Prediction of Disordered Regions

Disopred

Disopred predicts two disordered regions in our protein. 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.

Result of the Disopred prediction. * shows that this amino acid belongs to a disordered regions, whereas . signs for a non-disordered region.

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

POODLE-L

POODLE-L found no disordered regions. Therefore, there is no disordered region with a length more than 40aa in our protein.

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

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:

Prediction of POODLE-S (High B-factor residues)

Prediction of POODLE-S (missing residues)

Prediction of POODLE-I

Prediction of POODLE-L

Comparison of the different POODLE variants

POODLE-L doesn't find any disordered regions. This is the result we expected, because our protein doesn't posses any disordered regions.

Both POODLE-S variants found several short disordered regions, which is a false positive result. Interesstingly, there seems to be more missing electrons in the electron density map, than residues with high B-factor value.

POODLE-I found the same result as POODLE-S with high B-factor, which was expected, because POODLE-I combines POODLE-L and POODLE-S (high B-factor).

Therefore, the predictions of short disordered regions are wrong results. Only the prediction of POODLE-L is correct.

In general, these predictions are used, if nothing is known about the protein. Therefore, normally we don't know, that the prediction is wrong. Because of that, we want to trust the result and we want to check if the disordered regions overlap with the functionally important residues, because it seems that disordered regions are functionally very important. We check this for POODLE-S with missing residues and POODLE-I, because POODLE-S with high B-factor values shows the same result as POODLE-I.

functional residues			disordered
residue position	amino acid	function	POODLE-S (missing)	POODLE-I
323	E	active site	ordered	ordered
115	N	Glycolysation	ordered	ordered
157	N	Glycolysation	ordered	ordered
259	N	Glycolysation	ordered	ordered
58 (connected with 104)	C	Disulfide bond	disordered	ordered
104 (connected with 58)	C	Disulfide bond	disordered	ordered
277 (connected with 328)	C	Disulfide bond	ordered	ordered
328 (connected with 277)	C	Disulfide bond	ordered	ordered
505 (connected with 522)	C	Disulfide bond	ordered	ordered
522 (connected with 505)	C	Disulfide bond	ordered	ordered

As you can see in the table above, only one disulfide bond is located in a disordered region, all other functionally important residues are located in ordered regions. This is a further good hint, that the predictions are wrong.

IUPred

We tested the three different IUPred variants, which are offered by the webserver.

IUPred (short)

Result of the IUPred prediction, which is focus on short disordered regions.

As you can see in the picture, 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.

IUPred (long)

Next we take a look to the prediction of the long disordered regions:

Result of the IUPred prediction, which is focus on long disordered regions.

The picture above 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 posses any disordered regions.

IUPred (with structural information)

As last, we analysed the prediction of IUPred with the additional usage of structural information.

Result of the IUPred prediction with additional structural information

As before, the method did not find any disordered regions. 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.

Meta-Disorder

Meta-Disorder did not predict any disordered region in our protein. 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.