Evolutionary divergence of the paralogs Methoprene tolerant (Met) and germ cell expressed (gce) within the genus Drosophila

Juvenile hormone (JH) signaling underpins both regulatory and developmental pathways in insects. However, the JH receptor is poorly understood. Methoprene tolerant (Met) and germ cell expressed (gce) have been implicated in JH signaling in Drosophila. We investigated the evolution of Met and gce across 12 Drosophila species and found that these paralogs are conserved across at least 63 million years of dipteran evolution. Distinct patterns of selection found using estimates of dN/dS ratios across Drosophila Met and gce coding sequences, along with their incongruent temporal expression profiles in embryonic Drosophila melanogaster, illustrate avenues through which these genes have diverged within the Diptera. Additionally, we demonstrate that the annotated gene CG15032 is the 5′ terminus of gce.In mosquitoes and beetles, a single Met-like homolog displays structural similarity to both Met and gce, and the intron locations are conserved with those of gce. We found that Tribolium and mosquito Met orthologs are assembled from Met- and gce-specific domains in a modular fashion. Our results suggest that Drosophila Met and gce experienced divergent evolutionary pressures following the duplication of an ancestral gce-like gene found in less derived holometabolous insects.     

Density functional theoretical study of the structure, bonding and electrochemistry of N2S2 nitrosyl complexes of iron and cobalt

Density functional calculations are used to study the structure, bonding and properties of the N₂S₂ nitrosyl complexes (bme-pda)M(NO) and (bme-dach)M(NO) M = Fe, Co. The complexes studied in this work have been previously shown to exhibit unusual structural and electrochemical properties. Calculated optimal geometries and vibrational frequencies are compared to experimental data and found to be in excellent agreement. A very small energy barrier for rotation of the NO ligand relative to the S-donor atoms of the N₂S₂ ligand is calculated. The similarity in reduction potentials of Fe and Co complexes is investigated using molecular orbital analysis and calculation of absolute reduction potentials. It is concluded that reduction of the Fe complexes may produce triplet-state products. Such products are determined to be of lower energy than singlet-state products, and also consistent with the observed reduction potentials of the Fe and Co complexes.     

Synthesis, structure and photocatalytic activity of a remarkably bent, cofacial ethene-linked diiron (III) μ-oxobisporphyrin

Synthesis and characterization of cis and trans 1,2-bis[Chloroiron(III) 5-(2,3,7,8,12,13,17,18-octaethylporphyrinyl)]ethenes are described. Upon treatment with 5% NaOH, cis form of the molecule immediately converts to remarkably bent diiron (III)-μ-oxo bisporphyrin which transforms to cis bisChloroFe(III)porphyrin again by the addition of 5% HCl. This facile transformation is reversible with sharp change in color in which the bisporphyrin platform ‘open’ and ‘close’ its binding pockets with very high vertical flexibility in a single molecular framework. Single crystal X-ray structural characterization reveals cis diiron(III)-μ-oxo bisporphyrin in which Fe-O-Fe unit is remarkable bent with 150.9(2)° angle. Two porphyrin rings in the molecule are not slipped but face-to-face in a fully eclipsed geometry and are placed so close that some of the carbon atoms from each of the macrocycles are driven to be essentially less than the van der Waals contacts (<3.4 Å). Two rings in the oxo-bridged dimer also make the interplanar angle of 27.7° instead of expected angle of 60° due to the bridging alkenic bond. EPR, ¹H NMR and Mössbauer spectral data are indicative of strong anti-ferromagnetic coupling between two high-spin iron(III) centers via bridging oxo group. The complex catalyzes the rapid photoinduced oxygenation of phosphites under mild condition using aerial O₂. Electrochemical data reveals that the diiron(III)-μ-oxo bisporphyrin in dichloromethane undergoes four reversible/quasi-reversible one electron oxidation and one electron reductions. The presence of two porphyrin macrocycles within a short distance in the μ-oxo species makes the porphyrin core highly nonplanar and more electron rich that might responsible for easier oxidations compared to [Fe(OEP)]₂O.     

Frequency domain magnetic resonance and magnetic circular dichroism studies on Ni4 cubane molecular nanomagnets: A magnetic anisotropy investigation

A study of the magnetic anisotropies of three Ni cubane single-molecule magnets (SMM), [Ni(hmp)(MeOH)Cl]₄·H₂O (1·H₂O) (hmpH = (2-hydroxymethyl)pyridine) [Ni(hmp)(dmb)Cl]₄ (2) (dmb = 3,3-dimethylbutanol) and [Ni(hmp)(dmp)Cl]₄ (3) (dmp = 2,2-dimethylpropanol) is reported. Frequency domain magnetic resonance spectroscopic (FDMRS) studies on 1, 2 and 3 as powder pellets reveal zero-field splitting (ZFS) for the spin ground states of these compounds in the solid state. The ZFS of the complexes 1 and 2 were determined and the presence of different molecular species was found in both complexes while only one species was found in 3. The nesting of the variable temperature variable field (VTVH) curves observed from magnetic circular dichroism (MCD) measurements on 1 in solution confirms the presence of ZFS. Virtually all the bands observed in the magnetic circular dichroism spectra possess the same sign, which may be related to the ferromagnetic exchange coupling. In addition, MCD measurements of a dilute solution demonstrate the molecular origin of the magnetic anisotropy in 1.     

A new copper(II) complex of unsymmetrical tetradentate ligand generated in situ: synthesis and molecular structure

A new copper(II) complex with tetradentate unsymmetrical ligand was prepared by one-pot condensation of methyl-2-pyrrole carboxylate, diethylenetriamine and copper(II) sulfate. The complex was characterized by elemental analysis, electronic and IR spectral, as well as X-ray crystal structure determination. The X-ray structure of the molecule reveals the copper(II) center is in a square planar environment through coordination by two nitrogen atoms of the amine, one amide nitrogen atom and one nitrogen atom of the pyrrole moieties, respectively. The copper(II) complex is neutral due to deprotonation of the amide and pyrrole groups.     

Myospora metanephrops (n. g., n. sp.) from marine lobsters and a proposal for erection of a new order and family (Crustaceacida; Myosporidae) in the Class Marinosporidia (Phylum Microsporidia)

In this study we describe, the first microsporidian parasite from nephropid lobsters. Metanephrops challengeri were captured from an important marine fishery situated off the south coast of New Zealand. Infected lobsters displayed an unusual external appearance and were lethargic. Histology was used to demonstrate replacement of skeletal and other muscles by merogonic and sporogonic stages of the parasite, while transmission electron microscopy revealed the presence of diplokaryotic meronts, sporonts, sporoblasts and spore stages, all in direct contact with the host sarcoplasm. Analysis of the ssrDNA gene sequence from the lobster microsporidian suggested a close affinity with Thelohania butleri, a morphologically dissimilar microsporidian from marine shrimps. Whilst morphological features of the lobster parasite are consistent with members of the family Nosematidae, molecular data place the parasite closer to members of the family Thelohanidae. Due to the contradiction between morphological and molecular taxonomic data, we propose the erection of a new genus in which the lobster parasite is the type species (Myospora metanephrops). Furthermore, we recommend the erection of a new family (Myosporidae) and a new order (Crustaceacida) to contain this genus. The taxonomic framework presented could be further applied to the re-classification of existing members of the Phylum Microsporidia.     

Molecular Cloning of Pigeon UDP-galactose:��-d-Galactoside ��1,4-Galactosyltransferase and UDP-galactose:��-d-Galactoside ��1,4-Galactosyltransferase, Two Novel Enzymes Catalyzing the Formation of Gal��1�C4Gal��1�C4Gal��1�C4GlcNAc Sequence

We previously found that pigeon IgG possesses unique N-glycan structures that contain the Galα1–4Galβ1–4Galβ1–4GlcNAc sequence at their nonreducing termini. This sequence is most likely produced by putative α1,4- and β1,4-galactosyltransferases (GalTs), which are responsible for the biosynthesis of the Galα1–4Gal and Galβ1–4Gal sequences on the N-glycans, respectively. Because no such glycan structures have been found in mammalian glycoproteins, the biosynthetic enzymes that produce these glycans are likely to have distinct substrate specificities from the known mammalian GalTs. To study these enzymes, we cloned the pigeon liver cDNAs encoding α4GalT and β4GalT by expression cloning and characterized these enzymes using the recombinant proteins. The deduced amino acid sequence of pigeon α4GalT has 58.2% identity to human α4GalT and 68.0 and 66.6% identity to putative α4GalTs from chicken and zebra finch, respectively. Unlike human and putative chicken α4GalTs, which possess globotriosylceramide synthase activity, pigeon α4GalT preferred to catalyze formation of the Galα1–4Gal sequence on glycoproteins. In contrast, the sequence of pigeon β4GalT revealed a type II transmembrane protein consisting of 438 amino acid residues, with no significant homology to the glycosyltransferases so far identified from mammals and chicken. However, hypothetical proteins from zebra finch (78.8% identity), frogs (58.9–60.4%), zebrafish (37.1–43.0%), and spotted green pufferfish (43.3%) were similar to pigeon β4GalT, suggesting that the pigeon β4GalT gene was inherited from the common ancestors of these vertebrates. The sequence analysis revealed that pigeon β4GalT and its homologs form a new family of glycosyltransferases.     

An integrated molecular dynamics (MD) and experimental study of higher order human telomeric quadruplexes

Structural knowledge of telomeric DNA is critical for understanding telomere biology and for the utilization of telomeric DNA as a therapeutic target. Very little is known about the structure of long human DNA sequences that may form more than one quadruplex unit. Here, we report a combination of molecular dynamics simulations and experimental biophysical studies to explore the structural and dynamic properties of the human telomeric sequence (TTAGGG)₈TT that folds into two contiguous quadruplexes. Five higher order quadruplex models were built combining known single human telomeric quadruplex structures as unique building blocks. The biophysical properties of this sequence in K⁺ solution were experimentally investigated by means of analytical ultracentrifugation and UV spectroscopy. Additionally, the environments of loop adenines were probed by fluorescence studies using systematic single‐substitutions of 2‐aminopurine for the adenine bases. The comparison of the experimentally determined properties with the corresponding quantities predicted from the models allowed us to test the validity of each of the structural models. One model emerged whose properties are most consistent with the predictions, and which therefore is the most probable structure in solution. This structure features contiguous quadruplex units in an alternating hybrid‐1‐hybrid‐2 conformation with a highly ordered interface composed of loop residues from both quadruplexes © 2010 Wiley Periodicals, Inc. Biopolymers 93:533–548, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Synthesis and conformational analysis of carbasugar bioisosteres of α-l-iduronic acid and its methyl glycoside

The synthesis of two novel carbasugar analogues of α-l-iduronic acid is described in which the ring-oxygen is replaced by a methylene group. In analogy with the conformational equilibrium described for α-l-IdopA, the conformation of the carbasugars was investigated by ¹H and ¹³C NMR spectroscopy. Hadamard transform NMR experiments were utilised for rapid acquisition of ¹H,¹³C-HSQC spectra and efficient measurements of heteronuclear long-range coupling constants. Analysis of ¹H NMR chemical shifts and J_H,H coupling constants extracted by a total-lineshape fitting procedure in conjunction with J_H,C coupling constants obtained by three different 2D NMR experiments, viz., ¹H,¹³C-HSQC-HECADE, J-HMBC and IPAP-HSQC-TOCSY-HT, as well as effective proton-proton distances from 1D ¹H,¹H T-ROE and NOE experiments showed that the conformational equilibrium ⁴C₁?²S_5a?¹C₄ is shifted towards ⁴C₁ as the predominant or exclusive conformation. These carbasugar bioisosteres of α-l-iduronic acid do not as monomers show the inherent flexibility that is anticipated to be necessary for biological activity.     

3DSDSCAR—a three dimensional structural database for sialic acid-containing carbohydrates through molecular dynamics simulation

The inherent flexibility and lack of strong intramolecular interactions of oligosaccharides demand the use of theoretical methods for their structural elucidation. In spite of the developments of theoretical methods, not much research on glycoinformatics is done so far when compared to bioinformatics research on proteins and nucleic acids. We have developed three dimensional structural database for a sialic acid-containing carbohydrates (3DSDSCAR). This is an open-access database that provides 3D structural models of a given sialic acid-containing carbohydrate. At present, 3DSDSCAR contains 60 conformational models, belonging to 14 different sialic acid-containing carbohydrates, deduced through 10 ns molecular dynamics (MD) simulations. The database is available at the URL: http://www.3dsdscar.org.