Part 5: Algorithm to computationally estimate the effect of Pi for 4 LDH enzymes
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In order to estimate whether Pi has an activatory or an inhibitory effect on the enzymes, the computed probe binding energies (from GRID results, Part 4) were compared with those for the LDH from L. plantarum whose activity is known to be unaffected by Pi.

The binding energies of the Pi probe in the allosteric binding site (AS) and the COO probe in the catalytic binding site (CS) of LDH from L. plantarum were defined as E¬AS,threshold and ECS,threshold, respectively. For the other LDH enzymes, the activity was considered to be enhanced by Pi, if the binding energy of the Pi probe in the allosteric binding site, EPi ≤ E-AS,threshold. When the binding energy of Pi in the catalytic site EPi ≥ ECS,threshold, no inhibition by Pi was anticipated. The magnitude of activation and inhibition by Pi was assessed by computing and analyzing the following energy differences: ΔEAS = EPi - EAS,threshold; ΔECS = EPi - ECS,threshold; = EPi - ECOO¬. A strong enhancement of enzyme activity (designated by letter A) was assigned, if ΔEAS ≤ -2 kcal/mol. The letter a designates weak activation, when -2 ≤ ΔEAS ≤ 0 kcal/mol. Strong inhibition (I) was assigned when both ΔECS


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Organism: Lactic acid bacteria

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Created: 10th Jun 2014 at 14:19

Last updated: 10th Jun 2014 at 14:49

Last used: 22nd Aug 2019 at 14:16

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