Modeling of angiogenin-3 '-NMP complex

Angiogenin belongs to the Ribonuclease superfamily and has a weak enzymatic activity that is crucial for its biological function of stimulating blood vessel growth. Structural studies on ligand bound Angiogenin will go a long way in understanding the mechanism of the protein as well as help in designing drugs against it. In this study we present the first available structure of nucleotide ligand bound Angiogenin obtained by computer modeling. The importance of this study in itself notwithstanding, is a precursor to modeling a full dinucleotide substrate onto Angiogenin. Bovine Angiogenin, the structure of which has been solved at a high resolution, was earlier subjected to Molecular Dynamics simulations for a nanosecond. The MD structures offer better starting points for docking as they offer lesser obstruction than the crystal structure to ligand binding. The MD structure with the least serious short contacts was modeled to obtain a steric free Angiogenin - 3' mononucleotide complex structure. The structures were energetically minimized and subjected to a brief spell of Molecular Dynamics. The results of the simulation show that all the li,ligand-Angiogenin interactions and hydrogen bonds are retained, redeeming the structure and docking procedure. Further, following ligand - protein interactions in the case of the ligands 3'-CMP and 3'-UMP we were able to speculate on how Angiogenin, a predominantly prymidine specific ribonuclease prefers Cytosine to Uracil in the first base position.

Synthesis, Structures, and Magnetic Behavior of a Series of Copper(II) Azide Polymers of Cu-4 Building Clusters and Isolation of a New Hemiaminal Ether as the Metal Complex

Four new neutral copper azido polymers, Cu-4(N-3)(8)(L-1)(2)](n) (1), Cu-4(N-3)(8)(L-2)(2)](n) (2), Cu-4(N-3)(8)(L-3)(2)](n) (3), and Cu-9(N-3)(18)(L-4)(4)](n) (4) L1-4 are formed in situ by reacting pyridine-2-carboxaldehyde with 22-(methylamino)ethyl]pyridine (mapy, L-1), N,N-dimethylethylenediamine (N,N-dmen, L-2), N,N-diethylethylenediamine (N,N-deen, L-3), and N,N,2,2-tetramethylpropanediamine (N,N,2,2-tmpn, L-4)], have been synthesized by using 0.5 mol equiv of the chelating tridentate ligands with Cu-(NO3)(2)center dot 3H(2)O and an excess of NaN3. Single-crystal X-ray structures show that the basic unit of these complexes, especially 1-3, contains very similar Cu-4(II) building blocks. The overall structure of 3 is two-dimensional, while the other three complexes are one-dimensional in nature. Complex 1 represents a unique example containing hemiaminal ether arrested by copper(R). Complexes 1 and 2 have a rare bridging azido pathway: both end-on and end-to-end bridging azides between a pair of Cu-II centers. Cryomagnetic susceptibility measurements over a wide range of temperature exhibit dominant ferromagnetic behavior in all four complexes. Density functional theory calculations (B3LYP functional) have been performed on complexes 1-3 to provide a qualitative theoretical interpretation of their overall ferromagnetic behavior.

Metallo-beta-lactamase and phosphotriesterase activities of some zinc(II) complexes

Metallo-beta-lactamases (m beta l) and phosphotriesterase (PTE) are zinc(II) enzymes, which hydrolyze the beta-lactam antibiotics and toxic organophosphotriesters, respectively. In the present work, we have synthesized a few asymmetric phenolate-based ligands by sequential Mannich reaction and their corresponding zinc(II) complexes. These zinc(II) complexes were studied for their m beta l and PTE activities. It is shown that the zinc(II) complexes can hydrolyze oxacillin, the beta-lactam antibiotic, at much higher rates as compared to the hydrolysis of p-nitrophenyl diphenylphosphate (PNPDPP), the phosphotriester. Among the complexes studied, the binuclear asymmetric complex 1 having a water molecule coordinated to one of the zinc(II) ions exhibits much better mbl activity than the mononuclear complexes. However, the mononuclear zinc(II) complexes having labile chloride ions exhibit significant PTE activity, which can be ascribed to the replacement of chloride ions by hydroxide ions during hydrolysis reactions. (C) 2011 Elsevier B.V. All rights reserved.

Bis(acetylacetonato-kappa 2 O,O')(pyridine-kappa N)zinc(II)

In the title compound, Zn(C5H7O2)(2)(C5H5N)], the metal atom has square-pyramidal coordination geometry with the basal plane defined by the four O atoms of the chelating acetylacetonate ligands and with the axial position occupied by the pyridine N atom. The crystal packing is characterized by a C-H...O hydrogen-bonded ribbon structure approximately parallel to 10 ].

Magneto-structural correlation in (mu-alkoxo/hydroxo)(mu-carboxylato)dicopper(II) systems: Synthesis, X-ray structure and magnetic properties of aquo(mu-hydroxo) (mu-arylcarboxylato)bis(N,N,N ',N '-tetramethylethane-1,2-diamine)dicopper(II) diperchlorate

Asymmetrically dibridged dicopper(II) complexes, [Cu-2(OH)(O2CC6H4-p-Me)(tmen)(2)(H2O)](ClO4)(2) (1) and [Cu-2(OH)(O2CC6H4-p-OMe)(tmen)(2)(H2O)](ClO4)(2) (2) (tmen = N,N,N',N'-tetramethylethane-1,2-diamine), were prepared and structurally characterized. Complex 1 crystallizes in the monoclinic space group P2(1)/a with a = 17.718(2), b = 9.869(1), c = 19.677(2) Angstrom, beta = 115.16(1)degrees, V = 3114.3(6) Angstrom(3) and Z = 4. The structure was refined to R(wR(2)) = 0.067(0.178). Complex 2 crystallizes in the monoclinic space group P2(1)/a with a = 17.695(3), b = 9.574(4), c = 20.104(2) Angstrom, beta = 114.18(1)degrees, V = 3107(1) Angstrom(3) and Z = 4. The final residuals are R(wR(2)) = 0.067(0.182). The complexes have a [Cu-2(mu-OH)(mu-OH)(mu-O2CAr)](2+) core with tmen Ligands occupying the terminal sites of the core. In addition, one copper is axially bound to a water molecule. The Cu ... Cu distances and the Cu-OH Cu angles in the core are 3.394(1) Angstrom, 124.4(2)degrees for 1 and 3.374(1) Angstrom, 123.3(3)degrees for 2. The complexes show axial X-band EPR spectral features in methanol glass at 77 K giving g(perpendicular to) = 2.02, g(parallel to) = 2.3 (A(parallel to) = 165 x 10(-4) cm(-1)) and a visible band near similar to 630 nm in methanol. The complexes are weakly antiferromagnetic. A theoretical fit of the magnetic susceptibility data in the temperature range 40-295 K gives -J = 10 cm(-1), g = 2.05 for 1 and -J = 10 cm(-1), g = 2.0 for 2. Plots of -2J versus the Cu-OH-Cu angle (phi) in this class of asymmetrically dibridged dicopper(II) complexes having d(x2-y2)-d(x2-y2) magnetic orbitals show a linear magneto-structural correlation: -2J(cm(-1)) = 11.48 phi(deg) - 1373.

Molecular mimicry by antiidiotypic monoclonal antibody to gonadotropin releasing hormone

Antipeptide and antiidiotypic antibodies to several receptors are known to mimic their respective ligands in transducing signals on binding their receptors. In our attempts to study gonadotropin releasing hormone receptor, antipeptide and antiidiotypic monoclonal antibodies specific to the receptor were established earlier. The antipeptide mAb F1G4 was to a synthetic peptide corresponding to the extracellular domain of human GnRH receptor and the antiidiotypic mAb 4D10C1 was to the idiotype of a GnRH specific mAb. Here we report the physiological effects of the two mAbs on binding the receptor, as investigated using in vitro cultures of(a) human term placental villi and (b) rat pituitaries. The mAb 4D10C1 exerted a dose-dependent release of human chorionic gonadonopin in cultures of human term placental villi as well as luteinising and follicle stimulating hormones in cultures of rat pituitaries.

Structures of the catalytic site mutants D99A and H48Q and the calcium-loop mutant D49E of phospholipase A(2)

Crystal structures of the active-site mutants D99A and H48Q and the calcium-loop mutant D49E of bovine phospholipase A(2) have been determined at around 1.9 Angstrom resolution. The D99A mutant is isomorphous to the orthorhombic recombinant enzyme, space group P2(1)2(1)2(1), The H48Q and the calcium-loop mutant D49E are isomorphous to the trigonal recombinant enzyme, space group P3(1)21, The two active-site mutants show no major structural perturbations. The structural water is absent in D99A and, therefore, the hydrogen-bonding scheme is changed. In H48Q, the catalytic water is present and hydrogen bonded to Gln48 N, but the second water found in native His48 is absent. In the calcium-loop mutant D49E, the two water molecules forming the pentagonal bipyramid around calcium are absent and only one O atom of the Glu49 carboxylate group is coordinated to calcium, resulting in only four ligands.

EPR and photoluminescence studies of ZnO:Mn nanophosphors prepared by solution combustion route

Nanocrystalline ZnO:Mn (0.1 mol%) phosphors have been successfully prepared by self propagating, gas producing solution combustion method. The powder X-ray diffraction of as-formed ZnO:Mn sample shows, hexagonal wurtzite phase with particle size of similar to 40 nm. For Mn doped ZnO, the lattice parameters and volume of unit cell (a=3.23065 angstrom, c=5.27563 angstrom and V=47.684 (angstrom)(3)) are found to be greater than that of undoped ZnO (a=3.19993 angstrom, c=5.22546 angstrom and V=46.336 (angstrom)(3)). The SEM micrographs reveal that besides the spherical crystals, the powders also contained several voids and pores. The TEM photograph also shows the particles are approximately spherical in nature. The FTIR spectrum shows two peaks at similar to 3428 and 1598 cm(-1) which are attributed to O-H stretching and H-O-H bending vibration. The PL spectra of ZnO:Mn indicate a strong green emission peak at 526 nm and a weak red emission at 636 nm corresponding to T-4(1) -> (6)A(1) transition of Mn2+ ions. The EPR spectrum exhibits fine structure transition which will be split into six hyperfine components due to Mn-55 hyperfine coupling giving rise to all 30 allowed transitions. From EPR spectra the spin-Hamiltonian parameters have been evaluated and discussed. The magnitude of the hyperfine splitting (A) constant indicates that there exists a moderately covalent bonding between the Mn2+ ions and the surrounding ligands. The number of spins participating in resonance (N), its paramagnetic susceptibility (chi) have been evaluated. (C) 2011 Elsevier B.V. All rights reserved.

Molecular self-assembly of cadmium-triazolate complexes via hydrogen bonding: Synthesis, structures and photoluminescent properties

Two new cadmium coordination polymers namely Cd(HAmTrz-COO)(4)(NH4+)(2)] 1; and Cd(HAmTrz)(2)I-2](n) 2; (HAmTrz-COOH = 3-amino-1,2,4-triazole-5-carboxylic acid), have been prepared based on HAmTrz-COOH as ligand. The crystal structures of 1 and 2 have been determined by single-crystal X-ray diffraction technique. In coordination-complex 1 four triazole ligands coordinate via N1 nitrogen leading to a tetrahedral geometry around cadmium ion, while in 2 the ligand prefers to coordinate to the metal in a bidentate bridging mode. The structures of both the coordination polymers can be envisaged as 3D hydrogen bonded networks. Thermogravimetric analysis shows that 2 is more stable than 1 owing to different coordination numbers of cadmium atoms. Photoluminescence properties of both the compounds have been investigated in the solid state. (C) 2011 Elsevier B.V. All rights reserved.

Insights into the Regulatory Characteristics of the Mycobacterial Dephosphocoenzyme A Kinase: Implications for the Universal CoA Biosynthesis Pathway

Being vastly different from the human counterpart, we suggest that the last enzyme of the Mycobacterium tuberculosis Coenzyme A biosynthetic pathway, dephosphocoenzyme A kinase (CoaE) could be a good anti-tubercular target. Here we describe detailed investigations into the regulatory features of the enzyme, affected via two mechanisms. Enzymatic activity is regulated by CTP which strongly binds the enzyme at a site overlapping that of the leading substrate, dephosphocoenzyme A (DCoA), thereby obscuring the binding site and limiting catalysis. The organism has evolved a second layer of regulation by employing a dynamic equilibrium between the trimeric and monomeric forms of CoaE as a means of regulating the effective concentration of active enzyme. We show that the monomer is the active form of the enzyme and the interplay between the regulator, CTP and the substrate, DCoA, affects enzymatic activity. Detailed kinetic data have been corroborated by size exclusion chromatography, dynamic light scattering, glutaraldehyde crosslinking, limited proteolysis and fluorescence investigations on the enzyme all of which corroborate the effects of the ligands on the enzyme oligomeric status and activity. Cysteine mutagenesis and the effects of reducing agents on mycobacterial CoaE oligomerization further validate that the latter is not cysteine-mediated or reduction-sensitive. These studies thus shed light on the novel regulatory features employed to regulate metabolite flow through the last step of a critical biosynthetic pathway by keeping the latter catalytically dormant till the need arises, the transition to the active form affected by a delicate crosstalk between an essential cellular metabolite (CTP) and the precursor to the pathway end-product (DCoA).

DNA binding properties of novel dansylated distamycin analogues in which the fluorophore is directly conjugated to the N-methyl-pyrrole carboxamide backbone

Polyamides that are structural analogues of the naturally occurring DNA minor groove binding antibiotic distamycin (Dst) are promising candidates as gene modulators. Developing strategies for the large scale screening and monitoring of the cellular distribution of such ligands would aid the faster discovery of molecules, which would have eventual utility in molecular biology and medicine. Attachment of fluorescent tags would be a useful step towards this end. A fundamental question in this connection is whether the tag modifies the DNA binding affinity of the parent compounds. Towards answering this question, we have developed two oligopeptides that bear the dansyl (N, N-dimethylaminonaphthalene sulfonamido fluorophore) coupled directly to the N-terminus of the conjugated N-methylpyrrole carboxamide network, and possess three or four N-methyl pyrrole carboxamide units (abbreviated as Dn3 and Dn4 respectively). DNA binding abilities of these molecules were assessed from fluorescence titration experiments, duplex-DNA T-m analysis (employing both UV and fluorescence spectroscopy), induced circular dichroism measurements (ICD), salt dependence of ICD and apparent binding constant measurements (K-app) employing ethidium bromide (EtBr) displacement assay. Both these molecules 'reported' DNA binding in the form of an enhanced fluorescence emission. As judged from the ICD measurements, salt dependence of ICD, T-m analysis and K-app measurements, the binding affinities of the molecules that possessed dansyl group at their N-termini were lower than the ones with equivalent number of amide units, but possessed N-methylpyrrole carboxamide unit at their N-termini. These results would have implications in the future design of fluorescent polyamides.

Effect of molecular association and reactivity on substitution in chromium(III)-salprn complexes

A new chromium(III)-Schiff base complex, [Cr(5-chlorosalprn)(H2O)(2)]ClO4, where salprn=N,N'-propylenebis(salicylideneimine) has been prepared and characterized by electrospray ionization mass spectrometric (ESIMS) analysis and other spectroscopic techniques. Single crystal X-ray data reveal that the complex assumes a trans-diaquo structure, [Cr(C17H18Cl2N2O4)]ClO4.H2O. The effect of phenyl ring substituents on the rate of formation of [O=Cr-V Schiff base](+) has been investigated. The bimolecular rate constant for the formation of O=Cr-V species by the [Cr(Schiff base)(H2O)(2)]ClO4, where the Schiff base=salprn, (1) and 5-chlorosalprn, (2) with PhOI was compared. In the case of (2) the rate was found to be faster by an order of magnitude at pH=4 compared to (1). The introduction of a chloro-substituent on the phenyl ring not only influences the rate of redox reactivity but also the pKa values of aquo ligands of the complexes, indicating the difference in the electronic environment around the metal ion in both (1) and (2).

The design and synthesis of redox core-alpha amino acid composites based on thiol-disulfide exchange mechanism and a comparative study of their zinc abstraction potential from [CCXX] boxes in proteins

The design and synthesis of agents that can abstract zinc from their [CCXX] (C=cysteine; X=cysteine/histidine) boxes by thioldisulfide exchange-having as control, the redox parities of the core sulfur ligands of the reagent and the enzyme, has been illustrated, and their efficiency demonstrated by monitoring the inhibition of the transcription of calf thymus DNA by E. coli RNA polymerase, which harbors two zinc atoms in their [CCXX] boxes of which one is exchangeable. Maximum inhibition possible with removal of the exchangeable zinc was seen with redox-sulfanilamide-glutamate composite. In sharp contrast, normal chelating agents (EDTA, phenanthroline) even in a thousand fold excess showed only marginal inhibition, thus supporting an exchange mechanism for the metal removal. (C) 2002 Elsevier Science Ltd. All rights reserved.

The first bis(phosphine) monoxide (BPMO) complexes of copper(I)

Copper(l) complexes of bis(phosphine) monoxide ligands, bis(diphenylphosphino)ethane monoxide (dppeo) and bis(diphenylphosphino)methane monoxide (dppmo) have been prepared and characterized. One of the complexes with dppeo was characterized by X-ray crystal structure analysis confirming Cu(I) coordination to hard and soft donors. The stability of these complexes in solution was probed via spectroscopic and electrochemical studies. Copper(I) is more readily oxidized in the presence of the hard 0 donor ligands. In solution, they readily exchange the hard donor O, for soft ligands. Although copper(l) prefers soft ligands and is more stable towards oxidation in their presence, it coordinates to hard donors when there is electrostatic or an entropy driven advantage. (C) 2002 Elsevier Science Ltd. All rights reserved.

Probing the Allosteric Mechanism in Pyrrolysyl-tRNA Synthetase Using Energy-Weighted Network Formalism

Pyrrolysyl-tRNA synthetase (PyIRS) is an atypical enzyme responsible for charging tRNA(Pyl) with pyrrolysine, despite lacking precise tRNA anticodon recognition. This dimeric protein exhibits allosteric regulation of function, like any other tRNA synthetases. In this study we examine the paths of allosteric communication at the atomic level, through energy-weighted networks of Desulfitobacterium hafniense PyIRS (DhPyIRS) and its complexes with tRNA(Pyl) and activated pyrrolysine. We performed molecular dynamics simulations of the structures of these complexes to obtain an ensemble conformation-population perspective. Weighted graph parameters relevant to identifying key players and ties in the context of social networks such as edge/node betweenness, closeness index, and the concept of funneling are explored in identifying key residues and interactions leading to shortest paths of communication in the structure networks of DhPylRS. Further, the changes in the status of important residues and connections and the costs of communication due to ligand induced perturbations are evaluated. The optimal, suboptimal, and preexisting paths are also investigated. Many of these parameters have exhibited an enhanced asymmetry between the two subunits of the dimeric protein, especially in the pretransfer complex, leading us to conclude that encoding of function goes beyond the sequence/structure of proteins. The local and global perturbations mediated by appropriate ligands and their influence on the equilibrium ensemble of conformations also have a significant role to play in the functioning of proteins. Taking a comprehensive view of these observations, we propose that the origin of many functional aspects (allostery rand half-sites reactivity in the case of DhPyIRS) lies in subtle rearrangements of interactions and dynamics at a global level.