Homology-modelling HEXA

Homology structure groups

We decided to choose every 5% one protein:

> 60% sequence identity
PDB id	name	similarity	single template
1ht6_A	AMY1, alpha-amylase iso	95%
3aj7_A	Oligo-1,6-glucosidase	90%
1h4p_A	Glucan 1,3-beta-glucosidase	85.2%
3bc9_A	AMYB, alpha amylase, ca	80.8%	X
2zum_A	458AA long hypothetical	75%
3bmv_A	Cyclomaltodextrin gluca	70.3%
2f2h_A	Putative family 31 gluc	64.8%
3emz_A	Xylanase, endo-1,4-beta	61%
> 40%
2dep_A	Xylanase B, thermostabl	54.9%
3cui_A	EXO-beta-1,4-glucanase;	49.5%	X
1vhc_A	Putative KHG/KDPG aldol	45.1%
2hk0_A	D-psicose 3-epimerase	40.8%
< 40%
2g0w_A	LMO2234 protein; putati	35.5%
3q94_A	Fructose-bisphosphate a	30.0%
3hn3_A	Beta-G1, beta-glucuroni	25.1%
3lut_A	Voltage-gated potassium	20.1%	X

Calculation of the models

Swissmodel

To calculate the models with Swiss-Model we used the [Webserver]. For the template with high sequence identity, we used the automated and the alignment method, for the other two templates we only used the alignment method.

The used alignments can be found [here].

Modeller

We used Modeller from the command line. Therefore we followed the instructions, described [here].

First of all, we created an alignment for each of our three selected sequences. In the next step we used Modeller to model the 3D structure of the protein.

For Modeller we used the Pir Alignment format, which can be found here: [3BC9], [3CUI], [3LUT]

iTasser

To calculate our models with iTasser we used the [Webserver]. We defined the target and template sequence, but this time without an alignment. We used the same template sequences as before.

Results

Swissmodel

3BC9:

todo

3CUI:

The detailed prediction can be found [here]

Swiss-Model also give same scores to give the user the possibility to estimate the quality of the predicted model, which are showed in the next paragraphes.

The most important score in the following table is the QMEAN4 score, because this score consists of the scores above and give the user the possibility to compare different results.

Global Score
Scoring function term	Raw score	Z score
C_beta interaction energy	202.24	-4.65
All-atom pairwise energy	9942.28	-6.16
Solvation energy	67.79	-8.08
Torsion angle energy	76.36	-7.72
QMEAN4 score	0.057	-11.76

Swiss-Modeler also returns some pictures, which show the qualitity of the model.

Predicted Structure:

Prediction the structure of HEXA_HUMAN with 3cui as template structure

Prediction of the wrong predicted residues

Model qualitity:

Visualisation of the QMEAN Z-Score for this model

Visualisation of the QMEAN score in comparison with a gaussian distribution

Quality of the model in comparison to a X-ray structure

Plot, which shows the wrong predicted residues of this model

3HN3:

The detailed prediction can be found [here]

Swiss-Model also give same scores to give the user the possibility to estimate the quality of the predicted model, which are showed in the next paragraphes.

The most important score in the following table is the QMEAN4 score, because this score consists of the scores above and give the user the possibility to compare different results.

Global Score
Scoring function term	Raw score	Z score
C_beta interaction energy	120.70	-5.31
All-atom pairwise energy	2585.98	-5.22
Solvation energy	71.87	-9.92
Torsion angle energy	80.43	-8.44
QMEAN4 score	0.010	-12.80

Swiss-Modeler also returns some pictures, which show the qualitity of the model.

Predicted Structure:

Prediction the structure of HEXA_HUMAN with 3hn3 as template structure

Prediction of the wrong predicted residues

Model qualitity:

Visualisation of the QMEAN Z-Score for this model

Visualisation of the QMEAN score in comparison with a gaussian distribution

Quality of the model in comparison to a X-ray structure

Plot, which shows the wrong predicted residues of this model

Modeller

3BC9:

Modeller calculated one model for 3BC9, which can be seen in the next picture:

3D structure of HEXA_HUMAN with 3BC9 as template predicted by Modeller.

3CUI:

Modeller calculated one model for 3CUI, which can be seen in the next picture:

3D structure of HEXA_HUMAN with 3CUI as template predicted by Modeller.

3HN3:

TODO Dienstag

Analysis

RMSD

To get the possibility to estimate the quality of the predicted models, we calculated the RMSD between the observed protein and the predicted protein. For this purpose, we used PyMol, because PyMol is able to superpose two 3D protein structures and to calculate the RMSD.
Therefore, we used following command:

align model1, model2

As an output, we got the superposed structures, the number of aligned residues and the RMSD.

We decided not to use the RMSD, which is calculated by Modeller, because we wanted to calculate the RMSD for each structure in the same way, to get comparative results. In the pictures, which show the superposed structures, the green one is always the target, whereas the red one is always the template.

Results for 3BC9:

	Swissmodel	Modeller	iTasser					3D-Jigsaw
			Model 1	Model 2	Model 3	Model 4	Model 5
RMSD	todo	26.271	1.075	16.450	19.716	10.824	20.450	already running
aligned atoms	todo	3981	3443	3757	3910	3647	3911	already running
Structural alignment	todo	Superposition with the structure predicted by Modeller	Superposition with the structure predicted by iTasser (Model 1)	Superposition with the structure predicted by iTasser (Model 2)	Superposition with the structure predicted by iTasser (Model 3)	Superposition with the structure predicted by iTasser (Model 4)	Superposition with the structure predicted by iTasser (Model 5)	already running