CALculating the Center Of Mass
Example 5
Application of CALCOM to evaluate the distance between two subunits of the miraculin dimer during the molecular dynamics simulations performed at different pH conditions.
Miraculin is a plant protein that displays the peculiar property of modifying taste by swiching sour into a sweet taste. Its monomer is flavourless at all pH as well as at high concentration; the dimer form elicits its taste-modifying activity at acidic pH; a tetrameric form is also reported as active. Two histidine residues, located in exposed regions, are the main responsible of miraculin activity, as demonstrated by mutagenesis studies.
We have performed molecular dynamics simulations at different pH conditions. The center of mass of monomers costituing each dimer and their distance has been calculated using CALCOM (Table 1).
The molecular dynamics simulations at different pH conditions have indicated that at acidic pH the dimer assumes a widely open conformation, in agreement with the hypotheses coming from other studies.
Table1
Distances expressed in Angstroms between two subunits composing the miraculin dimer during the molecular dynamics simulations at different pH conditions (i.e. 3, 4.5 and 7).
| Time simulation (ns) | pH3 | pH4.5 | pH7 |
|---|
| 1 | 38.41 | 37.22 | 38.58 |
| 2 | 39.44 | 37.07 | 37.20 |
| 3 | 40.03 | 36.75 | 37.18 |
| 4 | 41.71 | 35.95 | 37.28 |
| 5 | 40.03 | 38.98 | 35.81 |
| 6 | 40.53 | 37.51 | 36.50 |
| 7 | 39.80 | 37.24 | 36.03 |
| 8 | 40.66 | 36.55 | 36.39 |
| 9 | 40.99 | 37.18 | 36.32 |
| 10 | 41.53 | 37.52 | 36.94 |