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Ligand Molecules (ligand + molecule)
Selected AbstractsCooperativity and allostery in haemoglobin functionIUBMB LIFE, Issue 2 2008Chiara Ciaccio Abstract Tetrameric haemoglobins display a cooperative ligand binding behaviour, which has been attributed to the functional interrelationship between multiple ligand binding sites. The quantitative description of this feature was initially carried out with a phenomenological approach, which was limited to the functional effect of the occupancy by a ligand molecule of a binding site on further binding steps. However, subsequent development of structural,functional models for the description of the cooperativity in haemoglobin brought about a much deeper information on the interrelationships between ligand binding at the heme and structural variations occurring in the surrounding free subunits. This approach opened the way to the evolution of the concept of allostery, which is intended as the structural,functional effect exerted by the presence of a ligand in a binding site on other binding sites present in the same molecule. This concept can be applied to either sites for the same ligand (homotropic allostery) and for sites of different ligands (heterotropic allostery). Several models trying to take into account the continuous building up of structural and functional information on the physicochemical properties of haemoglobin have been developed along this line. © 2008 IUBMB IUBMB Life, 60(2): 112,123, 2008 [source] Electrospray mass spectrometric investigation of the binding of cis -parinaric acid to bovine beta-lactoglobulin and study of the ligand-binding site of the protein using limited proteolysisRAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 22 2003Tímea Imre The binding property of parinaric acid, a polyunsaturated fatty acid, to bovine , -lactoglobulin, has been studied by electrospray ionization mass spectrometry. Stable complexation was observed under acidic conditions in a molar ratio of 1:1. Competitive complexation experiments were performed using saturated and unsaturated fatty acid standards with different chain lengths and number of double bonds to study the specificity of the interaction. It can be concluded that formation of the parinaric acid,lactoglobulin complex is preferred even if the molar concentration of the other fatty acids is ten times higher. In cases of specific complex formation the protein must have an active site that is a good acceptor for the ligand molecule. Limited trypsinolysis was performed on the lactoglobulin molecule to identify which part is responsible for the complexation. An intermediate tryptic fragment with molecular mass of 5200,Da was found to have the same ability to bind parinaric acid as the intact protein. This disulfide-bonded residue, [41-70]S-S[149-162], might thus be involved in the specific complexation of parinaric acid to , -lactoglobulin. This conclusion is consistent with previous information on this binding site. Copyright © 2003 John Wiley & Sons, Ltd. [source] Organotin(IV) tryptophanylglycinates: potential non-steroidal antiinflammatory agents; crystal structure of dibutyltin(IV) tryptophanylglycinateAPPLIED ORGANOMETALLIC CHEMISTRY, Issue 9 2009Mala Nath Abstract Diorganotin(IV) derivatives of tryptophanylglycine (H2Trp,Gly) with general formula R2Sn(Trp,Gly), where R = Me, n -Bu, Ph and n -Oct, and triorganotin(IV) derivatives R,3 Sn(HTrp,Gly) where R, = Me, n -Bu and Ph, have been synthesized and structurally characterized in the ,solid state as well as in solution on the basis of various spectroscopic techniques, viz. FT-IR, multinuclear 1H, 13C and 119Sn NMR, 119Sn Mössbauer and single crystal X-ray diffraction. These investigations suggest that tryptophanylglycine in R2Sn(Trp,Gly) acts as dianionic tridentate coordinating through carboxylate oxygen [C(O)O,], amino nitrogen (NH2) and N,peptide, while in the case of R,3 Sn(HTrp,Gly), the ligand acts as monoanionic bidentate coordinating through C(O)O, and NH2. This is further confirmed by the single-crystal X-ray structure of n -Bu2Sn(Trp,Gly) which shows that two butyl groups and peptide nitrogen (N,peptide) are in the equatorial positions, while the two axial positions are occupied by the carboxylic oxygen [C(O)O,] and the amino nitrogen (NH2) atom from the same ligand molecule in the distorted trigonal,bipyramidal geometry around tin. The anti-inflammatory (using the carrageenan-induced paw edema bioassay in rats), cardiovascular activities and acute toxicity (LD50) of some of these compounds have been examined. All of the studied R2Sn(Trp,Gly) and Ph3Sn(HTrp,Gly) exhibit very high anti-inflammatory activities comparable to that of phenylbutazone along with high safety margin (LD50 > 400 mg kg,1) with no side effects on the cardiovascular system. Copyright © 2009 John Wiley & Sons, Ltd. [source] pH-dependent structural changes in haemoglobin component V from the midge larva Propsilocerus akamusi (Orthocladiinae, Diptera)ACTA CRYSTALLOGRAPHICA SECTION D, Issue 3 2010Takao Kuwada Haemoglobin component V (Hb,V) from the midge larva Propsilocerus akamusi exhibits oxygen affinity despite the replacement of HisE7 and a pH-dependence of its functional properties. In order to understand the contribution of the distal residue to the ligand-binding properties and the pH-dependent structural changes in this insect Hb, the crystal structure of Hb,V was determined under five different pH conditions. Structural comparisons of these Hb structures indicated that at neutral pH ArgE10 contributes to the stabilization of the haem-bound ligand molecule as a functional substitute for the nonpolar E7 residue. However, ArgE10 does not contribute to stabilization at acidic and alkaline pH because of the swinging movement of the Arg side chain under these conditions. This pH-dependent behaviour of Arg results in significant differences in the hydrogen-bond network on the distal side of the haem in the Hb,V structures at different pH values. Furthermore, the change in pH results in a partial movement of the F helix, considering that coupled movements of ArgE10 and the F helix determine the haem location at each pH. These results suggested that Hb,V retains its functional properties by adapting to the structural changes caused by amino-acid replacements. [source] Interaction of Zinc Oxide Clusters with Molecules Related to the Sulfur Vulcanization of Polyolefins ("Rubber")CHEMISTRY - A EUROPEAN JOURNAL, Issue 33 2006Ralf Steudel Prof. Dr. Abstract The vulcanization of rubber by sulfur is a large-scale industrial process that is only poorly understood, especially the role of zinc oxide, which is added as an activator. We used the highly symmetrical cluster Zn4O4 (Td) as a model species to study the thermodynamics of the initial interaction of various vulcanization-related molecules with ZnO by DFT methods, mostly at the B3LYP/6-31+G* level. The interaction energy of Lewis bases with Zn4O4 increases in the following order: CO Small Molecule-Controlled Spontaneous Growth of Rose-Like Se Crystals at Room TemperatureEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 7 2008Da-Wei Deng Abstract The spontaneous growth of rose-like Se crystals in aqueous solutions at room temperature is reported. The formation of rose-like Se crystals is based on the oxidation of Na2Se in the presence of thioglycerol solution at pH = 11 in a dark ambient atmosphere. In alkaline solutions, the growth evolution of rose-like Se crystals with aging time was followed by scanning electron microscopy (SEM), and an interesting formation process from initial Se monomers to amorphous Se (a-Se) spheres, and to the final rose-like complex structures of Se crystals was observed. Seven kinds of small molecules with different structures, including 1-thioglycerol (TG), mercaptamine (MA), L -cysteine (L -cys), 3-mercaptopropionic acid (MPA), thioglycolic acid (TGA), glycerol (GLY), and L -serine (L -ser), were used to manipulate the growth of Se crystals. The experimental results show that the structures of the small molecules play a key role in the growth of the Se crystals. The presence of thiols in the structure of the small molecules is favorable for the formation of the aggregates of Se crystals, and other termini, such as ,NH2, ,OH, or ,COO,, will determine whether the aggregates of Se crystals are made up of Se slices or Se prisms. These observations suggest that the ligand molecules have a crucial effect on the nucleation, monomers, and growth of nanocrystals. The selection of ligands can be extended to other important materials for further preparation of nanocrystals with desired shapes. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] Synthesis and Characterisation of Coordination Polymers of CuII and ZnII with 1,3-Bis(1,2,3,4-tetrazol-2-yl)propane , Rotational Freedom of the Donor Group Favours Structural DiversificationEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 18 2004Robert Bronisz Abstract The novel bidentate ligand 1,3-bis(1,2,3,4-tetrazol-2-yl)propane (pbtz), which possesses a flexible spacer, was synthesised in order to investigate the influence of the flexibility of ligand molecules on the architecture of coordination polymers. For that purpose the reactions between pbtz and M(ClO4)2·6H2O salts (M = CuII and ZnII) were performed. The complexes [{Cu(pbtz)3}(ClO4)2], and [{Zn(pbtz)3}(ClO4)2·2EtOH], were characterised by IR and UV/Vis spectroscopy and their crystal structures were determined by single-crystal X-ray diffraction measurements. In both compounds the pbtz ligand molecules act as N4,N4, connectors bridging the central atoms, and the 2-substituted tetrazole rings coordinate in a monodentate fashion to the central atoms forming M(tetrazole)6 cores. [{Cu(pbtz)3}(ClO4)2], was isolated as a 1D coordination polymer. The copper(II) ions are triply bridged by ligand molecules, leading to the formation of infinite 1D chains. A highly unusual manner of bridging, with the tethering of two neighbouring central atoms by the same kind of ligand molecules, although possessing different conformations, is observed. In [{Zn(pbtz)3}(ClO4)2·2EtOH], the six-coordinate zinc(II) ions, which are bridged by single ligand molecules, serve as topological nodes, leading to the formation of a 3D ,-polonium-type network. The crystal structure of the ZnII complex contains only one such net solvated by ethanol molecules. A conformational analysis of the ligand molecules in both compounds demonstrates that the flexibility of the pbtz and the ability of the tetrazole rings in particular to adopt various, relative orientations is responsible for the diversity of the architectures of the obtained complexes. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] Comparative Study of Activities between Verbascoside and Rutin by Docking MethodMOLECULAR INFORMATICS, Issue 1 2003Kun Gao Abstract Verbascoside and rutin possess anti-cancer properties and are capable of repairing DNA damaged by oxygen radicals, acting as powerful antioxidants. Based on kinetic measurements and experiments on tumor cells, docking studies of the two ligand molecules with the receptor telomeric DNA fragments have been carried out. The docking calculations performed using JUMNA software showed that the both molecules can be docked into the minor groove of telomeric DNA and form complexes with suitable geometry for electron transfer between guanine radical and ligands. The reaction mechanism via the electron transfer process is further confirmed through energy calculations for transition states using MOPAC 93 program. Complexes can be formed without major distortion of DNA structure and are further stabilized by the interaction of DNA with the saccharide side-groups. By comparing their energies, the difference of activities of the two compounds can be explained. [source] Pentacoordination versus tetracoordination in silicon derivatives of an O,N,O,-tridentate ligandACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2010Uwe Böhme Bis[2-(2-hydroxy-3-methoxybenzylideneamino)phenolato-,O]dimethylsilicon, C30H30N2O6Si, (II), was isolated from the reaction of 2-(2-hydroxy-3-methoxybenzylideneamino)phenol, (I), with dichlorodimethylsilane at 339,K. It consists of two ligand molecules and the Me2Si unit forming a dialkoxydimethylsilane with a tetracoordinate Si atom. [2-(3-Methoxy-2-oxidobenzylideneamino)phenolato-,3O,N,O,]dimethylsilicon, C16H17NO3Si, (III), was isolated from the same reaction conducted at 263,K. In this complex, the dianion of (I) is coordinated via two O atoms and an azomethine N atom to the pentacoordinate Si atom. According to quantum chemical calculations, (II) is the thermodynamically stable product and (III) is the kinetically favoured product. [source] Purification,chemical structure,electrical property relationship in gold nanoparticle liquids,APPLIED ORGANOMETALLIC CHEMISTRY, Issue 8 2010Robert I. MacCuspie Abstract Macroscopic assemblies of nanoparticles with fluid like characteristics, i.e. nanoparticle liquids (NPLs), are a new class of materials that exhibit unique properties compared with dispersions of nanoparticles in a molecularly distinct matrix phase. By focusing on reaction ratios, techniques to maximize concentration of reactants and quantification of chemical content during washing steps, a high degree of control over the purity of NPLs was maintained while allowing for easy scalability in batch sizes and synthesis throughput. A range of tertiary amines and quaternary ammoniums were used to successfully synthesize Au NPLs from a range of Au nanoparticles with nominal diameters from 6 to 20 nm and initially stabilized with either citrate or dodecanethiol. Stable Au NPLs after purification exhibited a sub-equivalence ratio of canopy to ligand molecules within the corona. This small canopy density most likely arose from the incommensurate areal density of anionic charge within the ligand shell relative to the larger size of the cationic canopy molecule, resulting in a population of cation,anion pairs too weakly bound to be retained in the initial assembly of the canopy post-purification. Finally, increasing either the volume fraction or molecular weight of the canopy was found to increase exponentially the electrical resistance of the bulk NPLs. Removal of excess canopy molecules created a conductive Au NPL that improved hot-current switching durability by at least two orders of magnitude beyond prior reports. Published in 2010 by John Wiley & Sons, Ltd. [source] Structure of a conserved hypothetical protein, TTHA0849 from Thermus thermophilus HB8, at 2.4,Å resolution: a putative member of the StAR-related lipid-transfer (START) domain superfamilyACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 12 2005Makoto Nakabayashi The crystal structure of a conserved hypothetical protein, TTHA0849 from Thermus thermophilus HB8, has been determined at 2.4,Å resolution as a part of a structural and functional genomics project on T. thermophilus HB8. The main-chain folding shows a compact ,+, motif, forming a hydrophobic cavity in the molecule. A structural similarity search reveals that it resembles those steroidogenic acute regulatory proteins that contain the lipid-transfer (START) domain, even though TTHA0849 shows comparatively weak sequence identity to polyketide cyclases. However, the size of the ligand-binding cavity is distinctly smaller than other START domain-containing proteins, suggesting that it catalyses the transfer of smaller ligand molecules. [source]
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