Calcium-permeable acid-sensing ion channel is a molecular target of the neurotoxic metal ion lead

Acid-sensing ion channels (ASICs) are emerging as fundamental players in the regulation of neural plasticity and in pathological conditions. Here we showed that lead (Pb2+), a well known neurotoxic metal ion, reversibly and concentration-dependently inhib

Characterization of acid-sensing ion channels in dorsal horn neurons of rat spinal cord

Acid-sensing ion channels (ASICs) are ligand-gated cation channels activated by extracellular protons. In periphery, they contribute to sensory transmission, including that of nociception and pain. Here we characterized ASIC-like currents in dorsal horn neurons of the rat spinal cord and their functional modulation in pathological conditions. Reverse transcriptase-nested PCR and Western blotting showed that three ASIC isoforms, ASIC1a, ASIC2a, and ASIC2b, are expressed at a high level in dorsal horn neurons. Electrophysiological and pharmacological properties of the proton-gated currents suggest that homomeric ASIC1a and/or heteromeric ASIC1a + 2b channels are responsible for the proton-induced currents in the majority of dorsal horn neurons. Acidification-induced action potentials in these neurons were compatible in a pH-dependent manner with the pH dependence of ASIC-like current. Furthermore, peripheral complete Freund's adjuvant-induced inflammation resulted in increased expression of both ASIC1a and ASIC2a in dorsal horn. These results support the idea that the ASICs of dorsal horn neurons participate in central sensory transmission/modulation under physiological conditions and may play important roles in inflammation-related persistent pain.

Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies

The entry of human immunodeficiency virus (HIV) into cells depends on a sequential interaction of the gp120 envelope glycoprotein with the cellular receptors CD4 and members of the chemokine receptor family. The CC chemokine receptor CCR5 is such a receptor for several chemokines and a major coreceptor for the entry of R5 HIV type-1 (HIV-1) into cells. Although many studies focus on the interaction of CCR5 with HIV-1, the corresponding interaction sites in CCR5 and gp120 have not been matched. Here we used an approach combining protein structure modeling, docking and molecular dynamics simulation to build a series of structural models of the CCR5 in complexes with gp120 and CD4. Interactions such as hydrogen bonds, salt bridges and van der Waals contacts between CCR5 and gp120 were investigated. Three snapshots of CCR5-gp120-CD4 models revealed that the initial interactions of CCR5 with gp120 are involved in the negatively charged N-terminus (Nt) region of CCR5 and positively charged bridging sheet region of gp120. Further interactions occurred between extracellular loop2 (ECL2) of CCR5 and the base of V3 loop regions of gp120. These interactions may induce the conformational changes in gp120 and lead to the final entry of HIV into the cell. These results not only strongly support the two-step gp120-CCR5 binding mechanism, but also rationalize extensive biological data about the role of CCR5 in HIV-1 gp120 binding and entry, and may guide efforts to design novel inhibitors.

Characterize dynamic conformational space of human CCR5 extracellular domain by molecular modeling and molecular dynamics simulation

The chemokine receptor CCR5 is the receptor for several chemokines and major coreceptor for R5 human immunodeficiency virus type-1 strains entry into cell. Three-dimensional models of CCR5 were built by using homology modeling approach and 1 ns molecular dynamics (MD) simulation, because studies of site-directed mutagenesis and chimeric receptors have indicated that the N-terminus (Nt) and extracellular loops (ECLs) of CCR5 are important for ligands binding and viral fusion and entry, special attention was focused on disulfide bond function, conformational flexibility, hydrogen bonding, electrostatic interactions, and solvent-accessible surface area of Nt and ECLs of this protein part. We found that the extracellular segments of CCR5 formed a well-packet globular domain with complex interactions occurred between them in a majority of time of MID simulation, but Nt region could protrude from this domain sometimes. The disulfide bond Cys20-Cys269 is essential in controlling specific orientation of Nt region and maintaining conformational integrity of extracellular domain. RMS comparison analysis between conformers revealed the ECL1 of CCR5 stays relative rigid, whereas the ECL2 and Nt are rather flexible. Solvent-accessible surface area calculations indicated that the charged residues within Nt and ECL2 are often exposed to solvent. Integrating these results with available experimental data, a two-step gp120-CCR5 binding mechanism was proposed. The dynamic interaction of CCR5 extracellular domain with gp120 was emphasized. (C) 2004 Elsevier B.V. All rights reserved.

Molecular docking and 3D-QSAR study of pyranmycin derivatives against 16S rRNA A site

To understand pharmacophore properties of pyranmycin derivatives and to design novel inhibitors of 16S rRNA A site, comparative molecular field analysis (CoMFA) approach was applied to analyze three-dimensional quantitative structure-activity relationship (3D-QSAR) of 17 compounds. AutoDock 3.0.5 program was employed to locate the orientations and conformations of the inhibitors interacting with 16S rRNA A site. The interaction mode was demonstrated in the aspects of inhibitor conformation, hydrogen bonding and electrostatic interaction. Similar binding conformations of these inhibitors and good correlations between the calculated binding free energies and experimental biological activities suggest that the binding conformations of these inhibitors derived from docking procedure were reasonable. Robust and predictive 3D-QSAR model was obtained by CoMFA with q(2) values of 0.723 and 0.993 for cross-validated and noncross-validated, respectively. The 3D-QSAR model built here will provide clear guidelines for novel inhibitors design based on the Pyranmycin derivatives against 16S rRNA A site. (c) 2005 Elsevier B.V. All rights reserved.

Molecular characterization of three Rana grylio virus (RGV) isolates and Paralichthys olivaceus lymphocystis disease virus (LCDV-C) in iridoviruses

Three Rana grylio virus (RGV) isolates and lymphocystis disease virus (LCDV-C) were molecularly characterized by antigenicity comparison, Western blot detection of viral polypeptides, restriction fragment length polymorphism analysis of viral genomes, and MCP sequence analysis. Significant antigenicity differences existed among the three RGV isolates and LCDV-C. Western blot detection indicated that the viral polypeptides of three RGV isolates could be recognized by the anti-RGV9807 serum, whereas no bands were observed in the LCDV-C, and significant differences exist among the band patterns of three RGV isolates. Restriction fragment length polymorphism (RFLP) analysis was performed by digesting genomic DNA of the four iridovirus isolates with restriction endonucleases HindIII, KpnI, XbaI and BamHI. On the whole, obvious discrepancies existed between LCDV-C and RGV isolates, and some significant band pattern differences were also revealed between RGV9808 and RGV9506 (or RGV9807) in the profiles of restriction endonucleases Xbal, Kpn I and BamHI. PCR amplification and sequence analysis of MCP gene sequence further revealed their phylogenetic relationship among the three RGV isolates, LCDV-C and other iridoviruses. RGV9506, RGV9807 and RGV9808 are clustered together with other ranaviruses, such as FV3, BIV, TFV and ENHV, although the RGV9808 is more close to EHNV than to other ranaviruses. Additionally, LCDV-C is clustered with LCDV-1, the type species of genus Lymphocystisvirus. The current study provides clear evidence that significant genetic difference exists among the three RGV isolates. Therefore, further work on comparative genomic studies will contribute significantly to understanding of their taxonomic position and pathological mechanism. (C) 2005 Elsevier B.V. All rights reserved.

Molecular and expression characterization of three gonadotropin subunits common alpha, FSH beta and LH beta in groupers

A SMART cDNA plasmid library was constructed from protogyous greasy grouper (Epinephelus coioides) pituitary, and the full-length cDNAs of three gonadotropin (GTH) subunits common alpha, FSH beta and LH beta were cloned and sequenced from the library. The nucleotide sequences of common alpha, FSH beta and LH beta subunit cDNAs are 647, 594 and 574 bp in length, and encode for mature peptides of 94, 99 and 115 aa, respectively. High homology was observed by amino acid sequence alignment and identity comparison of the grouper mature peptides of common alpha, FSH beta and LH beta with that of other fishes. Phylogenetic tree analyses of the three GTH mature subunits revealed similar phylogeny relationships among the studied fish species. Three polyclonal antibodies were prepared from the in vitro expressed common alpha, FSH beta and LH beta mature proteins, respectively. Western blot analysis and immunofluoresence localization were performed on two typical stages of ovarian development stages in red-spotted grouper. Significant differences in protein expression levels of three gonadotropin subunits were revealed between the two ovarian development stages. In the individuals with resting ovary, common alpha was almost not detected in pituitaries, and FSH beta and LH beta expression levels were very low. While in the individuals with developing ovary, the expression of all three gonadotropin subunits reached to a high level. Immunofluoresence localization indicated that the grouper FSH beta cells mainly distributed in the middle area of PPD, while the LH beta cells distributed more widely, including in the area similar to the FSH beta cells and at the external periphery of pituitary near to the PI side. The common alpha might be expressed in both FSH beta and LH beta cells. Double immunofluoresence localization further demonstrated FSH beta and LH beta expression in distinct cells in the PPD area, although the FSH beta and LH beta cells were detected in the identical area of PPD. (c) 2005 Elsevier Ireland Ltd. All rights reserved.

Molecular phylogeny of three subspecies of common carp Cyprinus carpio, based on sequence analysis of cytochrome b and control region of mtDNA

The complete cytochrome b and the control region of mtDNA (about 2070 bp in total) of 10 strains belonging to three subspecies of the common carp, including three wild subspecies (the Yangtze River wild common carp - Cyprinus carpio haematopterus, Yuanjiang River wild common carp Cyprinus carpio rubrofuscus and Volga River wild common carp - Cyprinus carpio carpio) and seven domestic strains (Xingguo red carp, Russian scattered scaled mirror carp, Qingtian carp, Japanese Koi carp, purse red carp, Big-belly carp, German mirror carp) were sequenced. Phylogenetic analysis indicated that the 10 strains form three distinct clades, corresponding to C. c. haematopterus, C. c. rubrofuscus and C. c. carpio respectively. Purse red carp, an endemic domestic strain in Jiangxi province of China, showed a higher evolution rate in comparison with the other strains of C. c. haematopterus, most probably because of intensive selection and a long history of domestication. Base variation ratios among the three subspecies varied from 0.78% (between C. c. haematopterus and C. c. rubrofuscus) to 1.47%(between C. c. carpio and C. c. rubrofuscus). The topography of the phylogenetic tree and the geographic distribution of three subspecies closely resemble each other. The divergence time between C. c. carpio and the other two subspecies was estimated to be about 0.9 Myr and about 0.5 Myr between C. c. haematopterus and C. c. rubrofuscus. Based on phylogenetic analysis, C. c. rubrofuscus might have diverged from C. c. haematopterus.

Evolution of InAs/GaAs(001) islands during the two- to three-dimensional growth mode transition in molecular-beam epitaxy

A detailed observation was made using atomic force microscopy on the two- to three-dimensional (2D-3D) growth mode transition in the molecular-beam epitaxy of InAs/GaAs(001). The evolution of the 3D InAs islands during the 2D-3D mode transition was divided into two successive phases. The first phase may be explained in terms of a critical phenomenon of the second-order phase transition.

Atomic hydrogen induced step bunching and fabrication of quantum wire arrays on GaAs (311)A substrate by molecular beam epitaxy

Atomic hydrogen assisted molecular beam epitaxy (MBE) is a novel type of epitaxial growth of nanostructures. The GaAs (311)A surface naturally forms one-dimensional step arrays by step bunching along the direction of (-233) and the space period is around 40nm. The step arrays extend over several mum without displacement. The InGaAs quantum wire arrays are grown on the step arrays as the basis. Our results may prompt further development of more uniform quantum wire and quantum dot arrays.

Effect of ion-induced damage on GaNAs/GaAs quantum wells grown by plasma-assisted molecular beam epitaxy

The effect of ion-induced damage on GaNAs/GaAs quantum wells (QWs) grown by molecular beam epitaxy employing a DC plasma as the N source was investigated. Ion-induced damage results in: (i) an observed disappearance of pendellosung fringes in the X-ray diffraction pattern of the sample; (ii) a drastic decrease in intensity and a broadening in the full-width at half-maximum of photoluminescence spectra. It was shown that ion-induced damage strongly affected the bandedge potential fluctuations of the QWs. The bandedge potential fluctuations for the samples grown with and without ion removal magnets (IRMs) are 44 and 63 meV, respectively. It was found that the N-As atomic interdiffusion at the interfaces of the QWs was enhanced by the ion damage-induced defects. The estimated activation energies of the N-As atomic interdiffusion for the samples grown with and without IRMs are 3.34 and 1.78 eV, respectively. (C) 2001 Elsevier Science B.V. All rights reserved.

The improvement characteristics of homoepitaxial GaAs grown by atomic hydrogen-assisted molecular beam epitaxy

The electrical activity of defects in GaAs grown on GaAs substrates doped with Si and Be by both conventional molecular beam epitaxy (MBE) and atomic hydrogen-assisted MBE (H-MBE) were characterized by deep level transient spectroscopy. The trap densities are significantly reduced in the homoepitaxial GaAs grown by H-MBE compared to that grown by MBE. The reduction of trap densities is attributed to in situ passivation of these defects by atomic H during the growth. The improvement characteristics of GaAs materials will be significance for fabrication of semiconductor devices.

Enhanced hydrogen desorption from Si sites during low-temperature Si1-xGex growth by disilane and solid-Ge molecular beam epitaxy

A phenomenological model is proposed to explain quantitatively the interesting compositional dependence on the Ge incorporation rate during low-temperature growth of Si1-xGex by disilane and solid-Ge molecular beam epitaxy, based on enhanced hydrogen desorption from Si sites due to the presence of Ge atoms. The hydrogen desorption rate constant for disilane on Si sites is fitted to an exponential function of Ge incorporation rate and a possible physical explanation is discussed. Simulated results are in excellent agreement with experimental data. (C) 1999 American Institute of Physics. [S0021-8979(99)02109-X].

Characterization of strain relaxation in As ion implanted Si1-xGex epilayers grown by gas source molecular beam epitaxy

Strain relaxation in the As ion implanted Si0.57Ge0.43 epilayers was studied by double-crystal x-ray diffractometry and transmission electron microscopy, and was compared to that in the nonimplanted Si0.57Ge0.43 epilayers. Experimental results show that after rapid thermal annealing (RTA) the x-ray linewidth of the As+-implanted Si0.57Ge0.43 epilayers is narrower than that of the nonimplanted epilayers, and than that of the partially relaxed as-grown samples, which is due primarily to low density of misfit dislocations in the As+-implanted SiGe epilayers. RTA at higher than 950 degrees C results in the formation of misfit dislocations for the nonimplanted structures, and of combinations of dislocations and precipitates (tentatively identified as GeAs) for the As+-implanted epilayers. The results mean that the strain relaxation mechanism of the As+-implanted Si1-xGex epilayers may be different from that of the nonimplanted Si1-xGex epilayers. (C) 1998 American Institute of Physics.

Kondo effect in a triangular triple quantum dots ring with three terminals

For a triangular triple quantum dots (TTQDs) ring with three terminals, when lowering one of the dot-lead coupling to realize the left-right (L-R) reflection symmetry coupling, the internal C-upsilon of the TTQDs is well preserved in the absence of many-body effect for the symmetric distribution of the dot-lead coupling on the molecular orbits. In the presence of Kondo effect, the decrement of one of the dot-lead couplings suppresses the inter-dot hopping. This happens especially for the coupled quantum dot (QD), which decouples with the other two ones gradually to form a localized state near the Fermi level As a result, the internal dynamic symmetry of the TTQDs ring is reduced to L-R reflection symmetry, and simultaneously, the linear conductance is lifted for the new forming molecular orbit near the Fermi level