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Ion channels and their viral companions are defined by their quaternary structure. The individual sub-units have to assemble into homo- or hetero-oligomers. Using Vpu of HIV-1, a putative viral channel forming protein (VCP), as a test case, the formation of a quaternary structure is monitored using coarse grained molecular dynamics (CGMD) simulations. Full length Vpu is generated by combining the helical transmembrane domain (TMD) with the cytoplasmic domain derived from NMR spectroscopy. Patches of 2 to 6 as well as patches of 16 and 32 Vpu proteins, Vpu-WT, containing unphosphorylated serines 52 and 56 are used to study assembly dynamics. The same patches are simulated for the Vpu double mutant, Vpu-DD, in which the two serines 52 and 56 are replaced by aspartic acid. Serines 52 and 56 in Vpu-WT allow short lived contacts between the cytoplasmic domains. Dimer formation is the first step for long lasting assemblies and is induced by the EYR motif. Roll-over movements allow rearrangement within the dimer. Independent of the number of Vpu proteins, Vpu-DD prefers smaller aggregates than Vpu-WT. In the case of simulation of 4 Vpu-WT proteins a pore-like assembly is directly identified with the TMD Ser-23 pointing towards a putative central pore axis.

Protein 3a is a 274 amino acid polytopic channel protein with three putative transmembrane domains (TMDs) encoded by severe acute respiratory syndrome corona virus (SARS-CoV). Synthetic peptides corresponding to each of its three individual transmembrane domains (TMDs) are reconstituted into artificial lipid bilayers. Only TMD2 and TMD3 induce channel activity. Reconstitution of the peptides as TMD1 1TMD3 as well as TMD2 1TMD3 in a 1 : 1 mixture induces membrane activity for both mixtures. In a 1 : 1 : 1 mixture, channel like behavior is almost restored. Expression of full length 3a and reconstitution into artificial lipid bilayers reveal a weak cation selective (PK � 2P Cl) rectifying channel. In the presence of nonphysiological concentration of Ca-ions the channel develops channel activity. V C 2013 Wiley Periodicals, Inc. Biopolymers 99: 628‐635, 2013.

Viral protein U (Vpu) encoded by human immunodeficiency virus type 1 (HIV-1) is a short integral membrane protein which is known to self-assemble within the lipid membrane and associate with host factors during the HIV-1 infectivity cycle. In this study, full-length Vpu (M group) from clone NL4-3 was over-expressed in human cells and purified in an oligomeric state. Various single and double mutations were constructed on its phosphorylation sites to mimic different degrees of phosphorylation. Size exclusion chromatography of wild-type Vpu and mutants indicated that the smallest assembly unit of Vpu was a dimer and over time Vpu formed higher oligomers. The rate of oligomerization increased when (i) the degree of phosphorylation at serines 52 and 56 was decreased and (ii) when the ionic strength was increased indicating that the cytoplasmic domain of Vpu affects oligomerization. Coarse-grained molecular dynamic simulations with models of wild-type and mutant Vpu in a hydrated lipid bilayer supported the experimental data in demonstrating that, in addition to a previously known role in downregulation of host factors, the phosphorylation sites of Vpu also modulate oligomerization.

Significant enhancement in supercapacitor performance has been achieved via a new RuO2 nanocomposite materials prepared by direct ruthenium sputtering on arrayed multi-walled carbon nanotubes supported by Ti-buffered Si wafer. XPS, HRTEM and SAED analyses reveal that as-prepared nanoparticles have a crystalline Ru metal core with RuO2 oxide coating. The nanocomposites convert to RuO2–CNx NTs with subsequent electrochemical cycling. At present, well-dispersed and strongly adhered RuO2 NPs have been densely populated on CNx NTs to obtain the overall specific capacitance (1380 F/g-RuO2), charging–discharging rate (up to 600 mV/s) and operation stability (5000 cycles). Thus, RuO2–CNx NTs nanocomposites would make a promising candidate for use in next-generation high efficiency miniaturized supercapacitors directly fabricated on Si substrate. Keywords: Supercapacitors, Direct growth, Well-aligned carbon nanotubes, RuO2 nanoparticles, Arrayed nanocomposites

Optical properties of amorphous silicon carbon nitride thin films as a function of carbon content have been studied by the spectral microreflectometry. The compositions of a-SiCN thin films deposited with different CH4 flow rates were analyzed by X-ray photoemission spectroscopy (XPS). It was found that the transmittance of a-SiCN thin films decreases with the increasing carbon content; the index of refraction n varies from ~2.0 to ~2.2 and the optical gap (Tauc gap) Eopt value progressively decreases from 4.1 to 3.3 eV while the carbon content changes from 0 to 25% in the films. In addition, a MSM (metal-semiconductor-metal) photodetector device based on the a-SiCN thin film demonstrates excellent selective sensing features with a large photo-to-dark current ratio about 1800 under illumination of the 250 nm UV light source, providing potential applications for low-cost UV detection. D 2004 Elsevier B.V. All rights reserved.

First-principles calculations have been carried to study the structural and electronic properties of the series of α-silicon carbon nitride crystals which have been successfully synthesized and demonstrate interesting mechanical, electronic, optical properties. The bulk modulus values of the SiCN structures have been observed to progressively increase up as more C atoms substituted for Si atoms in the crystal due to strong covalent CN bonds compared to SiN bonds. The band structure calculations indicate that the electronic properties of the α-SiCN crystals are closer to α-Si 3 N 4 than to α-C 3 N 4 . In addition, to improve the underestimation of local density approximation, we implement the generalized density functional scheme to correct the band gap values for SiCN crystals. The size of the band gap for α-Si 2 CN 4 after gap opening shows a value of 3.82 eV which demonstrates a good approximation with that of the Si-rich SiCN crystals measured by the piezoreflectance spectroscopy, ranging from 3.81 to 4.66 eV.

This study investigates the strong photoluminescence (PL) and X-ray excited optical luminescence observed in nitrogen-functionalized 2D graphene nanoflakes (GNFs:N), which arise from the significantly enhanced density of states in the region of {\pi} states and the gap between {\pi} and {\pi}* states. The increase in the number of the sp2 clusters in the form of pyridine-like N-C, graphite-N-like, and the C=O bonding and the resonant energy transfer from the N and O atoms to the sp2 clusters were found to be responsible for the blue shift and the enhancement of the main PL emission feature. The enhanced PL is strongly related to the induced changes of the electronic structures and bonding properties, which were revealed by the X-ray absorption near-edge structure, X-ray emission spectroscopy, and resonance inelastic X-ray scattering. The study demonstrates that PL emission can be tailored through appropriate tuning of the nitrogen and oxygen contents in GNFs and pave the way for new optoelectronic devices., Comment: 8 pages, 6 figures (including toc figure)

Viral channel-forming proteins comprise a class of viral proteins which, similar to their host companions, are made to alter electrochemical or substrate gradients across lipid membranes. These proteins are active during all stages of the cellular life cycle of viruses. An increasing number of proteins are identified as channel proteins, but the precise role in the viral life cycle is yet unknown for the majority of them. This review presents an overview about these proteins with an emphasis on those with available structural information. A concept is introduced which aligns the transmembrane domains of viral channel proteins with those of host channels and toxins to give insights into the mechanism of function of the viral proteins from potential sequence identities. A summary of to date investigations on drugs targeting these proteins is given and discussed in respect of their mode of action in vivo.

In this study, we have successfully demonstrated that a GaN nanowire (GaNNW) based extended-gate field-effect-transistor (EGFET) biosensor is capable of specific DNA sequence identification under label-free in situ conditions. Our approach shows excellent integration of the wide bandgap semiconducting nature of GaN, surface-sensitivity of the NW-structure, and high transducing performance of the EGFET-design. The simple sensor-architecture, by direct assembly of as-synthesized GaNNWs with a commercial FET device, can achieve an ultrahigh detection limit below attomolar level concentrations: about 3 orders of magnitude higher in resolution than that of other FET-based DNA-sensors. Comparative in situ studies on mismatches ("hotspot" mutations related to human p53 tumor-suppressor gene) and complementary targets reveal excellent selectivity and specificity of the sensor, even in the presence of noncomplementary DNA strands, suggesting the potential pragmatic application in complex clinical samples. In comparison with GaN thin film, NW-based EGFET exhibits excellent performance with about 2 orders higher sensitivity, over a wide detection range, 10(-19)-10(-6) M, reaching about a 6-orders lower detection limit. Investigations illustrate the unique and distinguished feature of nanomaterials. Detailed studies indicate a positive effect of energy band alignment at the biomaterials-semiconductor hybrid interface influencing the effective capacitance and carrier-mobility of the system.

The evolution of the optical properties of GaN nanowires (NWs) with respect to a sequence of surface functionalization processes is reported; from pristine hydroxylated to finally, 3-mercaptopropyltrimethoxysilane (MPTMS) functionalized GaN NWs. Photoluminescence, Raman, stationary, and time-resolved photoluminescence measurements were applied to investigate the GaN NWs with different surface conditions. A documented surface passivation effect of the GaN NWs induced by the MPTMS functionalization is determined based on our characterization results. A hypothesis associated with the surface band bending and the defect levels near the band edges is proposed to explain the observed experimental results. Original Publication:Chih-Wei Hsu, Abhijit Ganguly, Chin-Pei Chen, Chun-Chiang Kuo, Plamen Paskov, Per-Olof Holtz, Li-Chyong Chen and Kuei-Hsien Chen, Optical properties of functionalized GaN nanowires, 2011, JOURNAL OF APPLIED PHYSICS, (109), 5, 053523.http://dx.doi.org/10.1063/1.3552919Copyright: American Institute of Physicshttp://www.aip.org/

Viral protein of regulation (Vpr) encoded by human immunodeficiency virus type 1 (HIV-1) is a short auxiliary protein that is 96 amino acids in length. During the viral life cycle, Vpr is released into the blood serum and is able to enter cellular membranes of noninfected cells. In this study a short peptide, Vpr(55-83), was shown to exhibit ion-channel-like activity when reconstituted into (1) planar lipid bilayers and (2) lipid bilayers held at the tip of a glass pipette. The two set-ups led to differences in the oligomerization state of the peptide, which was reflected in differences in the conductance levels. Experiments under applied hydrostatic pressure affect the dynamics of the protein within the membrane.

We demonstrate a rationale for using GaN nanowires (GaNNWs) in label-free DNA-sensing using dual routes of electrochemical impedance spectroscopy (EIS) and photoluminescence (PL) measurements, employing a popular target DNA with anthrax lethal factor (LF) sequence. The in situ EIS reveals that both high surface area and surface band-bending in the nanowires, providing more binding sites and surface-enhanced charge transfer, respectively, are responsible for the enhanced sensitivity to surface-immobilized DNA molecules. The net electron-transfer resistance can be readily deconvoluted into two components because of the coexistence of two interfaces, GaN/DNA and DNA/electrolyte interfaces, in series. Interestingly, the former, decreasing with LF concentration (C(LF)), serves as a signature for the extent of hybridization, while the latter as a fingerprint for DNA modification. For PL-sensing, the band-edge emission of GaNNWs serves as a parameter for DNA modification, which quenches exponentially with C(LF) as the incident light is increasingly blocked from reaching the core nanowire by rapidly developing a UV-absorbing DNA sheath at high C(LF). Furthermore, successful application for detection of "hotspot" mutations, related to the human p53 tumor-suppressor gene, revealed excellent selectivity and specificity, down to picomolar concentration, even in the current unoptimized sensor design/condition, and in the presence of mutations and noncomplementary strands, suggesting the potential pragmatic application in complex clinical samples.

High oxygen reduction activity of methanol-tolerant catalysts was successfully reported using platinum nanoparticles embedded in cobalt-based nitrogen-containing complexes supported on carbon blacks (Pt–N-complex/C). The oxygen reduction reaction (ORR) of the Pt–N-complex/C was attributed to four-electron transfer pathway in which oxygen was directly reduced to water, yielding four electrons. In a methanol-containing solution, the platinum intrinsically favors the methanol oxidation reaction over the ORR, which is a major drawback for direct methanol fuel cells (DMFCs). In comparison, when the Pt–N-complex/C is introduced in a methanol-containing solution, not only is the methanol oxidation suppressed but also the four-electron-transfer in the ORR is maintained up to the diffusion-limiting region. Physicochemical characterization of the Pt–N-complex/C indicates that pyrrolic N-type poly-aromatic hydrocarbons were formed in a network structure around the catalysts and prevented them from the methanol oxidation reaction. In a DMFC test at elevated methanol concentrations, the one with the Pt–N-complex/C cathode showed superior stability over the one with the Pt-based cathode, which may offer a solution to the methanol crossover problem in DMFCs.

This study demonstrates the utility of functionalized GaN nanowires (GaNNWs) for electrochemical detection of nucleic acids, in aqueous solution, using cyclic voltammetry. In order to link probe DNA to the NW surface, we employed an organosulfur compound, 3-mercaptopropyl trimethoxysilane (MPTS), to functionalize the GaNNW surface. Interestingly, the MPTS-modified GaNNWs exhibited a potential window of 4.5 V, the widest reported to date, with very low background current, which provides an advantage for sensing DNA immobilization/hybridization, down to sub-pM concentration, via monitoring adenine and guanine oxidation. The oxidation of guanine was characterized by its peak potential and peak current, where the former serves as a fingerprint for DNA hybridization and the latter as a parameter for the extent of hybridization. Moreover, the GaNNW-based sensor exhibited excellent consistency in hybridization-dehybridization-rehybridization cycles.

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X-ray absorption near-edge structure (XANES) and x-ray emission spectroscopy (XES) measurements were used to investigate the effect of Mg doping in ZnO nanorods. The intensities of the features in the O K-edge XANES spectra of Zn{sub 1-x}Mg{sub x}O nanorods are lower than those of pure ZnO nanorods, suggesting that Mg doping increases the negative effective charge of O ions. XES and XANES spectra of O 2p states indicate that Mg doping raises (lowers) the conduction-band-minimum (valence-band-maximum) and increases the bandgap. The bandgap is found to increase linearly with the Mg content, as revealed by photoluminescence and combined XANES and XES measurements.

An ultrahigh photocurrent gain has been found in the ultraviolet-absorbed GaN nanowires with m-directional long axis grown by chemical vapor deposition. The quantitative results have shown the gain values at 5.0×104–1.9×105 of the GaN nanowires with diameters from 40to135nm are near three orders of magnitude higher than the values of 5.2×101–1.6×102 estimated from the thin film counterparts. The intensity-dependent gain study has shown that the gain value is very sensitive to the excitation intensity following an inverse power law and no gain saturation observed in this investigated intensity range from 0.75to250W∕m2. This behavior has strongly suggested a surface-dominant rather than trap-dominant high gain mechanism in this one-dimensional nanostructure. The strong carrier localization effect induced by the surface electric field in the GaN nanowires is also discussed.

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X-ray absorption near-edge structure (XANES) and scanning photoelectron microscopy (SPEM) measurements have been performed for Zn1−xCoxO and Zn1−xMgxO to elucidate the effects of the doping of Co and Mg, which have very different electronegativities, on the electronic structures of ZnO nanorods. The intensities of O K-edge near-edge features in the XANES spectra of Zn1−xCoxO and Zn1−xMgxO nanorods are found to be lower than those of ZnO, which suggests that both Co and Mg substitutions of the Zn ions enhance the effective charge on the O ion. The valence-band SPEM measurements show that Mg doping does not increase the density of near-Fermi-level states, which implies that Mg doping will not improve field emission of ZnO nanorods. It is surprising to find that both Co and Mg substitutions of Zn increase the numbers of O 2p dominated valence-band states, despite that Co and Mg have larger and smaller electronegativities than that of Zn.

Viral channel forming proteins are known for their capability to make the lipid membrane of the host cell and its subcellular compartments permeable to ions and small compounds. There is increasing evidence that some of the representatives of this class of proteins are also strongly interacting with host proteins and the effectiveness of this interaction seems to be high. Interaction of viral channel proteins with host factors has been proposed by bioinformatics approaches and has also been identified experimentally. An overview of the interactions with host proteins is given for Vpu from HIV-1, E5 from HPV-16 and p7 from HCV. This article is part of a Special Issue entitled: Viral Membrane Proteins — Channels for Cellular Networking.