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Deprotonated Form (deprotonated + form)
Selected AbstractsRhodopsin Regeneration is Accelerated via Noncovalent 11- cis Retinal,Opsin Complex,A Role of Retinal Binding Pocket of Opsin,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 4 2008Hiroyuki Matsumoto The regeneration of bovine rhodopsin from its apoprotein opsin and the prosthetic group 11- cis retinal involves the formation of a retinylidene Schiff base with the , -amino group of the active lysine residue of opsin. The pH dependence of a Schiff base formation in solution follows a typical bell-shaped profile because of the pH dependence of the formation and the following dehydration of a 1-aminoethanol intermediate. Unexpectedly, however, we find that the formation of rhodopsin from 11- cis retinal and opsin does not depend on pH over a wide pH range. These results are interpreted by the Matsumoto and Yoshizawa (Nature258 [1975] 523) model of rhodopsin regeneration in which the 11- cis retinal chromophore binds first to opsin through the , -ionone ring, followed by the slow formation of the retinylidene Schiff base in a restricted space. We find the second-order rate constant of the rhodopsin formation is 6100 ± 300 mol,1 s,1 at 25°C over the pH range 5,10. The second-order rate constant is much greater than that of a model Schiff base in solution by a factor of more than 107. A previous report by Pajares and Rando (J Biol Chem264 [1989] 6804) suggests that the lysyl ,-NH2 group of opsin is protonated when the , -ionone ring binding site is unoccupied. The acceleration of the Schiff base formation in rhodopsin is explained by stabilization of the deprotonated form of the lysyl ,-NH2 group which might be induced when the , -ionone ring binding site is occupied through the noncovalent binding of 11- cis retinal to opsin at the initial stage of rhodopsin regeneration, followed by the proximity and orientation effect rendered by the formation of noncovalent 11- cis retinal,opsin complex. [source] Coordination polymers and hydrogen-bonded assemblies of 2,2,-[2,5-bis(carboxymethoxy)-1,4-phenylene]diacetic acid with ammonium, lanthanum and zinc cationsACTA CRYSTALLOGRAPHICA SECTION C, Issue 9 2010Hatem M. Titi We report the synthesis of the 2,2,-[2,5-bis(carboxymethoxy)-1,4-phenylene]diacetic acid (TALH4) ligand and the structures of its adducts with ammonium, namely diammonium 2,2,-[2,5-bis(carboxymethyl)-1,4-phenylenedioxy]diacetate, 2NH4+·C14H12O102,, (I), lanthanum, namely poly[[aquabis[,4 -2,2,-(2-carboxylatomethyl-5-carboxymethyl-1,4-phenylenedioxy)diacetato]dilanthanum(III)] monohydrate], {[La2(C14H11O10)2(H2O)]·H2O}n, (II), and zinc cations, namely poly[[{,4 -2,2,-[2,5-bis(carboxymethyl)-1,4-phenylenedioxy]diacetato}zinc(II)] trihydrate], {[Zn(C14H12O10)]·3H2O}n, (III), and poly[[diaqua(,2 -4,4,-bipyridyl){,4 -2,2,-[2,5-bis(carboxymethyl)-1,4-phenylenedioxy]diacetato}dizinc(II)] dihydrate], {[Zn2(C14H10O10)(C10H8N2)(H2O)2]·2H2O}n, (IV), the formation of all four being associated with deprotonation of TALH4. Adduct (I) is a diammonium salt of TALH22,, with the ions located on centres of crystallographic inversion. Its crystal structure reveals a three-dimensional hydrogen-bonded assembly of the component species. Reaction of TALH4 with lanthanum trinitrate hexahydrate yielded a two-dimensional double-layer coordination polymer, (II), in which the LaIII cations are nine-coordinate. With zinc dinitrate hexahydrate, TALH4 forms 1:1 two-dimensional coordination polymers, in which every ZnII cation is linked to four neighbouring TALH22, anions and each unit of the organic ligand is coordinated to four different tetrahedral ZnII cation connectors. The crystal structure of this compound accommodates molecules of disordered water at the interface between adjacent polymeric layers to give (III), and it has been determined with low precision. Another polymer assembly, (IV), was obtained when zinc dinitrate hexahydrate was reacted with TALH4 in the presence of an additional 4,4,-bipyridyl ligand. In the crystal structure of (IV), the bipyridyl and TAL4, entities are located on two different inversion centres. The ternary coordination polymers form layered arrays with corrugated surfaces, with the ZnII cation connectors revealing a tetrahedral coordination environment. The two-dimensional polymers in (II),(IV) are interconnected with each other by hydrogen bonds involving the metal-coordinated and noncoordinated molecules of water. TALH4 is doubly deprotonated, TALH22,, in (I) and (III), triply deprotonated, viz. TALH3,, in (II), and quadruply deprotonated, viz. TAL4,, in (IV). This report provides the first structural characterization of TALH4 (in deprotonated form) and its various supramolecular adducts. It also confirms the potential utility of this tetraacid ligand in the formulation of coordination polymers with metal cations. [source] Computational Study of the Phosphoryl Transfer Catalyzed by a Cyclin-Dependent KinaseCHEMISTRY - A EUROPEAN JOURNAL, Issue 30 2007Marco De, Vivo Dr. Abstract A cyclin-dependent kinase, Cdk2, catalyzes the transfer of the ,-phosphate from ATP to a threonine or serine residue of its polypeptide substrates. Here, we investigate aspects of the reaction mechanism of Cdk2 by gas-phase density functional calculations, classical molecular dynamics, and Car,Parrinello QM/MM simulations. We focus on the role of the conserved Asp127 and on the nature of the phosphoryl transfer reaction mechanism catalyzed by Cdk2. Our findings suggest that Asp127 is active in its deprotonated form by assisting the formation of the near-attack orientation of the substrate serine or threonine. Therefore, the residue does not act as a general base during the catalysis. The mechanism for the phosphoryl transfer is a single SN2-like concerted step, which shows a phosphorane-like transition state geometry. Although the resulting reaction mechanism is in agreement with a previous density functional study of the same catalytic reaction mechanism (Cavalli et,al., Chem. Comm.2003, 1308,1309), the reaction barrier is considerably lower when QM/MM calculations are performed, as in this study (,42,kcal,mol,1 QM vs. ,24,kcal,mol,1 QM/MM); this indicates that important roles for the catalysis are played by the protein environment and solvent waters. Because of the high amino acid sequence conservation among the whole family of cyclin-dependent kinases (CDKs), these results could be general for the CDK family. [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] | ||||||||||