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Exogenous Ligand (exogenous + ligand)
Selected AbstractsSystematic Regulation of the Enzymatic Activity of Phenylacetaldoxime Dehydratase by Exogenous LigandsCHEMBIOCHEM, Issue 12 2006Katsuaki Kobayashi Dr. Abstract Phenylacetaldoxime dehydratase from Bacillus sp. OxB-1 (OxdB) contains a heme that acts as the active site for the dehydration reaction of aldoxime. Ferrous heme is the active form, in which the heme is five coordinate with His282 as a proximal ligand. In this work, we evaluated the functional role of the proximal ligand for the catalytic properties of the enzyme by "the cavity mutant technique". The H282G mutant of OxdB lost enzymatic activity, although the heme, which was five coordinate with a water molecule (or OH,) as an axial ligand, existed in the protein matrix. The enzymatic activity was rescued by imidazole or pyridine derivatives that acted as the exogenous proximal ligand. By changing the electron-donation ability of the exogenous ligand with different substituents, the enzymatic activity could be regulated systematically. The stronger the electron-donation ability of the exogenous ligand, the higher was the restored enzymatic activity. Interestingly, H282G OxdB with 2-methyl imidazole showed a higher activity than the wild-type enzyme. Kinetic analyses revealed that the proximal His regulated not only the affinity of substrate binding to the heme but also the elimination of the OH group from the substrate. [source] Reactivation pathway of the hydrogenase H-cluster: Density functional theory studyINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2007Stefan Motiu Abstract This work puts forth a reaction pathway for the reactivation of exogenous ligand inhibited H-cluster, the active site of Fe-only hydrogenases. The H-cluster is a dimetal complex, Fe,Fe, with the metal centers bridged by di(thiomethyl)amine. Exogenous ligands, H2O, and OH,, are bound to the distal iron (Fed). Density functional theory (DFT) calculations on the native and ruthenium-modified H-cluster have been performed using the B3LYP functional with 6-31+G** and 6-311+G** basis sets. We have ascertained that there is a thermodynamically favorable pathway for the reactivation of the OH, inhibited H-cluster, which proceeds by an initial protonation of the Fed,OH, complex. The proposed reaction pathway has all its intermediate reactions ensue exothermically. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Funnel Complexes with CoII and NiII: New Probes into the Biomimetic Coordination Ability of the Calix[6]arene-Based Tris(imidazole) SystemEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 9 2004Olivier Sénèque Abstract The coordination properties of the calix[6]arene-based tris(imidazole) ligand X6Me3Imme3 were further explored with CoII and NiII. This imidazole system stabilizes tetrahedral mononuclear CoII complexes with an exchangeable fourth exogenous ligand (water, alcohol, amide) located at the heart of the hydrophobic calixarene cavity. With a weak donor ligand such as a nitrile, both four-coordinate tetrahedral and five-coordinate trigonal bipyramidal complexes were obtained. The latter contains a second nitrile molecule trans to the included guest nitrile. These complexes were characterized in solution as well as in the solid state. The NiII complexes are square-based pyramidal five-coordinate edifices with a guest nitrile inside the cavity and a water molecule outside. A comparison with previously described ZnII and CuII complexes emphasizes the flexibility of this ligand. A comparison with carbonic anhydrase, a mononuclear zinc enzyme with a tris(histidine) coordination core, shows that X6Me3Imme3 displays many structural features of this enzyme except for the cis coordination of the exogenous ligands. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2004) [source] Proximal ligand motions in H93G myoglobinFEBS JOURNAL, Issue 19 2002Stefan Franzen Resonance Raman spectroscopy has been used to observe changes in the iron,ligand stretching frequency in photoproduct spectra of the proximal cavity mutant of myoglobin H93G. The measurements compare the deoxy ferrous state of the heme iron in H93G(L), where L is an exogenous imidazole ligand bound in the proximal cavity, to the photolyzed intermediate of H93G(L)*CO at 8 ns. There are significant differences in the frequencies of the iron,ligand axial out-of-plane mode ,(Fe,L) in the photoproduct spectra depending on the nature of L for a series of methyl-substituted imidazoles. Further comparison was made with the proximal cavity mutant of myoglobin in the absence of exogenous ligand (H93G) and the photoproduct of the carbonmonoxy adduct of H93G (H93G-*CO). For this case, it has been shown that H2O is the axial (fifth) ligand to the heme iron in the deoxy form of H93G. The photoproduct of H93G-*CO is consistent with a transiently bound ligand proposed to be a histidine. The data presented here further substantiate the conclusion that a conformationally driven ligand switch exists in photolyzed H93G-*CO. The results suggest that ligand conformational changes in response to dynamic motions of the globin on the nanosecond and longer time scales are a general feature of the H93G proximal cavity mutant. [source] Reactivation pathway of the hydrogenase H-cluster: Density functional theory studyINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 5 2007Stefan Motiu Abstract This work puts forth a reaction pathway for the reactivation of exogenous ligand inhibited H-cluster, the active site of Fe-only hydrogenases. The H-cluster is a dimetal complex, Fe,Fe, with the metal centers bridged by di(thiomethyl)amine. Exogenous ligands, H2O, and OH,, are bound to the distal iron (Fed). Density functional theory (DFT) calculations on the native and ruthenium-modified H-cluster have been performed using the B3LYP functional with 6-31+G** and 6-311+G** basis sets. We have ascertained that there is a thermodynamically favorable pathway for the reactivation of the OH, inhibited H-cluster, which proceeds by an initial protonation of the Fed,OH, complex. The proposed reaction pathway has all its intermediate reactions ensue exothermically. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Searching for Neuroglobin's role in the brainIUBMB LIFE, Issue 8-9 2007Karin Nienhaus Abstract Neuroglobin is a small globin that plays an important role in the protection of brain neurons from ischemic and hypoxic injuries. The molecular mechanisms by which Ngb performs its physiological function are still under debate. Suggestions include oxygen storage and delivery, scavenging of NO and/or reactive oxygen species, oxygen sensing and signal transduction. In recent years, the molecular structures of Ngb with carbon monoxide bound to the heme iron and without an exogenous ligand have been solved, and interesting structural changes have been noticed upon ligand binding. Moreover, equilibrium and kinetic properties of the reactions with ligands have been examined in great detail. Here we summarize the molecular properties of Ngb and discuss them in relation to the potential physiological functions. [source] Systematic Regulation of the Enzymatic Activity of Phenylacetaldoxime Dehydratase by Exogenous LigandsCHEMBIOCHEM, Issue 12 2006Katsuaki Kobayashi Dr. Abstract Phenylacetaldoxime dehydratase from Bacillus sp. OxB-1 (OxdB) contains a heme that acts as the active site for the dehydration reaction of aldoxime. Ferrous heme is the active form, in which the heme is five coordinate with His282 as a proximal ligand. In this work, we evaluated the functional role of the proximal ligand for the catalytic properties of the enzyme by "the cavity mutant technique". The H282G mutant of OxdB lost enzymatic activity, although the heme, which was five coordinate with a water molecule (or OH,) as an axial ligand, existed in the protein matrix. The enzymatic activity was rescued by imidazole or pyridine derivatives that acted as the exogenous proximal ligand. By changing the electron-donation ability of the exogenous ligand with different substituents, the enzymatic activity could be regulated systematically. The stronger the electron-donation ability of the exogenous ligand, the higher was the restored enzymatic activity. Interestingly, H282G OxdB with 2-methyl imidazole showed a higher activity than the wild-type enzyme. Kinetic analyses revealed that the proximal His regulated not only the affinity of substrate binding to the heme but also the elimination of the OH group from the substrate. [source] Allosteric Tuning of the Intra-Cavity Binding Properties of a Calix[6]arene through External Binding to a ZnII Center Coordinated to Amino Side ChainsCHEMISTRY - A EUROPEAN JOURNAL, Issue 7 2007Ulrich Darbost Dr. Abstract Molecular recognition by calix[6]arene-based receptors bearing three primary alkylamino side chain arms (1) is described. Complexation of ZnII ion provides the dinuclear ,-hydroxo complex , XRD characterization of which, together with solution studies, provided evidence of its hosting of neutral polar organic guests G. Treatment of this complex with a carboxylic acid or a sulfonamide (XH) results in the formation of mononuclear species , one of which (X = Cl) has been characterized by XRD. A dicationic complex is obtained upon treatment of with a mixture of an alkylamine and a strong acid. Each of these ZnII complexes features a tetrahedral metal ion bound to the three amino arms of ligand 1 and to an exogenous ligand (either HO,, X,, or RNH2) sitting outside of the cavity. As a result, the metal ion structures the calixarene core, constraining it in a cone conformation suitable for guest hosting. The receptor properties of these compounds have been explored in detail and are compared with those of the trisammonium receptor , based on the same calixarene core, as well as those of the trisimidazole-based dicationic Zn funnel complexes. This study reveals very different host properties, in spite of the common hydrophobic, ,-basic, and hydrogen-bonding acceptor properties of the calixarene cores. A harder external ligand produces a less polarized receptor that is consequently particularly sensitive to the hydrogen-bonding ability of its guest. The less electron-rich the apical ligand, and a fortiori the trisammonium host, the more sensitive the receptor to the dipole moment of the guest. All this stands in contrast with the funnel Zn complexes, in which the coordination link plays a dominant role. It is also shown that the asymmetry of an exo -coordinated enantiopure amino ligand is sensed by the guest. This supramolecular system nicely illustrates how the receptor properties of a hydrophobic cavity can be allosterically tuned by the environment. [source] Role of Toll-like receptor 4 in the initiation and progression of atherosclerotic diseaseEUROPEAN JOURNAL OF CLINICAL INVESTIGATION, Issue 5 2004G. Pasterkamp Abstract The family of Toll-like receptors (TLRs) initiates an innate immune response after recognition of pathogen-associated molecular patterns (PAMPs). Evidence is accumulating that TLRs, and particularly TLR4, are important players in the initiation and progression of atherosclerotic disease. Not only exogenous ligands but also endogenous ligands that are expressed during arterial injury are recognized by TLR4. Mouse knockout studies and epidemiological studies of human TLR4 polymorphisms have demonstrated that the TLR4 might play a role in the initiation and progression of atherosclerosis. This review will summarize the latest progression in research on the role of TLR4 in arterial occlusive disease In addition, the potential of intervention in TLR4 signalling to influence progression of atherosclerotic disease is discussed. [source] Over-expression of Toll-like receptors and their ligands in small-for-size graftHEPATOLOGY RESEARCH, Issue 3 2010Weiwei Jiang Aim:, Toll-like receptors (TLRs) participate in several physiological and pathological processes of transplantation, including inflammation and allograft rejection, but the expression of TLRs and their ligands remains undetermined in small-for-size graft transplantation. Methods:, A non-arterialized partial liver transplantation model was used. The expression of TLR2 and TLR4 mRNA and protein, CD14 and Myeloid Differentiation-2 (MD-2) mRNA, as well as TLR2 and TLR4 exogenous ligands (endotoxin) and endogenous ligands [heat shock protein (HSP) 60 and 70] were assessed. The signaling pathways induced by TLR2 and TLR4 were also assessed. Results:, In small-for-size liver graft, the expression of mRNA and protein of TLR2 and TLR4, CD14 and MD-2 mRNA, as well as endogenous ligands of TLR2 and TLR4 such as HSP60 and HSP70 was quickly and significantly increased after reperfusion, and reached a peak at 3 h after reperfusion. The levels of exogenous ligands (endotoxin) were increased and reached a peak at 6 h after reperfusion. The appearance of TLR2 and TLR4 mRNA was accompanied by increased HSP 60 and 70 mRNA within 24 h after reperfusion. In the small-for-size group, the peak levels of TLRs and their endogenous ligands appeared earlier than those in the full size group; the peak levels of TLRs and their endogenous and exogenous ligands were higher than those in the full size group. Conclusion:,TLR2 and TLR4, as well as their endogenous and exogenous ligands were activated in small-for-size liver graft transplantation. [source] Structural and ligand-binding properties of serum albumin species interacting with a biomembrane interfaceJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 11 2007Takamitsu Kosa Abstract In the process of drug development, preclinical testing using experimental animals is an important aspect, for verification of the efficacy and safety of a drug. Serum albumin is a major binding protein for endogenous and exogenous ligands and regulates their distribution in various tissues. In this study, the structural and drug-binding properties of albumins on a biomembrane surface were investigated using reverse micelles as a model membrane. In reverse micelles, the secondary structures of all albumins were found, to varying degrees, to be intermediate between the native and denatured states. The tertiary structures of human and bovine albumin were similar to those of the native and intermediate states, respectively, whereas those of the dog, rabbit, and rat were in a denatured state. Thus, bovine albumin is an appropriate model for studying structural changes in human albumin in a membrane-water phase. Binding studies also showed the presence of species difference in the change in binding capacity of albumins during their interaction with reverse micelles. Among the albumins, rat albumin appears to be a good model for the protein-mediated drug uptake of human albumin in a biomembrane environment. These findings are significant in terms of the appropriate extrapolation of pharmacokinetics and pharmacodynamics data in various animals to humans. © 2007 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 96: 3117,3124, 2007 [source] Cleavage of the iron-methionine bond in c-type cytochromes: Crystal structure of oxidized and reduced cytochrome c2 from Rhodopseudomonas palustris and its ammonia complexPROTEIN SCIENCE, Issue 1 2002Silvano Geremia Abstract The three-dimensional structures of the native cytochrome c2 from Rhodopseudomonas palustris and of its ammonia complex have been obtained at pH 4.4 and pH 8.5, respectively. The structure of the native form has been refined in the oxidized state at 1.70 Å and in the reduced state at 1.95 Å resolution. These are the first high-resolution crystal structures in both oxidation states of a cytochrome c2 with relatively high redox potential (+350 mV). The differences between the two oxidation states of the native form, including the position of internal water molecules, are small. The unusual six-residue insertion Gly82-Ala87, which precedes the heme binding Met93, forms an isolated 310 -helix secondary structural element not previously observed in other c-type cytochromes. Furthermore, this cytochrome shows an external methionine residue involved in a strained folding near the exposed edge of the heme. The structural comparison of the present cytochrome c2 with other c-type cytochromes has revealed that the presence of such a residue, with torsion angles , and , of approximately ,140 and ,130°, respectively, is a typical feature of this family of proteins. The refined crystal structure of the ammonia complex, obtained at 1.15 Å resolution, shows that the sulphur atom of the Met93 axial ligand does not coordinate the heme iron atom, but is replaced by an exogenous ammonia molecule. This is the only example so far reported of an X-ray structure with the heme iron coordinated by an ammonia molecule. The detachment of Met93 is accompanied by a very localized change in backbone conformation, involving mainly the residues Lys92, Met93, and Thr94. Previous studies under typical denaturing conditions, including high-pH values and the presence of exogenous ligands, have shown that the detachment of the Met axial ligand is a basic step in the folding/unfolding process of c-type cytochromes. The ammonia adduct represents a structural model for this important step of the unfolding pathway. Factors proposed to be important for the methionine dissociation are the strength of the H-bond between the Met93 and Tyr66 residues that stabilizes the native form, and the presence in this bacterial cytochrome c2 of the rare six-residue insertion in the helix 310 conformation that increases Met loop flexibility. [source] | |||||||||||||