Phosphoryl Transfer Processes Research Articles

Phosphoryl Transfer Processes Promoted by a Trifunctional Calix[4]arene Inspired by DNA Topoisomerase I.

The cone-calix[4]arene derivative (1H3)2+, decorated at the upper rim with two guanidinium units and a phenolic hydroxyl in an ABAH functionalization pattern, effectively promotes the cleavage of the DNA model compound bis(p-nitrophenyl) phosphate (BNPP) in 80% DMSO solution at pH values in the range 8.5-12.0. The pH dependence of the kinetics was found to be fully consistent with the results of the potentiometric titration of the triprotic acid (1H3)2+. At pH 9.5, the rate enhancement of p-nitrophenol liberation from BNPP relative to background hydrolysis is 6.5 × 104-fold at 1 mM concentration of the calix[4]arene derivative. Experimental data clearly point to the effective cooperation of the three active units and to the involvement of the phenolate moiety as a nucleophile in the phosphoryl transfer step. Subsequent liberation of a second equivalent of p-nitrophenol from the phosphorylated calixarene intermediate is conceivably promoted by the "built-in" guanidine/guanidinium catalytic dyad.

Influence of additional metal ions on the ratio of conversion rates of intermediate products of the hydrolysis of adenosine-5′-triphosphoric acid catalyzed by the Cu2+ ion: 1. Experimental study of the influence of Mg2+ ions in the ascending branch of the dependence of the initial hydrolysis rate on pH

The hydrolysis of the dimeric complex (CuATP2−)2 to CuADP− and inorganic phosphate Pi is irreversible. The main intermediate hydrolysis product, whose formation should be taken into account at relatively early steps of hydrolysis, is the pentacovalent intermediate IntK formed in parallel with the hydrolysis to CuADP− and Pi through the common intermediate product (CuATP2−)2OH− (DOH−) in step 1, which is the replacement of the nucleophile (OH−) at the Cu2+ ion by OH− at the positively charged phosphorus atom. The influence of the addition of Mg2+ ions is studied (depending on their concentration) on the rate constants of step 1 in the region of pH in the ascending branch of the dependence of the initial hydrolysis rate on pH at two values of pH: 6.48 and 6.70. This region of pH is sensitive to both the rate constant of DOH− formation and the rate constants of step 1. The rate constant for the formation of DOH− from D remains unchanged. An increase in the concentration of Mg2+ decreases the value of ATP conversion, above which the stationary hydrolysis regime is observed. The ratio [IntK]/[DOH−] is higher when the stationary regime is attained. The applicability of the method proposed for the formation of the attacking nucleophile and the proposed sequence of steps to the enzymatic phosphoryl transfer processes is discussed.

ChemInform Abstract: Why Did Nature Select Phosphate for Its Dominant Roles in Biology?

AbstractReview: 49 refs.

Why did nature select phosphate for its dominant roles in biology?

Evolution has placed phosphate mono- and diesters at the heart of biology. The enormous diversity of their roles has called for the evolution of enzyme catalysts for phosphoryl transfer that are among the most proficient known. A combination of high-resolution X-ray structure analysis and 19F NMR definition of metal fluoride complexes of such enzymes, that are mimics of the transition state for the reactions catalysed, has delivered atomic detail of the nature of such catalysis for a range of phosphoryl transfer processes. The catalytic simplicity thus revealed largely explains the paradox of the contrast between the extreme stability of structural phosphate esters and the lability of phosphates in regulation and signaling processes. A brief survey of the properties of oxyacids and their esters for other candidate elements for these vital roles fails to identify a suitable alternative to phosphorus, thereby underpinning Todd’s Hypothesis “Where there’s life there’s phosphorus” as a statement of truly universal validity.

Why did Nature select phosphate for its dominant roles in biology?

Evolution has placed phosphate mono- and diesters at the heart of biology. The enormous diversity of their roles has called for the evolution of enzyme catalysts for phosphoryl transfer that are among the most proficient known. A combination of high-resolution X-ray structure analysis and 19F NMR definition of metal fluoride complexes of such enzymes, that are mimics of the transition state for the reactions catalysed, has delivered atomic detail of the nature of such catalysis for a range of phosphoryl transfer processes. The catalytic simplicity thus revealed largely explains the paradox of the contrast between the extreme stability of structural phosphate esters and the lability of phosphates in regulation and signalling processes. A brief survey of the properties of oxyacids and their esters for other candidate elements for these vital roles fails to identify a suitable alternative to phosphorus, thereby underpinning Todd’s Hypothesis “Where there’s life there’s phosphorus” as a statement of truly universal validity.

06/01716 Investigation of humic acid N with X-ray photoelectron spectroscopy: Effect of acid hydrolysis and comparison with 15N cross polarization/magic angle spinning nuclear magnetic resonance spectroscopy : Abe, T. et al. Organic Geochemistry, 2005, 36, (11), 1490–1497

Phosphoryl group transfer is central to genetic replication, cellular signalling and many metabolic processes. Understanding the mechanisms of phosphorylation and phosphate ester and anhydride cleavage is key to efforts towards biotechnological and biomedical exploitation of phosphate-handling enzymes. Analogues of phosphate esters and anhydrides are indispensable tools, alongside protein mutagenesis and computational methods, for the dissection of phosphoryl transfer mechanisms. Hydrolysable and non-hydrolysable phosphate analogues have provided insight into the nature and sites of phosphoryl transfer processes. Kinetic isotope effects and crystallography using transition state analogues have painted more detailed pictures of transition states and how enzymes work to stabilise them.

DFT calculations and parameterization of the approximate valence bond method to describe the phosphoryl transfer reaction in a model system

AbstractDensity functional theory (DFT) calculations have been performed at the B3LYP/6‐31G+(d,p) level for a model phosphodiester system to describe a transphosphorylation reaction that mimics the phosphoryl transfer process in serine/threonine protein kinases. The DFT energy and electrostatic potential data have been used to extend the parameterization of the approximate valence bond (AVB) method. AVB mimics well the DFT results and is planned for use as a fast potential energy generator to simulate phosphoryl transfer processes in protein kinases using the quantum classic molecular dynamics approach. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002

IsopolarvsIsosteric Phosphonate Analogues of Nucleotides

Abstract A range of β,γ-bridged phosphonate analogues of ATP and of β,β-bridged analogues of Ap4A has been synthesised. Some of their metal binding characteristics and inhibition of enzymatic phosphoryl transfer processes can be described in terms of the relative importance of steric and electronic features of the nucleotide analogues.