Active site guanines are critical for self-cleavage reactions of several ribozymes, but their precise functions in catalysis are unclear. To learn whether protonated or deprotonated forms of guanine predominate in the active site, microscopic pKa values were determined for ionization of 8-azaguanosine substituted for G8 in the active site of a fully functional hairpin ribozyme in order to deter...

Hybrid quantum mechanics:molecular mechanics (QM/MM) calculations of absolute deprotonation energies are performed with periodic boundary conditions for Brønsted sites of aluminosilicate bilayers with various Al/Si ratios (two-dimensional zeolite). The supercell method is applied and density functional theory is used. Much lower values are obtained (1042, 1069 and 1091 kJ mol(-1) for Al/Si = 1/...

M.PvuII is a DNA methyltransferase from the bacterium Proteus vulgaris that catalyzes methylation of cytosine at the N4 position. This enzyme also displays promiscuous activity catalyzing methylation of adenine at the N6 position. In this work we use QM/MM methods to investigate the reaction mechanism of this promiscuous activity. We found that N6 methylation in M.PvuII takes place by means of ...

Voltammetric experiments performed in phosphate buffer at constant pH 8.0 on platinum and stainless steel revealed clear reduction currents, which were correlated to the concentrations of phosphate. On the basis of the reactions proposed previously, a model was elaborated, assuming that both H2PO4 and HPO4 2 underwent cathodic deprotonation, and including the acid–base equilibriums. A kinetic m...

A combination of experimental methods, photoelectron-imaging spectroscopy, flowing afterglow-photoelectron spectroscopy and the flowing afterglow-selected ion flow tube technique, and electronic structure calculations at the B3LYP/6-311++G(d,p) level of density functional theory (DFT) have been employed to study the mechanism of the reaction of the hydroxide ion (HO-) with 1H-1,2,3-triazole. Fo...

The sulfonated tripodal polyaza-polycatechol-amine ligand tris(2,3-hydroxy-5-sulfobenzylamine) ethyl)amine (STRENCAT) was synthesized and its protonation constants determined by potentiometry at 25 degrees C and in 0.1 mol dm(-3) NaClO(4). In the adopted experimental conditions (2.5 < p[H(+)] < 11.5), six of the virtual thirteen protonation constants of STRENCAT were determined. The deprotonati...

Photoactive yellow proteins (PYPs) constitute a new class of eubacterial photoreceptors, containing a deprotonated thiol ester-linked 4-hydroxycinnamic acid chromophore. Interactions with the protein dramatically change the (photo)chemical properties of this cofactor. Here we describe the reconstitution of apoPYP with anhydrides of various chromophore analogues. The resulting hybrid PYPs, their...

The short and intermediate time scale dynamics of the photoacid pyranine (1-hydroxy-3,6,8-pyrenetrisulfonic acid, commonly referred to as HPTS) are studied with visible pump-probe spectroscopy in various solvents to elucidate the nature of its proton-transfer kinetics in water. The observed time dependences of HPTS are compared with those of the methoxy derivative, MPTS. A global fitting proced...