Microarray-based Raman spectroscopic assay for kinase inhibition by gold nanoparticle probes

In this paper, a microarray-based surface-enhanced Raman spectroscopic (SERS) assay for detection of kinase functionality and inhibition has been reported. Biotinylated anti-phosphoserinen antibodies mark the phosphorylation and inhibition events and gold nanoparticles are attached to the antibodies by standard avidin-biotin chemistry, followed by silver deposition for SERS signal enhancement. The avidin conjugated fluorescein is used as SERS probe. The alpha-catalytic subunit of cyclic adenosine 5'-monophosphate (cAMP) dependent protein kinase (PKA), its well known substrate, kemptide, and three inhibitors, H89, HA1077, and KN62 have been chosen here to establish the SERS assay. As expected, highly selective inhibition of PKA is demonstrated with the inhibitor H89 and the inhibition assay enable to detect kinase inhibition as well as derive IC50 (half maximal inhibitory concentration) plots.

Microarray-based kinase inhibition assay by gold nanoparticle probes

We report on the development of a new class of kinase microarray for the detection of kinase inhibition based on marking peptide phosphorylation/biotinylation events by attachment of gold nanoparticles followed by silver deposition for signal enhancement. The alpha-catalytic subunit of cyclic adenosine 5'-monophosphate-dependent protein kinase (PKA), and its well-known substrate, kemptide, were used for the purpose of monitoring phosphorylation and inhibition. As expected, highly selective inhibition of PKA is demonstrated with the four inhibitors: H89, HA1077, mallotoxin, and KN62. Furthermore, an inhibition assay demonstrates the ability to detect kinase inhibition as well as derive IC50 (half-maximal inhibitory concentration) plots.

QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by “GAMESS”, and the rest atoms are treated as MM part calculated by “TINKER”. The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with theQMpart with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(1 0 0) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the imidazole rings are attached to the substrate more tightly than other bases in this peptide.

The Interaction Between Shock Waves and Solid Spheres Arrays in a Shock Tube

When a shock wave interacts with a group of solid spheres, non-linear aerodynamic behaviors come into effect. The complicated wave reflections such as the Mach reflection occur in. the wave propagation process. The wave interactions with vortices behind each sphere's wake cause fluctuation in the pressure profiles of shock waves. This paper reports an experimental study for the aerodynamic processes involved in the interaction between shock waves and solid spheres. A schlieren photography was applied to visualize the various shock waves passing through solid spheres. Pressure measurements were performed along different downstream positions. The experiments were conducted in both rectangular and circular shock tubes. The data with respect to the effect of the sphere array, size, interval distance, incident Mach number, etc., on the shock wave attenuation were obtained.

Adsorption of His-tagged peptide to Ni, Cu and Au (100) surfaces: Molecular dynamics simulation

Molecular dynamics (MD) simulations are performed to study the interaction of His-tagged peptide with three different metal surfaces in explicit water. The equilibrium properties are analyzed by using pair correlation functions (PCF) to give an insight into the behavior of the peptide adsorption to metal surfaces in water solvent. The intermolecular interactions between peptide residues and the metal surfaces are evaluated. By pulling the peptide away from the peptide in the presence of solvent water, peeling forces are obtained and reveal the binding strength of peptide adsorption on nickel, copper and gold. From the analysis of the dynamics properties of the peptide interaction with the metal surfaces, it is shown that the affinity of peptide to Ni surface is the strongest, while on Cu and An the affinity is a little weaker. In MD simulations including metals, the His-tagged region interacts with the substrate to an extent greater than the other regions. The work presented here reveals various interactions between His-tagged peptide and Ni/Cu/Au surfaces. The interesting affinities and dynamical properties of the peptide are also derived. The results give predictions for the structure of His-tagged peptide adsorbing on three different metal surfaces and show the different affinities between them, which assist the understanding of how peptides behave on metal surfaces and of how designers select amino sequences in molecule devices design. (c) 2007 Elsevier Ltd. All rights reserved.

QM/MM and Classical Molecular Dynamics Simulation of Histidine-Tagged Peptide Immobilization on Nickel Surface

The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by "GAMESS", and the rest atoms are treated as MM part calculated by "TINKER". The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with the QM part with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(100) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the in-tidazole rings are attached to the substrate more tightly than other bases in this peptide.

Friction properties of bio-mimetic nano-fibrillar arrays

Nano-fibrillar arrays are fabricated using polystyrene materials. The average diameter of each fiber is about 300 nm. Experiments show that such a fibrillar surface possesses a relatively hydrophobic feature with a water contact angle of 142 degrees. Nanoscale friction properties are mainly focused on. It is found that the friction force of polystyrene nano-fibrillar surfaces is obviously enhanced in contrast to polystyrene smooth surfaces. The apparent coefficient of friction increases with the applied load, but is independent of the scanning speed. An interesting observation is that the friction force increases almost linearly with the real contact area, which abides by the fundamental Bowden-Tabor law of nano-scale friction.

Molecular Modeling and Affinity Determination of scFv Antibody: Proper Linker Peptide Enhances Its Activity

One of existing strategies to engineer active antibody is to link VH and VL domains via a linker peptide. How the composition, length, and conformation of the linker affect antibody activity, however, remains poorly understood. In this study, a dual approach that coordinates molecule modeling, biological measurements, and affinity evaluation was developed to quantify the binding activity of a novel stable miniaturized anti-CD20 antibody or singlechain fragment variable (scFv) with a linker peptide. Upon computer-guided homology modeling, distance geometry analysis, and molecular superimposition and optimization, three new linker peptides PT1, PT2, and PT3 with respective 7, 10, and 15 residues were proposed and three engineered antibodies were then constructed by linking the cloned VH and VL domains and fusing to a derivative of human IgG1. The binding stability and activity of scFv-Fc chimera to CD20 antigen was quantified using a micropipette adhesion frequency assay and a Scatchard analysis. Our data indicated that the binding affinity was similar for the chimera with PT2 or PT3 and ~24-fold higher than that for the chimera with PT1, supporting theoretical predictions in molecular modeling. These results further the understanding in the impact of linker peptide on antibody structure and activity.

Formation mechanisms of uniform arrays of periodic nanoparticles and nanoripples on 6H-SiC crystal surface induced by femtosecond laser ablation

Uniform arrays of periodic nanoparticles with 80-nm period are formed on 6H-SiC crystal irradiated by circularly polarized 400-nm femtosecond laser pulses. In order to understand the formation mechanism, the morphology evolvement as a function of laser pulse energy and number is studied. Periodic nanoripples are also formed on the sample surface irradiated by linearly polarized 400-, 510- and 800-nm femtosecond laser pulses. All these results support well the mechanism that second-harmonic generation plays an important role in the formation of periodic nanostructures.

Lau cavity and phase locking of laser arrays

The Lau cavity is the self-imaging cavity with a phase corrector under the Lau reimaging condition. The author proposes the use of the Lau cavity to utilize both the Talbot and the Lau effects for phase locking one-dimensional and two-dimensional diode-laser arrays into a single-lobe coherent beam. Analyses on the self-reproducing of a coherent lasing field and the reimaging of initial incoherent radiation are given.

Dynamic readout of subdiffraction-limited pit arrays with a silver superlens

Recent theoretical and experimental results suggested that the silver superlens could be constructed through controlling silver thin film thickness and preparation conditions, and applied in subdiffraction-limited optical imaging and optical lithography. In this work, we report another significant application of silver superlens-ultrahigh density optical data storage. With the silver superlens the subdiffraction-limited pit arrays on an optical disk are dynamically read out and the carrier-to-noise ratio can reach 25 dB for the thin film thickness of 46 nm. The readout laser power and readout velocity have little effect on the carrier-to-noise ratio. Additionally, in our experiment the silver thin film thickness needs to be controlled in the range from 20 to 80 nm.

On the dynamic readout of sub-diffraction-limit pit arrays with a silver thin film

Fast moving arrays of periodic sub-diffraction-limit pits were dynamically read out via a silver thin film. The mechanism of the dynamic readout is analysed and discussed in detail, both experimentally and theoretically. The analysis and experiment show that, in the course of readout, surface plasmons can be excited at the silver/air interface by the focused laser beam and amplified by the silver thin film. The surface plasmons are transmitted into the substrate/silver interface with a large enhancement. The surface waves at the substrate/silver interface are scattered by the sinusoidal pits of sub-diffraction-limit size. The scattered waves are collected by a converging lens and guided into the detector for the readout.

Nano-polypyrrole supercapacitor arrays prepared by layer-by-layer assembling method in anodic aluminum oxide templates

A novel method for preparing nano-supercapacitor arrays, in which each nano-supercapacitor consisted of electropolymerized Polypyrrole (PPy) electrode / porous TiO2 separator / chemical polymerized PPy electrode, was developed in this paper. The nano-supercapacitors were fabricated in the nano array pores of anodic aluminum oxide template using the bottom-up, layer-by-layer synthetic method. The nano-supercapacitor diameter was 80 nm, and length 500 nm. Based on the charge/discharge behavior of nano-supercapacitor arrays, it was found that the PPy/TiO2/PPy array supercapacitor devices performed typical electrochemical supercapacitor behavior. The method introduced here may find application in manufacturing nano-sized electrochemical power storage devices in the future for their use in the area of microelectronic devices and microelectromechanical systems.