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Isomerization Mechanism (isomerization + mechanism)
Selected AbstractsIsomerization mechanism of aspartate to isoaspartate implied by structures of Ustilago sphaerogena ribonuclease U2 complexed with adenosine 3,-monophosphateACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2010Shuji Noguchi Aspartates in proteins are isomerized non-enzymatically to isoaspartate via succinimide in vitro and in vivo. In order to elucidate the mechanism of isoaspartate formation within the Asp45-Glu46 sequence of Ustilago sphaerogena ribonuclease U2 based on three-dimensional structure, crystal structures of ribonuclease U2 complexed with adenosine 3,-monophosphate have been solved at 0.96 and 0.99,Å resolution. The crystal structures revealed that the C, atom of Asp45 is located just beside the main-chain N atom of Glu46 and that the conformation which is suitable for succinimide formation is stabilized by a hydrogen-bond network mediated by water molecules 190, 219 and 220. These water molecules are suggested to promote the formation of isoaspartate via succinimide: in the succinimide-formation reaction water 219 receives a proton from the N atom of Glu46 as a general base and waters 190 and 220 stabilize the tetrahedral intermediate, and in the succinimide-hydrolysis reaction water 219 provides a proton for the N atom of Glu46 as a general acid. The purine-base recognition scheme of ribonuclease U2 is also discussed. [source] Structures of mannose-6-phosphate isomerase from Salmonella typhimurium bound to metal atoms and substrate: implications for catalytic mechanismACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2009S. R. Sagurthi Mannose-6-phosphate isomerase (MPI) catalyzes the interconversion of mannose 6-phosphate and fructose 6-phosphate. X-ray crystal structures of MPI from Salmonella typhimurium in the apo form (with no metal bound) and in the holo form (with bound Zn2+) and two other structures with yttrium bound at an inhibitory site and complexed with Zn2+ and fructose 6-phosphate (F6P) were determined in order to gain insights into the structure and the isomerization mechanism. Isomerization involves acid/base catalysis with proton transfer between the C1 and C2 atoms of the substrate. His99, Lys132, His131 and Asp270 are close to the substrate and are likely to be the residues involved in proton transfer. The interactions observed at the active site suggest that the ring-opening step is probably catalyzed by His99 and Asp270. An active-site loop consisting of residues 130,133 undergoes conformational changes upon substrate binding. Zn2+ binding induces structural order in the loop consisting of residues 50,54. The metal atom appears to play a role in substrate binding and is probably also important for maintaining the architecture of the active site. Isomerization probably follows the previously suggested cis -enediol mechanism. [source] How Does the Trans,Cis Photoisomerization of Azobenzene Take Place in Organic Solvents?CHEMPHYSCHEM, Issue 5 2010Giustiniano Tiberio Dr. Abstract The trans,cis photoisomerization of azobenzene-containing materials is key to a number of photomechanical applications, but the actual conversion mechanism in condensed phases is still largely unknown. Herein, we study the isomerization in a vacuum and in various solvents via a modified molecular dynamics simulation adopting an ab initio torsion,inversion force field in the ground and excited states, while allowing for electronic transitions and a stochastic decay to the fundamental state. We determine the trans,cis photoisomerization quantum yield and decay times in various solvents (n -hexane, anisole, toluene, ethanol, and ethylene glycol), and obtain results comparable with experimental ones where available. A profound difference between the isomerization mechanism in vacuum and in solution is found, with the often neglected mixed torsional,inversion pathway being the most important in solvents. [source] Ultrafast Photoisomerization of Photoactive Yellow Protein Chromophore Analogues in Solution: Influence of the Protonation StateCHEMPHYSCHEM, Issue 8 2006Agathe Espagne Dr. Abstract We investigate solvent viscosity and polarity effects on the photoisomerization of the protonated and deprotonated forms of two analogues of the photoactive yellow protein (PYP) chromophore. These are trans- p -hydroxybenzylidene acetone and trans- p -hydroxyphenyl cinnamate, studied in solutions of different polarity and viscosity at room temperature, by means of femtosecond fluorescence up-conversion. The fluorescence lifetimes of the protonated forms are found to be barely sensitive to solvent viscosity, and to increase with increasing solvent polarity. In contrast, the fluorescence decays of the deprotonated forms are significantly slowed down in viscous media and accelerated in polar solvents. These results elucidate the dramatic influence of the protonation state of the PYP chromophore analogues on their photoinduced dynamics. The viscosity and polarity effects are, respectively, interpreted in terms of different isomerization coordinates and charge redistribution in S1. A trans-to-cis isomerization mechanism involving mainly the ethylenic double-bond torsion and/or solvation is proposed for the anionic forms, whereas "concerted" intramolecular motions are proposed for the neutral forms. [source] Configurational stability of 2-benzoylcyclohexanone: Unexpected solvent effects on the rate of racemizationCHIRALITY, Issue 4 2005Gilbert E. Tumambac Abstract The kinetics of the racemization of 2-benzoylcyclohexanone 1 in hexanes, ethanol, and mixtures thereof have been investigated by time dependence of enantiomeric purity using enantioselective HPLC. In pure hexanes and ethanol, the racemization half-lives were determined as 552 and 23.8 min, respectively, at 66°C. Surprisingly, racemization of 1 in mixtures of hexanes and ethanol was found to involve an induction period followed by a sigmoidal decrease of the enantiomeric excess with half-lives varying between 11.5 and 24.0 min. This unexpected solvent influence on the rate of racemization of 1 was attributed to complex isomerization mechanisms involving three possibly interconverting enol tautomers of 1.Chirality 17:171,176, 2005. © 2005 Wiley-Liss, Inc. [source] | ||||||||||