Phosphoryl transfer reaction

HYBRID POTENTIALS FOR THE SIMULATION OF PHOSPHORYL TRANSFER REACTIONS... 

The AMl/d-PhoT model [33] is a parameterization of a modified AMl/d Hamiltonian developed specifically to model phosphoryl transfer reactions catalyzed by enzymes and ribozymes for use in linear-scaling calculations and combined QM/MM simulations. The model is currently parametrized for H, O, and P atoms to reproduce... 

Smooth COSMO solvation model. We have recently extended our smooth COSMO solvation model with analytical gradients [71] to work with semiempirical QM and QM/MM methods within the CHARMM and MNDO programs [72, 73], The method is a considerably more stable implementation of the conventional COSMO method for geometry optimizations, transition state searches and potential energy surfaces [72], The method was applied to study dissociative phosphoryl transfer reactions [40], and native and thio-substituted transphosphorylation reactions [73] and compared with density-functional and hybrid QM/MM calculation results. The smooth COSMO method can be formulated as a linear-scaling Green s function approach [72] and was applied to ascertain the contribution of phosphate-phosphate repulsions in linear and bent-form DNA models based on the crystallographic structure of a full turn of DNA in a nucleosome core particle [74],... 

Case Study Comparison of DFT Functionals on Model Phosphoryl Transfer Reactions... 

Mechanistically it was proposed that the substrate bridges both Zn(II) ions and replaces the apical amines in 28 while one of them attacks the phosphorus atom as an intramolecular nucleophile to perform the phosphoryl-transfer reaction (30). The presented observations are not re-... 

In every type of biological phosphoryl transfer reaction, a P-O bond of the leaving group (R2-OH) is broken and a new P-O bond is formed between phosphorus and the attacking group R -OH ... 

Magnesium has its role intimately intertwined with phosphate in many phosphoryl transfer reactions, as Mg-ATP in muscle contraction, in the stabilization of nucleic acid structures as well as in the catalytic activity of ribozymes (catalytic RNA molecules). It also serves as a structural component of enzymes, and is found as the metal centre in chlorophylls, which absorbs light energy in photosynthesis. 

Figure 10.3 In the phosphoryl-transfer reaction catalysed by hexokinase, the y-phosphoryl group of ATP undergoes inversion of configuration. (From Voet and Voet, 2004. Reproduced with permission from John Wiley Sons., Inc.)...

Figure 10.8 The phosphoglucomutase reaction proceeds via two phosphoryl-transfer reactions. (From Allen and Dunaway-Mariano, 2004. Copyright 2004, with permission from Elsevier.)...

Figure 10.13 Phosphoryl-transfer reactions. The figure shows (a) nucleotide polymerization, (b) nucleic acid hydrolysis, (c) first cleavage of an exon-intron junction by group I ribozyme (d) and by a group II ribozyme, (e) strand transfer during transposition and (f) exon ligation during RNA splicing. (From Yang et al., 2006. Copyright 2006, with permission from Elsevier.)...

Knowles, J.R. (1980) Enzyme-catalysed phosphoryl transfer reactions, Annu. Rev. Biochem., 49, 877-919. 

Acyl-phosphates can participate in so-called in-line phosphoryl transfer reactions, and depending on reaction conditions, acyl-phosphate compounds can form a metaphosphate anion ... 

A zinc(II) complex 22a with an alcohol-pendent polyamine has been synthesized (23). The alcoholic OH deprotonates with pifa of 8.6 (determined by pH-metric titration), yielding 22b. Reaction of 22 (2 mM) with a phosphotriester diethyl(4-nitrophenyl) phosphate (0.1 mM) in 10 mM TAPS buffer (pH 8.6) at 25°C seemed to promote phosphoryl-transfer reactions to 23, just like acyltransferred intermediates 10 and 16a in the reactions between Znn-macrocyclic complexes with an alcohol pendent and NA (see Scheme 4). The pH dependence of the first-order rate constants gave a sigmoidal curve with an inflection point around the pKa value of 8.6. The hydrolysis of the substrate phosphotriester to the phosphodiester product diethyl phosphate thus seemed to... 

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