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Several Ligands (several + ligand)
Selected AbstractsThe effects of physiologically important nonmetallic ligands in the reactivity of metallothionein towards 5,5,-dithiobis(2-nitrobenzoic acid)FEBS JOURNAL, Issue 18 2001A new method for the determination of ligand interactions with metallothionein The reaction of Cd5Zn2 -metallothionein (MT) with 5,5,-dithiobis(2-nitrobenzoic acid) (Nbs2) has been studied at different reagent stoichiometries, pH and temperature conditions and in the presence of several ligands. At stoichiometries of Nbs2 to MT from 0.5 to 5, the reaction followed first order kinetics. The first order rate constants obtained were independent from the concentration of Nbs2 but were linearly dependent on the concentration of MT. At higher Nbs2/MT stoichiometries, the reaction deviates from first order kinetics and the observed rate constant increases. The reactivity of MT towards Nbs2 has been probed at 4 µm concentration of both reagents where the reaction is monophasic and is characterized by a linear Arrhenius plot (Ea = 45.8 ± 2.7 kJ·mol,1). It has been demonstrated that metal release at low pH or subtraction from MT by EDTA substantially increases the reactivity of MT towards Nbs2. At the same time, a number of nonmetallic ligands moderately accelerate the reaction of MT with Nbs2 and hyperbolic dose,response curves were obtained. The data have been interpreted with the binding of ligands to MT and following MT. Ligand binding constants were calculated as follows: ATP, K = 0.31 ± 0.06 mm; ADP, K = 0.26 ± 0.07 mm. Several compounds such as AMP, S -methylglutathione, and phosphate had no effect on the reaction, but Zn2+ ions showed an inhibitory effect at micromolar concentrations. [source] Ligand Influence on Metathesis Activity of Ruthenium Carbene Catalysts: A DFT StudyADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 1-2 2007Bernd Abstract A survey of the concept of active and inactive ligand conformations in ruthenium alkene carbene complexes of the Grubbs catalyst type is presented. This concept is extended to a variety of anionic ligand atoms. Density functional theory calculations at the B3LYP/LACV3P**+//B3LYP/LACVP* level of theory were performed on the precatalyst, 14 valence-electron intermediate, alkene carbene conformers and ruthena(IV)cyclobutane model intermediates for several ligands, such as methoxide, methanethiolate, fluoride, mesylate, water, and ammonia. The rule of the superiority of metathesis catalysts with small and electron-withdrawing halogens does not apply to fluoride ligands. Alkoxides and thiolates also destabilize active carbene conformations, while mesylate ligands lead to a balanced energetic relation of active and inactive carbene orientations. Cationic ruthenium carbene species with aqua or ammine ligands are limited by unfavored ligand dissociation to 14 valence-electron intermediates. A guideline for the design of novel ligand systems for ruthenium carbene complexes as metathesis catalysts is proposed. [source] A new method for the gradient-based optimization of molecular complexesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2009Jan Fuhrmann Abstract We present a novel method for the local optimization of molecular complexes. This new approach is especially suited for usage in molecular docking. In molecular modeling, molecules are often described employing a compact representation to reduce the number of degrees of freedom. This compact representation is realized by fixing bond lengths and angles while permitting changes in translation, orientation, and selected dihedral angles. Gradient-based energy minimization of molecular complexes using this representation suffers from well-known singularities arising during the optimization process. We suggest an approach new in the field of structure optimization that allows to employ gradient-based optimization algorithms for such a compact representation. We propose to use exponential mapping to define the molecular orientation which facilitates calculating the orientational gradient. To avoid singularities of this parametrization, the local minimization algorithm is modified to change efficiently the orientational parameters while preserving the molecular orientation, i.e. we perform well-defined jumps on the objective function. Our approach is applicable to continuous, but not necessarily differentiable objective functions. We evaluated our new method by optimizing several ligands with an increasing number of internal degrees of freedom in the presence of large receptors. In comparison to the method of Solis and Wets in the challenging case of a non-differentiable scoring function, our proposed method leads to substantially improved results in all test cases, i.e. we obtain better scores in fewer steps for all complexes. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Pentraxins: Multifunctional proteins at the interface of innate immunity and inflammationBIOFACTORS, Issue 2 2009Livija Deban Abstract Pentraxins are a family of multimeric pattern recognition proteins highly conserved in evolution. On the basis of the primary structure of the protomer, pentraxins are divided into two groups: short pentraxins and long pentraxins. C reactive protein, the first pattern recognition receptor identified, and serum amyloid P component are classic short pentraxins produced in the liver in response to IL-6. Long pentraxins, including the prototype PTX3, are expressed in a variety of tissues. PTX3 is produced by a variety of cells and tissues, most notably dendritic cells and macrophages, in response to Toll-like receptor (TLR) engagement and inflammatory cytokines. Through interaction with several ligands, including selected pathogens and apoptotic cells, pentraxins play a role in complement activation, pathogen recognition and apoptotic cell clearance. In addition, PTX3 is involved in the deposition of extracellular matrix and female fertility. Unlike the classic short pentraxins CRP and SAP, PTX3 primary sequence and regulation are highly conserved in man and mouse. Thus, gene targeting identified PTX3 (and presumably other members of the family) as multifunctional soluble pattern recognition receptors acting as a nonredundant component of the humoral arm of innate immunity and involved in tuning inflammation, matrix deposition, and female fertility. © 2009 International Union of Biochemistry and Molecular Biology, Inc. [source] The structure of Staphylococcus aureus phosphopantetheine adenylyltransferase in complex with 3,-phosphoadenosine 5,-phosphosulfate reveals a new ligand-binding modeACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 10 2009Hyung Ho Lee Bacterial phosphopantetheine adenylyltransferase (PPAT) catalyzes the penultimate step in the coenzyme A (CoA) biosynthetic pathway. It catalyzes the reversible transfer of an adenylyl group from ATP to 4,-phosphopantetheine (Ppant) to form dephospho-CoA (dPCoA) and pyrophosphate. Previous structural studies have revealed how several ligands are recognized by bacterial PPATs. ATP, ADP, Ppant and dPCoA bind to the same binding site in a highly similar manner, while CoA binds to a partially overlapping site in a different mode. To provide further structural insights into ligand binding, the crystal structure of Staphylococcus aureus PPAT was solved in a binary complex with 3,-phosphoadenosine 5,-phosphosulfate (PAPS). This study unexpectedly revealed a new mode of ligand binding to PPAT, thus providing potentially useful information for structure-based discovery of inhibitors of bacterial PPATs. [source] | ||||||||||