is introduced as a quantification method, and results are compared with fluorescence microscopy. Experimental parameters, for example the applied voltage and duration of field application, are varied systematically, and the influence on the amount of immobilized proteins is investigated. A linear correlation to the duration of field application was found by atomic force microscopy, and both microscopical methods yield a square dependence of the amount of immobilized proteins on the applied voltage. While fluorescence microscopy allows real‐time imaging, atomic force microscopy reveals immobilized proteins obscured in fluorescence images due to low S/N. Furthermore, the higher spatial resolution of the atomic force microscope enables the visualization of the protein distribution on single nanoelectrodes. The electric field distribution is calculated and compared to experimental results with very good agreement to atomic force microscopy measurements.     

Strategies for protein-based nanofabrication: Ni-NTA as a chemical mask to control biologically imposed symmetry

Background: Technologies that improve control of protein orientation on surfaces or in solution, through designed molecular recognition, will expand the range of proteins that are useful for biosensors, molecular devices and biomaterials. A limitation of some proteins is their biologically imposed symmetry, which results in indistinguishable recognition surfaces. Here, we have explored methods for modifying the symmetry of an oligomeric protein that exhibits useful self-assembly properties.Results:Escherichia coli glutamine synthetase (GS) contains 24 solvent-exposed histidines on two symmetry-related surfaces. These histidines drive a metal-dependent self-assembly of GS tubes. Immobilization of GS on the affinity resin Ni²⁺-NTA followed by on-column modification with diethyl pyrocarbonate affords asymmetrically modified GS that self-assembles only to the extent of ‘short’ dimeric GS tubes, as demonstrated by electron microscopy, dynamic light scattering and atomic force microscopy. The utility of Ni²⁺-NTA as a chemical mask was also demonstrated for asymmetric modification of engineered cysteines adjacent to the natural histidines.Conclusions: Current genetic methods do not provide distinguishable recognition elements on symmetry-related surfaces of biologically assembled proteins. Ni²⁺-NTA serves as a mask to control chemical modification in vitro of residues within symmetry-related pairs, on proteins containing functional Histags. This strategy may be extended to modification of a wide range of amino acids with a myriad of reagents.     

Anodic Stripping Voltammetry: An AFM Study of Some Problems and Limitations

The use of anodic stripping voltammetry for quantitative analytical measurements using solid electrodes is addressed in the light of generic limitations arising from i) electrode heterogeneity, ii) electrode morphology, iii) inhibited electrodeposition, and iv) incomplete stripping of deposited metal in the anodic sweep. It is shown, using direct imaging of electrode surfaces via AFM and optical microscopy, that each of the preceding factors may produce significant deviations from ideal electrode behavior. The use of atomic force microscopy to fully characterize any developed ASV procedures is strongly recommended. To ensure reproducible and accurate stripping voltammetry, steps should be taken to minimize the effects discussed.     

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.     

In situ AFM study of proton-assisted electrochemical oxidation/reduction of microparticles of organic dyes

In situ atomic force microscopy (AFM) images of crystals of organic dyes alizarin, indigo and morin have been monitored during the course of their solid-state electrochemical oxidation/reduction in contact with aqueous acetate buffer. Such images indicate that proton-assisted reduction and oxidation processes are localized in a shallow layer in the vicinity of the particle/electrolyte interface, in agreement with expectances from the Lovric and Scholz model with significantly restricted proton diffusion across the solids.     

Molecular imaging of membrane proteins and microfilaments using atomic force microscopy

Atomic force microscopy (AFM) is an emerging technique for a variety of uses involving the analysis of cells. AFM is widely applied to obtain information about both cellular structural and subcellular events. In particular, a variety of investigations into membrane proteins and microfilaments were performed with AFM. Here, we introduce applications of AFM to molecular imaging of membrane proteins, and various approaches for observation and identification of intracellular microfilaments at the molecular level. These approaches can contribute to many applications of AFM in cell imaging.     

Evaluation of the arsenic binding capacity of plant proteins under conditions of protein extraction for gel electrophoretic analysis

As prerequisite for the investigation of arsenic-binding proteins in plants, the general influence of different extraction parameters on the binding behaviour of arsenic to the plant protein pool was investigated. The concentration of the extraction buffer affected the extraction yield both for proteins and for arsenic revealing an optimal buffer concentration of 5 mM Tris/HCl, pH 8. The addition of 1 or 2% (w/v) SDS to the extraction buffer produced a two- to threefold enhancement of the total protein extraction yield but strongly suppressed the simultaneous extraction of arsenic from 80 ± 8% extraction yield obtained without SDS to 48 ± 2% in presence of 2% (w/v) SDS. The arsenic binding capacity of the protein fraction obtained after extraction with Tris buffer and protein precipitation by trichloroacetic acid in acetone was estimated to be 1.4 ± 0.6% independently on the original spiking concentration of arsenic provided in the form of monomethylarsonate to the extracts. Due to the low total protein concentrations of the plant extracts that varied in the range from 75 to 412 μg mL⁻¹ depending on the extraction parameters, high arsenic concentrations of 263-1001 mg (kg protein mass)⁻¹ resulted for spiking concentrations of 10 mg As L⁻¹. The optimized protein isolation procedure was applied to plants grown under arsenic exposure and revealed a similar arsenic binding capacity as for the spiked protein extracts.     

原子力显微镜在生物大分子结构研究中的应用进展

评述了原子力显微镜（ａｔｏｍｉｃ ｆｏｒｃｅ ｍｉｃｒｏｓｃｏｐｙ,ＡＦＭ）的成镜模式与探针技术的发展以及在脱氧核糖核酸、蛋白质和多糖等生物大分子结构研究中的应用进展,并展望了原子力显微镜在此领域的发展前景。     

Dynamic imaging of single DNA-protein interactions using atomic force microscopy

Atomic force microscopy (AFM) imaging of static DNA-protein complexes, in air and in liquid, can be used to directly obtain quantitative and qualitative information on the structure of different complexes. For example, DNA length, the location of preferential binding sites for proteins and bending of DNA as a result of the complexation can all be measured. Recording consecutive AFM images of DNA and protein molecules under conditions that they are still able to move and interact, or dynamic AFM imaging, however, can reveal information on the dynamic aspects of the interactions between these molecules. Here, an overview is given of the technical challenges that need to be considered for successful dynamic AFM imaging studies of individual DNA-protein interactions. Necessary technical improvements to the AFM set-up and the development of new sample preparation methods are described in this paper.     

Effect of size and protein environment on electrochemical properties of gold nanoparticles on carbon electrodes

We studied the electrochemical properties of gold nanoparticles (GNPs) and their complexes with proteins using square-wave voltammetry. Effect of the nanoparticle size and detection procedure was explored upon the oxidation of GNPs on a glassy carbon electrode (GCE). For pre-characterized GNPs of 13, 35 and 78 nm diameter, the oxidation peak potential was + 0.98, + 1.03 and + 1.06 V vs. Ag/AgCl, respectively. The conjugation of GNPs with four different proteins was verified by UV–Vis spectroscopy and atomic force microscopy indicated the formation of protein shells around GNPs. This process hampered the oxidation of GNPs on bare GCE causing pronounced decrease in the current response by an average factor of 72. GCE modification with carbon nanotubes weakly influenced the sensitivity of GNP detection but resulted in a 14.5-fold signal increase averaged for all GNP–protein complexes. The acidic dissolution and electrodeposition of GNPs or their complexes adsorbed on GCE allowed superior signal amplification directly proportional to nanoparticle size. The results are useful for the optimization of voltammetric analysis of GNP–protein complexes and can be extended to the characterization of other metal nanostructures and their complexes with biological components.     

Chemical force microscopy: applications in surface characterisation of natural hydroxyapatite

Detailed mapping of surface chemistry with nanometer resolution has application throughout the physical and life sciences. The atomic force microscope (AFM) has provided a tool that, when using functionalised probes, is capable of providing chemical information with this level of spatial resolution. Here, we describe the technique of chemical force microscopy (CFM) and demonstrate the sensitivity of the technique using chemical force titrations against pH. We describe in detail the specific application of mapping the surface charge on natural hydroxyapatite from skeletal tissue and show that this new information leads to a better understanding of the binding of matrix proteins to the mineral surface.     

Imaging of reconstituted purple membranes by atomic force microscopy

The organization of bacteriorhodopsin (bR) within reconstituted purple membranes (RPM) was examined using atomic force microscopy (AFM). Five reconstituted species were examined: RPM 3 (bR/native polar lipids/dimyristoylphosphatidylcholine (DMPC) in a 1:9:14 molar ratio), RPM 4 (bR/native polar lipids in a 1:7 molar ratio), RPM 5 (bR/native polar lipids/1,2-di-O-phytanyl-sn-glycerol in a 1:3.5:6.1 molar ratio), RPM 6 (bR/native polar lipids/1,2-di-O-phytanyl-sn-glycero-3-phosphocholine in a 1:3.5:4.9 molar ratio), and RPM 7 (bR/native polar lipids/1,2-diphytanoyl-sn-glycero-3-[phospho-l-serine] in a 1:3.5:4.6 molar ratio). RPM 3 patches adsorbed onto mica exhibit domains of crystallized bR trimers arranged in a hexagonal packing structure, similar to those found in native purple membrane (NPM). These domains are enclosed by DMPC-rich regions. RPM 4 patches were observed to have larger domains of crystallized bR, with trimer orientation 30° different from that found in NPM. The bR-rich domains are enclosed by a large, protein-free, lipid-rich region. The topography of RPM 5 was difficult to resolve as the surface had no discernable patterns or structure. The topographies of RPM 6 and 7 were similar to that found in RPM 3 in that higher domains were formed within the patch adsorbed onto mica. They may contain protein-rich regions, but clear images of protein arrangement could not be obtained using AFM. This may be a result of imaging limitations or of the lack of organization of bR within these domains.     

蘸礁笔纳米平板印刷术(DPN)在蛋白质芯片中的应用

生物芯片技术以及其临床应用的快速发展,将驱动其研究平台的微型化,以达到更高的阵列排列密度、灵敏度和减少样品消耗;为了满足以上要求,阵列元素的尺寸必须由目前的微米尺度缩小到纳米尺度。蘸礁笔纳米平板印刷术(DPN,Dip-Pen Nanolithography),采取类似于“书写”的方式,能够直接在合适的基板表面制作各种的纳米尺度的蛋白阵列。DPN技术具有操作简单、材料选择灵活、分辨率高、能够精确控制被阵列分子的位置等优点,是在纳米尺度上制作生物分子的阵列首选。本文介绍了蘸礁笔纳米平板印刷术在蛋白质芯片中的应用。     

Competitive adsorption of proteins and low-molecular-weight surfactants: computer simulation and microscopic imaging

Proteins and low-molecular-weight (LMW) surfactants are used in the food industry as emulsifying (and foaming) ingredients and as stabilizers. These attributes are related to their ability to adsorb at fluid-fluid (and gas-fluid) interfaces lowering the interfacial (and surface) tension of liquids. Hence, the study of the properties of adsorbed layers of these molecules can be expected to lead to a better understanding of their effect on food products. Direct proof of the validity of mesoscopic models of systems of proteins and LMW surfactants can only be achieved by quantitative theoretical predictions being tested against both macroscopic and mesoscopic experiments. Computer simulation constitutes one of the few available tools to predict mathematically the behaviour of models of realistic complexity. Furthermore, experimental techniques such as atomic force microscopy (AFM) now allow high resolution imaging of these systems, providing the mesoscopic scale measurements to compare with the simulations. In this review, we bring together a number of related findings that have been generated at this mesoscopic level over the past few years. A useful simple model consisting of spherical particles interacting via bonded and unbonded forces is described, and the derived computer simulation results are compared against those from the imaging experiments. Special attention is paid to the adsorption of binary mixtures of proteins, mixtures of LMW surfactants, and also protein+surfactant mixed systems. We believe that further development of these mathematically well-defined physical models is necessary in order to achieve a proper understanding of the key physico-chemical processes involved.     

Fragile structured layers on surfaces in highly concentrated solutions of electrolytes of various valencies

In the present study a dynamic mode of atomic force microscopy for force measurements was employed to investigate the hydration repulsion force between charged surfaces in highly concentrated electrolyte solutions of NaCl, MgCl₂ and LaCl₃. A strong dependence of this repulsive force on the approaching rate of surfaces, the prehistory of their contact and the valency of cations was demonstrated. The phenomena were strongly pronounced in the cases of high scan rates, large surfaces and cations of high valency. The results obtained indicate that a fragile structure composed of water molecules, ions and hydrated ions exists outside of the primary layer of water molecules and ions adsorbed firmly on surfaces.     

Self-assembly and morphological characterization of two-component functional amyloid proteins

Functional amyloid has been increasingly applied as self-assembling nanostructures to construct multifunctional biomaterials. However, little has been known how different side domains, varied fusion positions and subunits affect self-assembly and morphologies of amyloid fibrils. Here, we constructed three groups of two-component amyloid proteins based on CsgA, the major protein components of Escherichia coli biofilms, to bridge these gaps. We showed that all fusion proteins have amyloid features, as indicated by Congo red assay. Atomic force microscopy (AFM) indeed reveals that these fusion proteins are able to self-assemble into fibrils, with an average diameter of 0.5-2 nm and length of hundreds of nanometers to several micrometers. The diameter of fibrils increases with the increase of the molecular weight of fusion domains, while the dynamic assembly of recombinant proteins was delayed as a result of the introduction of fusion domains. Moreover, fusion of the same functional domains but at intermediate position seems to cause the most interference on fibril assembly compared with those fused at C or Nterminus, as mainly short and irregular fibrils were detected. This phenomenon appears more pronounced for randomly coiled mussel foot proteins (Mfps) than for rigid chitin-binding domain (CBD). Finally, increase of the molecular weight of tandem repeats in protein monomer seemed to increase the fibril diameter of the resultant fibrils, but either reduction of the tandem repeats of CsgA to one single belta-sheet loop or increase in the number of tandem repeats of CsgAs from one to four produced shorter and intermittent fibrils compared with CsgA control protein. These studies therefore provide insights into self-assembly of two-component amyloid proteins and lay the foundation for rational design of multifunctional molecular biomaterials.     

Atomic force microscopy study of salivary pellicles formed on enamel and glass in vivo

This study was performed to evaluate the use of atomic force microscopy (AFM) in examining the surface of the adsorbed layer of salivary proteins (salivary pellicle) formed in vivo on dental enamel and glass surfaces. Enamel and glass test pieces were attached to the buccal surfaces of the upper first molar teeth in two adults using removable intraoral splints. The splints were carried intraorally over periods ranging from 10 min to1 h. Using the contact mode of AFM, pellicle structures could be recognised on intraorally exposed specimens compared to nonexposed enamel and glass surfaces. The surface of the adsorbed salivary pellicle was characterised by a dense globular appearance. The diameter of the globulelike protein aggregates adsorbed onto enamel and glass varied between 80 and 200 nm and 80 and 150 nm, respectively. The structure of the adsorbed protein layer was clearly visible on glass surfaces, even though minor differences in the protein layer between glass and enamel specimens were observed. This study indicates that AFM is a powerful tool for high-resolution examination of the salivary pellicle surface structure in its native (hydrated) state. AFM avoids artefacts due to fixing, dehydration and sputter-coating which occur with scanning electron microscopic analyses. Received: 29 November 2000 Accepted: 14 December 2000