The mechanism of the nucleotidyl transfer reaction catalyzed by yeast RNA polymerase I1 has been investigated using molec- ular mechanics and quantum mechanics methods. Molecular dynamics （MD） simulations were carri...The mechanism of the nucleotidyl transfer reaction catalyzed by yeast RNA polymerase I1 has been investigated using molec- ular mechanics and quantum mechanics methods. Molecular dynamics （MD） simulations were carried out using the TIP3 water model and generalized solvent boundary potential （GSBP） by CHARMM based on the X-ray crystal structure. Two models of the ternary elongation complex were constructed based on CHARMM MD calculations. All the species including reactants, transition states, intermediates, and products were optimized using the DFT-PBE method coupled with the basis set DZVP and the auxiliary basis set GEN-A2. Three pathways were explored using the DFT method. The most favorable reaction pathway involves indirect proton migration from the RNA primer 3＇-OH to the oxygen atom of a-phosphate via a solvent water mole- cule, proton rotation from the oxygen atom of a-phosphate to the 13-phosphate side, the RNA primer 3＇-O nucleophilic attack on the a-phosphorus atom, and P-O bond breakage. The corresponding reaction potential profile was obtained. The rate limit- ing step, with a barrier height of 21.5 kcal/mol, is the RNA primer 3＇-0 nucleophilic attack, rather than the commonly consid- ered proton transfer process. A high-resolution crystal structure including crystallographic water molecules is required for fur- ther studies.展开更多
The binding kinetics properties of three Ru（Ⅱ） complexes of [Ru（bpy） 2（dhipH 3）]（ClO4）2, [（bpy） 2Ru（eipcH）]（ClO4）2 and [（bpy） 2Ru（ebipcH 2）Ru（bpy） 2]（ClO4）4, where bpy2,2′-bipyridine, dhipH 33,...The binding kinetics properties of three Ru（Ⅱ） complexes of [Ru（bpy） 2（dhipH 3）]（ClO4）2, [（bpy） 2Ru（eipcH）]（ClO4）2 and [（bpy） 2Ru（ebipcH 2）Ru（bpy） 2]（ClO4）4, where bpy2,2′-bipyridine, dhipH 33,4-dihydroxyphenyl-（imidazo[4,5-f][1,10]phenanthroline）, eipcHN-ethyl-4-（imidazolo[4,5-f]-（1,10-phenanthrolin）-2-yl）carbazole, and ebipcH 2N-ethyl-4,7-bis（imidazolo[4,5-f]-（1,10-phenanthrolin）-2-yl）carbazole, with yeast-RNA were investigated by monitoring the decays in absorbance for π-π* absorption peaks at 286 nm with binding time. The decay curves for the complexes were well fitting to biexponential decay functions with half-life times for rapidly-decayed components being 0.006, 0.02 and 0.8 min, and those for slowly-decayed components being 0.7, 4.2 and 103 min, respectively. The rapidly- and slowly-decayed components are probably due to electrostatic interaction and aromatic base stacking of the RNA with the Ru（Ⅱ） complexes, respectively. The results indicate that not only binuclear complexes but also mononuclear complexes can slowly bind to the RNA depending on the molecular structures of the complexes.展开更多
基金supported by the Natural Sciences and Engineering Research Council of Canada (10174)the Project-sponsored by SRF for ROCS,SEM
文摘The mechanism of the nucleotidyl transfer reaction catalyzed by yeast RNA polymerase I1 has been investigated using molec- ular mechanics and quantum mechanics methods. Molecular dynamics （MD） simulations were carried out using the TIP3 water model and generalized solvent boundary potential （GSBP） by CHARMM based on the X-ray crystal structure. Two models of the ternary elongation complex were constructed based on CHARMM MD calculations. All the species including reactants, transition states, intermediates, and products were optimized using the DFT-PBE method coupled with the basis set DZVP and the auxiliary basis set GEN-A2. Three pathways were explored using the DFT method. The most favorable reaction pathway involves indirect proton migration from the RNA primer 3＇-OH to the oxygen atom of a-phosphate via a solvent water mole- cule, proton rotation from the oxygen atom of a-phosphate to the 13-phosphate side, the RNA primer 3＇-O nucleophilic attack on the a-phosphorus atom, and P-O bond breakage. The corresponding reaction potential profile was obtained. The rate limit- ing step, with a barrier height of 21.5 kcal/mol, is the RNA primer 3＇-0 nucleophilic attack, rather than the commonly consid- ered proton transfer process. A high-resolution crystal structure including crystallographic water molecules is required for fur- ther studies.
文摘The binding kinetics properties of three Ru（Ⅱ） complexes of [Ru（bpy） 2（dhipH 3）]（ClO4）2, [（bpy） 2Ru（eipcH）]（ClO4）2 and [（bpy） 2Ru（ebipcH 2）Ru（bpy） 2]（ClO4）4, where bpy2,2′-bipyridine, dhipH 33,4-dihydroxyphenyl-（imidazo[4,5-f][1,10]phenanthroline）, eipcHN-ethyl-4-（imidazolo[4,5-f]-（1,10-phenanthrolin）-2-yl）carbazole, and ebipcH 2N-ethyl-4,7-bis（imidazolo[4,5-f]-（1,10-phenanthrolin）-2-yl）carbazole, with yeast-RNA were investigated by monitoring the decays in absorbance for π-π* absorption peaks at 286 nm with binding time. The decay curves for the complexes were well fitting to biexponential decay functions with half-life times for rapidly-decayed components being 0.006, 0.02 and 0.8 min, and those for slowly-decayed components being 0.7, 4.2 and 103 min, respectively. The rapidly- and slowly-decayed components are probably due to electrostatic interaction and aromatic base stacking of the RNA with the Ru（Ⅱ） complexes, respectively. The results indicate that not only binuclear complexes but also mononuclear complexes can slowly bind to the RNA depending on the molecular structures of the complexes.
