Prediction of Disordered Regions
Contents
Disopred
Disopred predicts two disordered regions in our protein, which can be seen in Figure 1. The first region is at the beginning of the protein (first two residues) and the second region is at the end (last three regions). This prediction is wrong, because it is normal, that the electrons from the first and the last amino acids lack in the electron density map. So, our protein Hexosamidase A has no disordered regions.
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POODLE
We decided to test several POODLE variants and to compare the results.
POODLE-I
POODLE-I predicted five disordered regions:
start position | end position | length |
1 | 2 | 2 |
14 | 19 | 6 |
83 | 89 | 7 |
105 | 109 | 5 |
527 | 529 | 3 |
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POODLE-L
POODLE-L found no disordered regions. Therefore, there is no disordered region with a length more than 40 amio acids in our protein.
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POODLE-S (High B-factor residues)
This POODLE-S variant searches for high B-factor values in the crystallography, which implies uncertainty in the assignment of the atom positions.
POODLE-S predicted five disordered regions:
start position | end position | length |
0 | 2 | 2 |
13 | 19 | 7 |
83 | 88 | 6 |
105 | 109 | 5 |
526 | 529 | 4 |
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POODLE-S (missing residues)
POODLE-S (missing residues) predicts a disordered region, if there is an amino acid in the sequence record, but not on the electron density map.
Poodle-S found 6 disordered regions.
start position | end position | length |
17 | 18 | 2 |
53 | 61 | 9 |
78 | 109 | 33 |
153 | 153 | 1 |
280 | 280 | 1 |
345 | 345 | 1 |
Graphical Output:
On the plots above, it is possible to see where the disordered regions are. All peaks above the red line are predicted as disordered regions. As we wrote above in the table, the POODLS-S variant which uses high B-factor values for the prediction (Figure 2) predicts 5 disordered regions, POODLS-S with missing residues (Figure 3) predicts 6 disordered regions, POODLE-I (Figure 4) predicts 5 disordered regions and POODLE-L (Figure 5) does not predict any disordered regions.
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IUPred
We tested the three different IUPred variants, which are offered by the webserver.
IUPred (short)
As you can see in the picture (Figure 6), IUPred which is focus on short disordered regions found only at the beginning and at the end of the protein a disordered region. This may be wrong, because at the beginning and at the end there are often regions without defined secondary structure, but also without function.
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IUPred (long)
Next we take a look to the prediction of the long disordered regions:
The picture above (Figure 7) shows the result of this prediction. There is no disordered region predicted, not even at the beginning or at the end of the protein. This prediction is quite good, because the HEXA_HUMAN protein does not possess any disordered regions.
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IUPred (with structural information)
As last, we analysed the prediction of IUPred with the additional usage of structural information.
As before, the method did not find any disordered regions, which can be seen in Figure 8. Therefore, the method predict three times the right result. Only by the method with focus on short disordered regions was a prediction of two disordered regions, but these regions were located at the beginning and at the end of the protein, which is obviously wrong.
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Meta-Disorder
Meta-Disorder did not predict any disordered region in our protein, which can be seen on Figure 9. The different methods of which Meta-Disorder consists predicted some disordered regions, but Meta-Disorder build the consensus over all of these methods, and therefore it did not predict any disordered regions.
Graphical representation of the result:
The result is very good, because HEXA_HUMAN does not have any disordered regions. Therefore, the prediction of Meta-Disorder is right.
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