How dopamine transporter interacts with dopamine: insights from molecular modeling and simulation

By performing homology modeling, molecular docking, and molecular dynamics simulations, we have developed three-dimensional (3D) structural models of both dopamine transporter and dopamine transporter-dopamine complex in the environment of lipid bilayer and solvent water. According to the simulated structure of dopamine transporter-dopamine complex, dopamine was orientated in a hydrophobic pocket at the midpoint of the membrane. The modeled 3D structures provide some detailed structural and mechanistic insights concerning how dopamine transporter (DAT) interacts with dopamine at atomic level, extending our mechanistic understanding of the dopamine reuptake with the help of Na(+) ions. The general features of the modeled 3D structures are consistent with available experimental data. Based on the modeled structures, our calculated binding free energy (DeltaG(bind) = -6.4 kcal/mol) for dopamine binding with DAT is also reasonably close to the experimentally derived DeltaG(bind) value of -7.4 kcal/mol. Finally, a possible dopamine-entry pathway, which involves formation and breaking of the salt bridge between side chains of Arg(85) and Asp(476), is proposed based on the results obtained from the modeling and molecular dynamics simulation. The new structural and mechanistic insights obtained from this computational study are expected to stimulate future, further biochemical and pharmacological studies on the detailed structures and mechanisms of DAT and other homologous transporters.     

Phosphorylation of eukaryotic initiation factor 2 by heme-regulated inhibitor kinase-related protein kinases in Schizosaccharomyces pombe is important for fesistance to environmental stresses

Protein synthesis is regulated by the phosphorylation of the alpha subunit of eukaryotic initiation factor 2 (eIF2alpha) in response to different environmental stresses. One member of the eIF2alpha kinase family, heme-regulated inhibitor kinase (HRI), is activated under heme-deficient conditions and blocks protein synthesis, principally globin, in mammalian erythroid cells. We identified two HRI-related kinases from Schizosaccharomyces pombe which have full-length homology with mammalian HRI. The two HRI-related kinases, named Hri1p and Hri2p, exhibit autokinase and kinase activity specific for Ser-51 of eIF2alpha, and both activities were inhibited in vitro by hemin, as previously described for mammalian HRI. Overexpression of Hri1p, Hri2p, or the human eIF2alpha kinase, double-stranded-RNA-dependent protein kinase (PKR), impeded growth of S. pombe due to elevated phosphorylation of eIF2alpha. Cells from strains with deletions of the hri1(+) and hri2(+) genes, individually or in combination, exhibited a reduced growth rate when exposed to heat shock or to arsenic compounds. Measurements of in vivo phosphorylation of eIF2alpha suggest that Hri1p and Hri2p differentially phosphorylate eIF2alpha in response to these stress conditions. These results demonstrate that HRI-related enzymes are not unique to vertebrates and suggest that these eIF2alpha kinases are important participants in diverse stress response pathways in some lower eukaryotes.     

High-Oleic Peanut Oils Produced by HpRNA-Mediated Gene Silencing of Oleate Desaturase

The quality of peanut oil largely depends on the quantity of oleic (18:1) and linoleic acids (18:2). These two acids comprise more than 80% of the total fatty acids in peanuts. The oleate desaturase (FAD2) gene is important for maintaining high oleic acid content. A partial conservative sequence of the FAD2 gene from peanut was selected. The sense and antisense 260-bp fragments were amplified and subcloned into pFGC1008 binary expression vectors. A total of 21 transgenic plants were obtained via Agrobacterium-mediated transformation. The resulting down-regulation of the FAD2 gene resulted in a 70% increase in oleic acid content in the seeds of transformed plants compared with a 37.93% increase in untransformed plants. The results demonstrated that the target genes were likely suppressed by hpRNA interference, a pathway capable of achieving phenotypic changes. The silencing of FAD2 enabled the development of peanut oils having novel combinations of oleic acid content that can be used in high-value applications, making this approach a reliable technique for the genetic modification of seed quality and the potential for enhancement of other traits as well.     

The red bayberry genome and genetic basis of sex determination

Morella rubra, red bayberry, is an economically important fruit tree in south China. Here, we assembled the first high‐quality genome for both a female and a male individual of red bayberry. The genome size was 313‐Mb, and 90% sequences were assembled into eight pseudo chromosome molecules, with 32 493 predicted genes. By whole‐genome comparison between the female and male and association analysis with sequences of bulked and individual DNA samples from female and male, a 59‐Kb region determining female was identified and located on distal end of pseudochromosome 8, which contains abundant transposable element and seven putative genes, four of them are related to sex floral development. This 59‐Kb female‐specific region was likely to be derived from duplication and rearrangement of paralogous genes and retained non‐recombinant in the female‐specific region. Sex‐specific molecular markers developed from candidate genes co‐segregated with sex in a genetically diverse female and male germplasm. We propose sex determination follow the ZW model of female heterogamety. The genome sequence of red bayberry provides a valuable resource for plant sex chromosome evolution and also provides important insights for molecular biology, genetics and modern breeding in Myricaceae family.     

Cloning of phospholipase D from grape berry and its expression under heat acclimation

To investigate whether phospholipase D (PLD, EC 3.1.4.4) plays a role in adaptive response of post-harvest fruit to environment, a PLD gene was firstly cloned from grape berry (Vitis Vinifera L. cv. Chardonnay) using RT-PCR and 3'- and 5'-RACE. The deduced amino acid sequence (809 residues) showed 84.7% identity with that of PLD from Ricinus communis. The secondary structures of this protein showed the characteristic C2 domain and two active sites of a phospholipid-metabolizing enzyme. The PLD activity and its expression in response to heat acclimation were then assayed. The results indicated PLD was significantly activated at enzyme activity, as well as accumulation of PLD mRNA and synthesis of new PLD protein during the early of heat acclimation, primary suggesting that the grape berry PLD may be involved in the heat response in post-harvest grape berry. This work offers an important basis for further investigating the mechanism of post-harvest fruit adaptation to environmental stresses.     

Resonance light scattering technique for determination of polychlorinated biphenyls with silver nanoparticles

In this paper, a simple and novel method for the determination of polychlorinated biphenyls (PCBs), using silver nanoparticles (AgNPs) as a resonance light scattering (RLS) probe, is proposed. Under optimized conditions, there existed linear relationships between the enhancing RLS intensity of the system and the concentrations of PCBs in the range 8.0 × 10^?8?1.0 × 10^?6 g mL^?1 for 2,4,4′‐trichlorbiphenyl (PCB28), 9.0 × 10^?8?1.0 × 10^?6 g mL^?1 for 2,2′,5,5′‐tetrachlorbiphenyl (PCB52) and 4.0 × 10^?8?1.0 × 10^?6 g mL^?1 for 3,3′,4,4′‐tetrachlorobiphenyl (PCB77). The corresponding detection limits (S/N = 3) were 2.6 × 10^?8 g mL^?1 for PCB28, 3.3 × 10^?8 g mL^?1 for PCB52 and 6.3 × 10^?9 g mL^?1 for PCB77, respectively. Finally, the mechanism of RLS enhancement was also studied. The results indicated that PCBs were adsorbed on the surface of AgNPs to form larger AgNP–PCB aggregates, resulting in the RLS enhancement of the system. Copyright © 2011 John Wiley & Sons, Ltd.     

Dynamically Tunable Electromagnetically Induced Transparency in Graphene and Split-Ring Hybrid Metamaterial

In this letter, a novel hybrid metamaterial consisting of periodic array of graphene nano-patch and gold split-ring resonator has been theoretically proposed to realize an active control of the electromagnetically induced transparency analog in the mid-infrared regime. A narrow transparency window occurs over a wide absorption band due to the coupling of the high-quality factor mode provided by graphene dipolar resonance and the low-quality factor mode of split-ring resonator magnetic resonance, which is interpreted in terms of the phase change and surface charge distribution. In addition to the obvious dependence of the spectral feature on the geometric parameters of the elements and the surrounding environmental dielectric constant, our proposed metamaterial shows great tunabilities to the transparency window by tuning the Fermi energy of the graphene nano-patch through electric gating and its electronic mobility without changing the geometric parameters. Furthermore, our proposed metamaterial combines low losses with very large group index associated with the resonance response in the transparency window, showing it suitable for slow light applications and nanophotonic devices for light filter and biosensing.     

Study of the inhibitory effect of fatty acids on the interaction between DNA and polymerase β

The binding of human DNA polymerase β (pol β) to DNA template-primer duplex and single-stranded DNA in the absence or presence of pol β inhibitors has been studied using a surface plasmon resonance biosensor. Two fatty acids, linoleic acid and nervonic acid, were used as potent pol β inhibitors. In the interaction between pol β and DNA, pol β could bind to ssDNA in a single binding mode, but bound to DNA template-primer duplexes in a parallel mode. Both pol β inhibitors prevented the binding of pol β to the single strand overhang and changed the binding from parallel to single mode. The affinities of pol β to the template-primer duplex region in the presence of nervonic acid or linoleic acid were decreased by 20 and 5 times, respectively. The significant inhibitory effect of nervonic acid on the pol β-duplex interaction was due to both a 2-fold decrease in the association rate and a 9-fold increase in the dissociation rate. In the presence of linoleic acid, no significant change of association rate was observed, and the decrease in binding affinity of pol β to DNA was mainly due to 7-fold increase in the dissociation rate. Published in Russian in Biokhimiya, 2009, Vol. 74, No. 7, pp. 1000–1006. These authors contributed equally.