Iron tetraanthracenotetraazaporphyrins: synthesis, structural characterization, ligand binding properties, and unexpected selectivity of a bis-"bowl" tetraazaporphyrin

The synthesis and characterization, by optical spectroscopy, mass spectrometry, superconducting quantum interference device (SQUID) magnetometry, and single-crystal X-ray diffraction, of six iron complexes of tetraanthracenotetraazaporphyrin (TATAP) are reported. Eight benzo groups, flanking the macrocycle periphery, form a nonpolar "bowl" on each face of the porphyrazine and prevent mu-oxo dimer formation. Fe(TATAP) readily binds THF, a variety of neutral nitrogenous axial ligands, and carbon monoxide. The equilibrium binding constants for the first two are higher than those of analogous porphyrins while those of the latter are smaller. We attribute these differences to the higher pi acidity of the porphyrazine ligand. Fe(TATAP) also shows different relative magnitudes of the successive equilibrium binding constants, K1 and K2, for hindered nitrogenous ligands when compared to those of porphyrin analogues. Surprisingly, Fe(TATAP), in toluene solution, shows no affinity for O2 when exposed to 1 atm partial pressure of O2 at 25 degrees C. These results are explained in terms of an unusually positive iron(III/II) redox potential when coordinated by the TATAP ligand.     

Development of lipid targeting Raman probes for in vivo imaging of Caenorhabditis elegans

A simple, sensitive, and highly specific lipid targeting Raman probe (Nile red coated silver nanoparticles) has been developed to image living nematode Caenorhabditis elegans (C. elegans). Our idea of imaging lipids in C. elegans is to combine the specificity of the fluorescent dye, Nile red, and the highly enhanced Raman scattering on the silver nanoparticles. Our strategy involves the fabrication of a lipid targeting probe, which is incorporated into the intracellular intestinal granules of C. elegans by incubating these worms in the solution containing Raman probes, resulting in an uptake and subsequent incorporation of these Raman probes into the intestinal granule, thus allowing fast visualization of lipid droplets through a conventional confocal imaging technique.     

Replication in UV-lrradiated Caenorhabditis elegans Embryos

Abstract— Replication continues in wild-type (but not rad mutant) Caenorhabditis elegans embryos even after exposure to massive fluences of UV radiation. It is of interest to elucidate the mechanism(s) for this "damage-resistant" DNA synthesis. In this study, DNA from unirradiated and UV-irradiated wild-type embryos was examined using the electron microscope. Large fluences of UV radiation (180 J m⁻²) had little effect on either replication bubble size or distances between bubbles in wild-type embryos, indicating that the damage-resistant DNA synthesis was not grossly aberrant. Conversely, UV irradiation significantly decreased center-to-center distances between bubbles in excision-repair-deficient rad-3 embryos. This suggests that the decreased DNA synthesis observed after UV irradiation in rad-3 embryos is due largely to blockage of elongation of DNA synthesis.     

Extended-ensemble docking to probe dynamic variation of ligand binding sites during large-scale structural changes of proteins

Proteins can sample a broad landscape as they undergo conformational transition between different functional states. At the same time, as key players in almost all cellular processes, proteins are important drug targets. Considering the different conformational states of a protein is therefore central for a successful drug-design strategy. Here we introduce a novel docking protocol, termed extended-ensemble docking, pertaining to proteins that undergo large-scale (global) conformational changes during their function. In its application to multidrug ABC-transporter P-glycoprotein (Pgp), extensive non-equilibrium molecular dynamics simulations employing system-specific collective variables are first used to describe the transition cycle of the transporter. An extended set of conformations (extended ensemble) representing the full transition cycle between the inward- and the outward-facing states is then used to seed high-throughput docking calculations of known substrates, non-substrates, and modulators of the transporter. Large differences are predicted in the binding affinities to different conformations, with compounds showing stronger binding affinities to intermediate conformations compared to the starting crystal structure. Hierarchical clustering of the binding modes shows all ligands preferably bind to the large central cavity of the protein, formed at the apex of the transmembrane domain (TMD), whereas only small binding populations are observed in the previously described R and H sites present within the individual TMD leaflets. Based on the results, the central cavity is further divided into two major subsites, first preferably binding smaller substrates and high-affinity inhibitors, whereas the second one shows preference for larger substrates and low-affinity modulators. These central subsites along with the low-affinity interaction sites present within the individual TMD leaflets may respectively correspond to the proposed high- and low-affinity binding sites in Pgp. We propose further an optimization strategy for developing more potent inhibitors of Pgp, based on increasing its specificity to the extended ensemble of the protein, instead of using a single protein structure, as well as its selectivity for the high-affinity binding site. In contrast to earlier in silico studies using single static structures of Pgp, our results show better agreement with experimental studies, pointing to the importance of incorporating the global conformational flexibility of proteins in future drug-discovery endeavors.

Functional states of P-glycoprotein formed during its full transition cycle (red to blue), captured by molecular dynamics simulations, form a structural framework for extended-ensemble docking of small-molecule ligands of diverse activities.     

Complexes built with a scorpion-type tripodal ligand and metal ions: syntheses, structural features, electrochemical properties and magnetic properties

The complexes [Fe(bpz*mpy)₂](ClO₄)₂ (1a), [Cu(bpz*mpy)₂](ClO₄)₂ (1b) and [Ag(bpz*mpy)(Ph₃P)](ClO₄) · H₂O (2) (bpz*mpy = pyridin-2-yl-bis(3,5-dimethylpyrazol-1-yl)methane) have been synthesized and characterized by physicochemical and spectroscopic methods. X-ray crystallographic analysis reveals that the central Fe^II and Cu^II ions in complexes 1a and 1b are located on a twofold rotation axis and have a distorted octahedral coordination sphere, while the Ag^I center in complex 2 is tetrahedrally coordinated. The electrochemical properties of complex 1b have been investigated. Furthermore, a variable temperature magnetic susceptibility study of complex 1a has also been performed over the measured temperature range 2–300 K.     

beta-Barrel transmembrane proteins: Geometric modelling, detection of transmembrane region, and structural properties

The location of the membrane lipid bilayer relative to a transmembrane protein structure is important in protein engineering. Since it is not present on the determined structures, it is essential to automatically define the membrane embedded protein region in order to test mutation effects or to design potential drugs. beta-Barrel transmembrane proteins, present in nature as outer membrane proteins (OMPs), comprise one of the two transmembrane protein fold classes. Lately, the number of their determined structures has increased and this enables the implementation and evaluation of structure-based annotation methods and their more comprehensive study. In this paper, we propose two new algorithms for (i) the geometric modelling of beta-barrels and (ii) the detection of the transmembrane region of a beta-barrel transmembrane protein. The geometric modelling algorithm combines a non-linear least square minimization method and a genetic algorithm in order to find the characteristics (axis, radius) of a shape with axial symmetry which best models a beta-barrel. The transmembrane region is detected by profiling the external residues of the beta-barrel along its axis in terms of hydrophobicity and existence of aromatic and charged residues. TbB-Tool implements these algorithms and is available in . A non-redundant set of 22 OMPs is used in order to evaluate the algorithms implemented and the results are very satisfying. In addition, we quantify the abundance of all amino acids and the average hydrophobicity for external and internal beta-stranded residues along the axis of beta-barrel, thus confirming and extending other researchers' results.     

A split ligand for lanthanide binding: facile evaluation of dimerizing proteins

Luminescence of lanthanides is attractive for biological applications due to its long lifetime and sharp emission profiles. We describe the split display of a lanthanide binding ligand that allows facile evaluation of dimerizing proteins. The split lanthanide ligand is cysteine reactive, and therefore should be readily applicable to a variety of protein systems.     

Synthesis and ligand binding properties of triptycene-linked porphyrin arrays

Multiporphyrin arrays are a complex class of molecules with numerous potential applications in energy transfer, photomedicine, and light harvesting. We have developed a facile/versatile route to a class of triptycene-linked porphyrin arrays via both Suzuki and Sonogashira cross-coupling methods, which makes use of the rigid three-pronged orientation of triptycene to construct trimeric porphyrin arrays linked either in the meso or β-position with various linker groups. In order to understand the properties of these potential antenna systems and probe their potential applications, the coordination behavior of zinc(II) derivatives with mono- and bidentate N-donor ligands was investigated. Depending on ligand concentration, both one- and two-point binding was observed with a bidentate ligand. Also/in addition, different cavity sizes, obtained by the use of different linker groups, resulted in differences in the binding properties of each trimeric system.     

Three novel lanthanide complexes with imidazole-4,5-dicarboxylate ligand: Hydrothermal syntheses, structural characterization, and properties

Three novel lanthanide complexes, namely, [Ce(Himdc)(H₂imdc)(H₂O)₃]·H₂O (1), {[Dy(Himdc)(Ox)_0.5(H₂O)₂]·H₂O}_n (2), and {[Nd(Himdc)(Ox)_0.5(H₂O)₂]·H₂O}_n (3) (H₃imdc = imidazole-4,5-dicarboxylic acid, Ox = oxalate), have been successfully prepared by the assembly of lanthanide ions and H₃imdc ligand under different synthetic conditions. All of the complexes have been characterized by means of elemental analysis, IR, TG analysis, luminescence spectroscopy as well as single-crystal X-ray diffraction analysis. The 3D supramolecular structure of 1 is constructed from 1D zig-zag chains through the hydrogen bonding interactions. Complex 2 possesses the chair-shaped secondary building units (SBUs) with Dy₆(Himdc)₄(Ox)₂ and meso-helical chains (P + M), resulting in a novel 2D structure based on the linkages of oxalate ligand. Complex 3 also presents 2D layer structure with uninodal 6-connected net topology, but crystallizes in the different space group and owns higher coordination number of the central metal atom than complex 2. The luminescence property of 2 is investigated in the solid state at room temperature.     

Effect of ligand binding on the intraminimum dynamics of proteins

Effects of ligand binding on protein dynamics are studied via molecular dynamics (MD) simulations on two different enzymes, dihydrofolate reductase (DHFR) and triosephosphate isomerase (TIM), in their unliganded (free) and liganded states. Domain motions in MD trajectories are analyzed by collectivities and rotation angles along the principal components (PCs). DHFR in the free state has well‐defined domain rotations, whereas rotations are slightly damped in the binary complex with nicotinamide adenine dinucleotide phosphate (NADPH), and remarkably distorted in the presence of NADP⁺, showing that NADP⁺ is solely responsible for the loss of correlation of the domains in DHFR. Although mean square fluctuations of MD simulations in the same PC subspaces are similar for different ligation states, linear stochastic time series models show that backbone flexibility along the first five PCs is decreased upon NADPH and NADP⁺ binding in subpicosecond scale. This shows that mobility of the protein along the PCs is closely related with intraminimum dynamics, and alterations in ligation states may change the intraminimum dynamics significantly. Low vibrational frequencies of the alpha‐carbon atoms of DHFR are determined from the time series models of a larger number of low indexed PCs, and it is found that number of modes in the lowest frequencies is reduced upon ligand binding. A similar result is obtained for TIM in the unliganded and dihydroxyacetone phosphate bound states. We suggest that stochastic time series modeling is a promising method to be used in determining subtle perturbations in protein dynamics. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Computational study of ligand binding in lipid transfer proteins: Structures,interfaces, and free energies of protein‐lipid complexes

Plant nonspecific lipid transfer proteins (nsLTPs) bind a wide variety of lipids, which allows them to perform disparate functions. Recent reports on their multifunctionality in plant growth processes have posed new questions on the versatile binding abilities of these proteins. The lack of binding specificity has been customarily explained in qualitative terms on the basis of a supposed structural flexibility and nonspecificity of hydrophobic protein‐ligand interactions. We present here a computational study of protein‐ligand complexes formed between five nsLTPs and seven lipids bound in two different ways in every receptor protein. After optimizing geometries in molecular dynamics calculations, we computed Poisson‐Boltzmann electrostatic potentials, solvation energies, properties of the protein‐ligand interfaces, and estimates of binding free energies of the resulting complexes. Our results provide the first quantitative information on the ligand abilities of nsLTPs, shed new light into protein‐lipid interactions, and reveal new features which supplement commonly held assumptions on their lack of binding specificity. © 2012 Wiley Periodicals, Inc.     

Synthesis,structural and spectral properties of Au complexes: luminescence properties and their non‐covalent DNA binding studies

Gold complexes of 1,3‐ bis‐pyridylimidazolium chloride ( L1 ), 1,3‐bis‐[2,6‐diisopropylphenyl]imidazolium chloride ( L2 ) and 1,3‐bis‐[benzyl]benzimidazolium chloride ( L3 ) were synthesized and characterized by analytical methods. For the complexes, electronic spectral results show that there is a marked difference in the band feature observed in the spectra, ascribed to the greater relativistic effect of gold. In fluorescence studies, the complexes develop emission bands in the visible region (400–600 nm) after excitation at around 350 nm. Au complex–DNA binding was studied, and it was observed that genomic DNA isolated from the U373‐GB cell line was fragmented and in some cases degraded by the Au complexes. Furthermore, the intensity of the DNA band increased when concentration of the metal complex was augmented. This study shows that the DNA cleavage is mediated by the Au complex. Copyright © 2013 John Wiley & Sons, Ltd.     

Profiling of Caenorhabditis elegans proteins using two-dimensional gel electrophoresis and matrix assisted laser desorption/ionization-time of flight-mass spectrometry

The nematode Caenorhabditis elegans (C. elegans) is the first animal whose whole 97 Mb genome sequence, encoding ca. 19000 open reading frames (ORF's), has been essentially determined. We tried to establish a 2-DE map of the nematode proteome by means of two-dimensional polyacrylamide gel electrophoresis (2-D PAGE). A soluble protein fraction of mixed stages of the worm, wild-type strain N2, was applied to 2-D PAGE. After Coomassie Brilliant Blue (CBB) staining, 1200 spots were detected and 140 major spots were excised from the gel and subjected to in-gel digestion with Achromobacter protease I (lysyl endopeptidase). Resulting peptides were analyzed by matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) followed by peptide mass fingerprinting for protein identification. With this approach we have obtained a two-dimensional electrophoresis (2-DE) protein map in which 69 spots were localized as landmarks for comparison of expression profiles to elucidate the basis of various biological events.     

Computational analysis,structural modeling and ligand binding site prediction of Plasmodium falciparum 1-deoxy-d-xylulose-5-phosphate synthase

Malaria remains one of the most serious infectious diseases in the world. There are five human species of the Plasmodium genus, of which Plasmodium falciparum is the most virulent and responsible for the vast majority of malaria related deaths. The unique biochemical processes that exist in Plasmodium falciparum provide a useful way to develop novel inhibitors. One such biochemical pathway is the methyl erythritol phosphate pathway (MEP), required to synthesize isoprenoid precursors. In the present study, a detailed computational analysis has been performed for 1-deoxy-d-xylulose-5-phosphate synthase, a key enzyme in MEP. The protein is found to be stable and residues from 825 to 971 are highly conserved across species. The homology model of the enzyme is developed using three web-based servers and Modeller software. It has twelve disordered regions indicating its druggability. Virtual screening of ZINC database identifies ten potential compounds in thiamine diphosphate binding region of the enzyme.     

Preparation of Dendrobium officinale Flower Anthocyanin and Extended Lifespan in Caenorhabditis elegans

The Dendrobium officinale flower is a non-medicinal part of the plant, rich in a variety of nutrients and bioactive ingredients. The purpose of this article was to explore the preparation conditions of anthocyanins (ACNs) from the D. officinale flower. Subsequently, its anti-aging effects were evaluated with Caenorhabditis elegans. Results showed that the ACNs had antioxidant activities on scavenging free radicals (DPPH· and ABTS⁺·), and the clearance rate was positively correlated with the dose. Additionally, ACNs significantly increased the activity of superoxide dismutase (SOD) in C. elegans, which was 2.068-fold higher than that of the control. Treatment with ACNs at 150 μL extended the lifespan of C. elegans by 56.25%, and treatment with ACNs at 50 μL promoted fecundity in C. elegans. Finally, the protective effect of ACNs enhanced stress resistance, thereby increasing the survival numbers of C. elegans, which provided insights for the development and practical application of functional products.     

UV PHOTOBIOLOGY OF THE NEMATODE Caenorhabditis elegans: ACTION SPECTRA, ABSENCE OF PHOTOREACTIVATION and EFFECTS OF CAFFEINE

Action spectra for UV inactivation of reproduction in Caenorhabditis elegans have been obtained for strains N2 (wild-type) and rad-3 (radiation-sensitive). Use of a dye laser radiation source, providing high intensity in a narrow wavelength band, has permitted more detail (14 wavelengths between 260 and 320 nm) than available in the spectra for other multicellular organisms. Overall sensitivity of N2 is similar to that of wild-type Escherichia coli; that of rad-3 is 30-fold higher between 265 and 310 nm; relative sensitivity decreases above 310 nm but also seems to increase for irradiation below 265 nm. Tests for photoreactivation and for modification of survival by post-irradiation treatment with caffeine were negative.