Nuclear magnetic resonance studies of the N-terminal fragment of adenosine diphosphate ribosylation factor 1 in micelles and bicelles: influence of N-myristoylation

The N-terminal fragment of adenosine diphosphate (ADP) ribosylation factor 1 (ARF1) is proposed to be involved in the guanosine triphosphate- (GTP-) dependent, reversible association of the protein with membranes through the interaction of not only the N-linked myristoyl chain but also its highly conserved N-terminal hydrophobic residues. Based on the N-terminal sequence of this protein, specifically (13)C- and (15)N-labeled peptides were synthesized with and without an N-myristoyl anchor. The behavior, including structure, dynamics, and orientation, of these peptides in a lipid environment was then studied through a combination of solution (1)H nuclear magnetic resonance (NMR) techniques in micelles and heteronuclear solid-state NMR experiments in magnetically aligned bicelles. The work presented is an extension of the previously reported characterization of the myristoylated N-terminal fragment of ARF1 [Losonczi and Prestegard (1998) Biochemistry 37, 706-716] to include a comparison to a nonmyristoylated analogue. Results indicate that both myristoylated and nonmyristoylated peptides are alpha-helical in a lipid environment and that N-myristoylation does not greatly influence the structure of the peptides. Evidence is presented suggesting association of the peptides with bilayer disks through a combination of edge and surface interactions.     

CHROMOSOMES IN TWENTY-FIVE SPECIES OF CHINESE MEM-BRACIDS (HOMOPTERA: MEMBRACIDAE)*

Abstract Chromosomes in 25 species of Membracidae are recorded. Numbers, size and behaviors of the chromosomes during meiosis and mitosis are used as specific or generic features for the taxonomy of this group. Chromosome numbers vary from n=5 to 12, and sex mechanism are of XO type except two species with neo-XY system. The histogram indicates that 2n=11 with XO sex mechanism is the modal chromosome number, and another type n=10 is also commonly found in this family.     

A NEW SPECIES OF GENUS HABROPHLEBIODES ULMER (EPHEMEROPTERA: LEPTOPHLEBIIDAE)

Abstract  The present paper deals with a new species Habrophlebiodes zijinensis sp. nov. collected in Nanjing, Jiangsu Povince, China.     

Structural Basis of Multifunctional Bovine Mitochondrial Cytochrome bc 1 Complex

The mitochondrial cytochrome bc ₁ complex is a multifunctional membrane protein complex. Itcatalyzes electron transfer, proton translocation, peptide processing, and superoxide generation.Crystal structure data at 2.9 Å resolution not only establishes the location of the redox centersand inhibitor binding sites, but also suggests a movement of the head domain of the iron–sulfurprotein (ISP) during bc ₁ catalysis and inhibition of peptide-processing activity during complexmaturation. The functional importance of the movement of extramembrane (head) domain ofISP in the bc ₁ complex is confirmed by analysis of the Rhodobacter sphaeroides bc ₁ complexmutants with increased rigidity in the ISP neck and by the determination of rate constants foracid/base-induced intramolecular electron transfer between [2Fe–2S] and heme c ₁ in nativeand inhibitor-loaded beef complexes. The peptide-processing activity is activated in bovineheart mitochondrial bc ₁ complex by nonionic detergent at concentrations that inactivate electrontransfer activity. This peptide-processing activity is shown to be associated with subunits Iand II by cloning, overexpression and in vitro reconstitution. The superoxide-generation siteof the cytochrome bc ₁ complex is located at reduced b _L and Q^–. The reaction is membranepotential-, and cytochrome c-dependent.     

Mapping and Expression Analysis of Chicken NDRG1 and NDRG3 Genes

N-myc downstream-regulated genes 1 and 3 (NDRG1 and NDRG3) are members of the alpha/beta hydrolase superfamily. Phylogenetic analysis of the family demonstrated that human NDRG1 and 3 belong to a subfamily. The mapping and gene expression patterns of these genes represent one step toward further investigation into their possible roles in the chicken (Gallus gallus). To map these genes in the chicken chromosome, a 6000 rads chicken-hamster radiation hybrid panel (ChickRH6) was used. Primers were designed according to the published human sequences for amplification of those two genes. We compared the corresponding human mRNA sequences with the predicted coding sequences of the chicken NDRG1 and 3 genes and found that the assembled contigs shared a high percentage of similarity with the human genes. PCR of samples from ChickRH6 revealed that the locations of NDRG1 and 3 are linked to the markers MYC (58 cRs away, LOD score 4.52) and SEQ0265 (10 cRs away, LOD score 17.81), respectively. This result adds two new markers to the chicken RH map, and it reinforces that the RH technique is indeed a powerful tool for mapping genes due to its rapidity, precision, convenience, and reproducibility. In addition, we detected the gene expression and distribution of chicken NDRG1 and 3 in seven tissues, including heart, liver, spleen, lung, muscle, brain, and thymus, by RT-PCR, and found that NDRG1 is relatively ubiquitously expressed in all the tested tissues and highly expressed in heart and liver, whereas NDRG3 is high in heart, muscle, and brain.     

G-Quadruplex structure: a target for anticancer therapy and a probe for detection of potassium

G-Quadruplexes are four-stranded DNA structures that play important regulatory roles in the maintenance of telomere length by inhibiting telomerase activity. Telomeres are specialized functional DNA-protein structures consisting of a variable number of tandem G-rich repeats together with a group of specific proteins. Telomere losses during cell replication are compensated by telomerase, which adds telomeric repeats onto the chromosome ends in the presence of its substrate--the 3 -overhang. Recently, quadruplexes have been considered as a potential therapeutic target for human cancer because they can inhibit telomerase activity, and some quadruplex-interacting drugs can induce senescence and apoptosis of cancer cells. In addition, due to the potassium preference to the other cations, especially sodium ions, quadruplexes have been suggested for developing potassium detection probes with higher sensitivity and selectivity. This review will illustrate these two aspects to provide further understanding of G-quadruplex structures.     

Large-scale phosphoproteome analysis of human liver tissue by enrichment and fractionation of phosphopeptides with strong anion exchange chromatography

The mixture of phosphopeptides enriched from proteome samples are very complex. To reduce the complexity it is necessary to fractionate the phosphopeptides. However, conventional enrichment methods typically only enrich phosphopeptides but not fractionate phosphopeptides. In this study, the application of strong anion exchange (SAX) chromatography for enrichment and fractionation of phosphopeptides was presented. It was found that phosphopeptides were highly enriched by SAX and majority of unmodified peptides did not bind onto SAX. Compared with Fe(3+) immobilized metal affinity chromatography (Fe(3+)-IMAC), almost double phosphopeptides were identified from the same sample when only one fraction was generated by SAX. SAX and Fe(3+)-IMAC showed the complementarity in enrichment and identification of phosphopeptides. It was also demonstrated that SAX have the ability to fractionate phosphopeptides under gradient elution based on their different interaction with SAX adsorbent. SAX was further applied to enrich and fractionate phosphopeptides in tryptic digest of proteins extracted from human liver tissue adjacent to tumorous region for phosphoproteome profiling. This resulted in the highly confident identification of 274 phosphorylation sites from 305 unique phosphopeptides corresponding to 168 proteins at false discovery rate (FDR) of 0.96%.     

Fate and protective effect of marrow stromal cells after subretinal transplantation

Engraftment of marrow stromal cells (MSCs) has been proposed as a therapeutic approach for degenerative diseases. In this study we investigated the fate and dynamic progress of grafted MSCs in living retina with the aim of evaluating the use of transplanted MSCs to treat retinal degeneration. Approximately 1×10⁵ gfp -MSCs in 2 μl phosphate-buffered saline were injected into the subretinal space of adult Sprague-Dawley rats. Two weeks later, approximately 0.174%±0.082% of the transplanted cells had survived and diffused into the subretinal space. Nine weeks after transplantation the surviving gfp -MSCs accounted for 0.049%±0.023% of the number of cells injected and were mainly located at the injection site. The same number of MSCs were transplanted into the left eye subretinal space of 3-week-old hereditary retinal degenerative Royal College of Surgeons rats, and phosphate-buffered saline was injected into their right eyes as a control. Five weeks after transplantation, the amount of rudimentary photo-receptors was more significantly increased in grafted eyes than in control eyes. The results indicated that grafted MSCs could survive and rescue retinal degeneration.     

NaKtide, a Na/K-ATPase-derived Peptide Src Inhibitor, Antagonizes Ouabain-activated Signal Transduction in Cultured Cells

We have previously shown that the Na/K-ATPase binds and inhibits Src. Here, we report the molecular mechanism of Na/K-ATPase-mediated Src regulation and the generation of a novel peptide Src inhibitor that targets the Na/K-ATPase/Src receptor complex and antagonizes ouabain-induced protein kinase cascades. First, the Na/K-ATPase inhibits Src kinase through the N terminus of the nucleotide-binding domain of the α1 subunit. Second, detailed mapping leads to the identification of a 20-amino acid peptide (NaKtide) that inhibits Src (IC₅₀ = 70 nm) in an ATP concentration-independent manner. Moreover, NaKtide does not directly affect the ERK and protein kinase C family of kinases. It inhibits Lyn with a much lower potency (IC₅₀ = 2.5 μm). Third, highly positively charged leader peptide conjugates including HIV-Tat-NaKtide (pNaKtide) readily enter cultured cells. Finally, the following functional studies of pNaKtide demonstrate that this conjugate can specifically target the Na/K-ATPase-interacting pool of Src and act as a potent ouabain antagonist in cultured cells: 1) pNaKtide, unlike PP2, resides in the membranes. Consistently, it affects the basal Src activity much less than that of PP2. 2) pNaKtide is effective in disrupting the formation of the Na/K-ATPase/Src receptor complex in a dose-dependent manner. Consequently, it blocks ouabain-induced activation of Src, ERK, and hypertrophic growth in cardiac myocytes. 3) Unlike PP2, pNaKtide does not affect IGF-induced ERK activation in cardiac myocytes. Taken together, we suggest that pNaKtide may be used as a novel antagonist of ouabain for probing the physiological and pathological significance of the newly appreciated signaling function of Na/K-ATPase and cardiotonic steroids.The Na/K-ATPase is expressed in most eukaryotic cells and is essential for maintaining the transmembrane ion gradient by pumping Na⁺ out of and K⁺ into cells (1). Structurally, the enzyme consists of two non-covalently linked α and β subunits. Similar to other P-ATPases, the Na/K-ATPase α subunit has 10 transmembrane domains with both the N and C termini located in the cytoplasm (2, 3). Based on the published crystal structures of Na/K-ATPase (4), the α subunit consists of several well-characterized domains. The actuator (A)² domain consists of the N terminus and the second cytosolic domain (CD2) connected to transmembrane helices M2 and M3, and the highly conserved discontinuous phosphorylation (P) domain is close to the plasma membrane, while the nucleotide-binding (N) domain is relatively isolated (2). There is a significant amount of movement of both the A and N domains during the ion-pumping cycle as in the SR Ca²⁺-ATPase (4–6). It appears that the A domain rotates, while the N domain closes during the transport cycle. Interestingly, these domains have also been implicated in interacting with many protein partners, including inositol 1,4,5-trisphosphate receptors, phosphoinositide 3-kinase, phospholipase C-γ (PLC-γ), ankyrin, and cofilin (7–12).Src, a member of the Src family non-receptor kinases, plays an important role in the signal transduction pathways of many extracellular stimuli such as cytokines, growth factors, and stress responses (13) and has been considered as a promising target for therapeutic intervention in certain cancers (14) and bone diseases (15). Several endogenous inhibitors of Src have been documented previously, including the C-terminal Src kinase, CSK-homologous kinase, Wiscott-Aldrich syndrome protein, RACK1, and caveolin (16–19).Previously, we and others (20) have demonstrated that binding of cardiotonic steroids (CTS) such as ouabain to the Na/K-ATPase stimulates multiple protein kinase cascades. Moreover, the knock-out of Src prevents these cascades from being activated (10, 21, 22). More recently, we have observed that the Na/K-ATPase interacts directly with Src via at least two binding motifs. One of these interactions is between the CD2 of the α1 subunit and the Src SH2, and the other involves the third cytosolic domain (CD3) of the α1 subunit and the Src kinase domain. We propose that the formation of the Na/K-ATPase/Src complex serves as a receptor for ouabain to stimulate the aforementioned protein kinase cascades. Specifically, the CD3-Src kinase interaction maintains Src in an inactive form whereas the binding of ouabain to the Na/K-ATPase disrupts this interaction, resulting in the assembly and activation of different pathways including ERK cascades, PLC/PKC pathway and mitochondrial production of reactive oxygen species (23). Thus, the Na/K-ATPase functions as an endogenous negative Src regulator. This proposition is consistent with the fact that the basal Src activity is inversely correlated to the amount of Na/K-ATPase α1 subunit in both cultured cells (24) and in α1 heterozygous mouse tissues (25). Therefore, to better understand how the molecular interactions between the Na/K-ATPase and Src regulate Src activity, we have further mapped the Src-binding domains in the CD3 of α1. These studies led to the identification of a peptide Src inhibitor (pNaKtide) and the demonstration that pNaKtide can act as a novel ouabain antagonist capable of inhibiting ouabain-induced activation of protein kinase cascades and hypertrophic growth in cardiac myocytes.