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Ligand Conformations (ligand + conformation)
Selected AbstractsThree-Dimensional Lanthanoid-Containing Coordination Frameworks: Structure, Magnetic and Fluorescent PropertiesEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 4 2005Hong-Tao Zhang Abstract Two lanthanoid-containing 3D coordination polymers, [Gd2L3(H2O)2]n (1) and {[TbL1.5(H2O)]·0.5H2O}n (2) (L = succinate), have been prepared by hydrothermal reaction. The difference in structure between the two 3D coordination polymers is a result of the flexibility of the ligand conformation. The magnetic properties of 1 and 2 have been investigated in the 1.8,300 K range. Both complexes exhibit ferromagnetic interaction between lanthanoid ions. AC magnetic measurements revealed long-range magnetic order in complex 2. Especially 2 integrates the ferromagnetic, fluorescent and porous properties into a single entity. This motif may be developed to achieve new multifunctional molecular-based materials. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] Enhanced docking with the mining minima optimizer: Acceleration and side-chain flexibilityJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 16 2002Visvaldas Kairys Abstract The ligand,protein docking algorithm based on the Mining Minima method has been substantially enhanced. First, the basic algorithm is accelerated by: (1) adaptively determining the extent of each energy well to help avoid previously discovered energy minima; (2) biasing the search away from ligand positions at the surface of the receptor to prevent the ligand from staying at the surface when large sampling regions are used; (3) quickly testing multiple different ligand positions and orientations for each ligand conformation; and (4) tuning the source code to increase computational efficiency. These changes markedly shorten the time needed to discover an accurate result, especially when large sampling regions are used. The algorithm now also allows user-selected receptor sidechains to be treated as mobile during the docking procedure. The energies associated with the mobile side chains are computed as if they belonged to the ligand, except that atoms at the boundary between side chains and the rigid backbone are treated specially. This new capability is tested for several well-known ligand/protein systems, and preliminary application to an enzyme whose substrate is unknown,the recently solved hypothetical protein YecO (HI0319) from Haemophilus influenzae,indicates that side-chains relaxations allow candidate substrates of various sizes to be accommodated. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1656,1670, 2002 [source] The kinetics of competitive antagonism of nicotinic acetylcholine receptors at physiological temperatureTHE JOURNAL OF PHYSIOLOGY, Issue 4 2008Deeptankar Demazumder Detailed information about the ligand-binding site of nicotinic acetylcholine receptors has emerged from structural and mutagenesis experiments. However, these approaches provide only static images of ligand,receptor interactions. Kinetic measurements of changes in protein function are needed to develop a more dynamic picture. Previously, we measured association and dissociation rate constants for competitive inhibition of current through embryonic muscle acetylcholine receptor channels at 25°C. Little is known about competitive antagonism at physiological temperatures. Here, we performed measurements at 37°C and used thermodynamics to estimate the energetics of antagonism. We used rapid solution exchange protocols to determine equilibrium and kinetics of inhibition of acetylcholine-activated currents in outside-out patches by (+)-tubocurarine, pancuronium and cisatracurium. Kinetic rates as high as 600 s,1 were resolved by this technique. Binding was primarily enthalpy driven. The 12°C increase in temperature decreased equilibrium antagonist binding by 1.7- to 1.9-fold. In contrast, association and dissociation rate constants increased 1.9- to 6.0-fold. Activation energies for dissociation were 90 ± 6, 106 ± 8 and 116 ± 10 kJ mol,1 for cisatracurium, (+)-tubocurarine and pancuronium, respectively. The corresponding apparent activation energies for association were 38 ± 6, 85 ± 6 and 107 ± 13 kJ mol,1. The higher activation energy for association of (+)-tubocurarine and pancuronium compared with cisatracurium is notable. This may arise from either a more superficial binding site for the large antagonist cisatracurium compared to the other ligands, or from a change in receptor conformation upon binding of (+)-tubocurarine and pancuronium but not cisatracurium. Differences in ligand desolvation and ligand conformation are not likely to be important. [source] Exploring the binding site of the human muscarinic M3 receptor: Homology modeling and docking studyINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 8 2007Liliana Ostopovici Abstract The human muscarinic M3 receptor (hM3) and its interactions with selective agonists and antagonists were investigated by means of combined homology and docking approach. Also, two pharmacophoric models for the hM3 agonist and antagonist binding sites were proposed. The three-dimensional (3D) structure of hM3 receptor was modeled based on the high-resolution X-ray structure of bovine rhodopsin from the Protein Data Bank (PDB). To validate the reliability of the model obtained, the main chain torsion angles phi (,) and psi (,) were examined in a Ramachandran plot, and all omega angles were measured for peptidic bond planarity. The characteristics of the active site, the position, and the orientation of ligands in situ, as well as the binding modes of the representative agonists and antagonists, were analyzed by applying a molecular docking technique using the AutoDock 3.0.5 program. Specific interactions responsible for recognition of the hM3 receptor, like ionic bond formed between protonated amine of the ligands and the Asp3.6 side chain were identified. Structure,reactivity relationships have been explained by analyzing the 3D structure of the hM3 model and the ligand conformations resulted from molecular docking simulation. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [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] Protein,protein docking with multiple residue conformations and residue substitutionsPROTEIN SCIENCE, Issue 6 2002David M. Lorber Abstract The protein docking problem has two major aspects: sampling conformations and orientations, and scoring them for fit. To investigate the extent to which the protein docking problem may be attributed to the sampling of ligand side-chain conformations, multiple conformations of multiple residues were calculated for the uncomplexed (unbound) structures of protein ligands. These ligand conformations were docked into both the complexed (bound) and unbound conformations of the cognate receptors, and their energies were evaluated using an atomistic potential function. The following questions were considered: (1) does the ensemble of precalculated ligand conformations contain a structure similar to the bound form of the ligand? (2) Can the large number of conformations that are calculated be efficiently docked into the receptors? (3) Can near-native complexes be distinguished from non-native complexes? Results from seven test systems suggest that the precalculated ensembles do include side-chain conformations similar to those adopted in the experimental complexes. By assuming additivity among the side chains, the ensemble can be docked in less than 12 h on a desktop computer. These multiconformer dockings produce near-native complexes and also non-native complexes. When docked against the bound conformations of the receptors, the near-native complexes of the unbound ligand were always distinguishable from the non-native complexes. When docked against the unbound conformations of the receptors, the near-native dockings could usually, but not always, be distinguished from the non-native complexes. In every case, docking the unbound ligands with flexible side chains led to better energies and a better distinction between near-native and non-native fits. An extension of this algorithm allowed for docking multiple residue substitutions (mutants) in addition to multiple conformations. The rankings of the docked mutant proteins correlated with experimental binding affinities. These results suggest that sampling multiple residue conformations and residue substitutions of the unbound ligand contributes to, but does not fully provide, a solution to the protein docking problem. Conformational sampling allows a classical atomistic scoring function to be used; such a function may contribute to better selectivity between near-native and non-native complexes. Allowing for receptor flexibility may further extend these results. [source] Hydrogen-bonded zigzag chains in 2,2,-dithiodibenzoic acid,1,3-di-4-pyridylpropane (1/1)ACTA CRYSTALLOGRAPHICA SECTION C, Issue 9 2009Li-Li Wang The title 1:1 cocrystal, C14H10O4S2·C13H14N2 or H2L·bpp, has the two components connected by O,H...N hydrogen bonds to generate a one-dimensional zigzag chain running along the crystallographic a direction. These chains are further stacked into a three-dimensional supramolecular network by weak C,H...O and C,H..., contacts. Comparison of the structural differences with previous findings suggests that deprotonated forms, hydrogen-bonding sites and flexible ligand conformations become significant factors that influence the topological arrangement and binding stoichiometry of the resulting cocrystals. [source] | ||||||||||