Physical and Kinetic Analysis of the Cooperative Role of Metal Ions in Catalysis of Phosphodiester Cleavage by a Dinuclear Zn(II) Complex

Citations Over TimeTop 1% of 2003 papers

Abstract

A dinuclear metal ion complex Zn(2)()(L2O) and its mononuclear analogue Zn(L1OH) were synthesized and studied as catalysts of the cleavage of the phosphate diester 2-hydroxypropyl-4-nitrophenyl phosphate (HPNP). X-ray crystal structure data, potentiometric titrations, and (1)H NMR spectra obtained over a wide range of pH values provide strong evidence that the alcohol linker in the complex Zn(2)()(L2O) is ionized below pH 6.0, while the alcohol group in the complex Zn(L1OH) remains protonated even at high pH. The ionizations observed at high pH correspond to the formation of the monohydroxo complexes, Zn(2)(L2O)(OH) and Zn(L1OH)(OH), with pK(a)'s of 8.0 and 9.2, respectively. The pH-rate profiles of second-order rate constants for metal-ion complex-catalyzed cleavage of HPNP are reported. These show downward curvature centered at the pK(a)'s for the respective zinc-bound waters, and limiting second-order rate constants at high pH of k(c) = 0.71 M(-)(1) s(-)(1) for Zn(2)()(L2O) and 0.061 M(-)(1) s(-)(1) for Zn(L1OH). The larger catalytic activity of Zn(2)()(L2O) compared with Zn(L1OH) is due to the cooperative role of the metal ions in facilitating the formation of the ionized zinc-bound water at close to neutral pH and in providing additional stabilization of the rate-limiting transition state for phosphodiester cleavage. Zn(2)()(L2O) complex (1 M) at pH 7.6 stabilizes the transition state for the uncatalyzed reaction by 9.3 kcal/mol. Assuming that the dissociation constant determined for a diethyl phosphate inhibitor is similar to that for substrate, then ca. 2.4 kcal/mol of these stabilizing interactions are expressed in the ground-state Michaelis complex, while the bulk of these interactions are only expressed as the reaction approaches the transition state for phosphodiester cleavage.

Related Papers

• → Hydrolysis of Phosphodiester Bonds within RNA Hairpin Loops in Buffer Solutions: the Effect of Secondary Structure on the Inherent Reactivity of RNA Phosphodiester Bonds(1999)17 cited
• → Mechanistic insights for β-cyclodextrin catalyzed phosphodiester hydrolysis(2014)5 cited
• → Hydrolytic Stability of Ribose Phosphodiester Bonds within Several Oligonucleotides at High Temperatures Using a Real-Time Monitoring Method for Hydrothermal Reactions(2001)9 cited
• → Promotion of stable triplex formation by partial incorporation of 2′,5′-phosphodiester linkages into triplex-forming oligonucleotides(2005)8 cited
• → Bonding through phosphodiester moiety: Its implications in pharmaceutical modifications(2023)