Difference between revisions of "Homology Modelling GLA"
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=Introduction= |
=Introduction= |
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In this task, we performed homology modelling of the protein [[Fabry_Disease#.CE.B1-galactosidase_A|α-galactosidase A]] with the programs MODELLER, SWISS-MODEL, iTasser and 3D-JIGSAW. Homology modelling relies on the following two assumptions. First, the structure of the protein is determined by its amino acid sequence. Second, the structure of a protein is more conserved than its amino acid sequence. Usually one performs homology modelling of a protein which structure is not known. In this case, we have several PDB structures of the α-galactosidase A available and hence we are able to evaluate the resulting models of the programs afterwards. |
In this task, we performed homology modelling of the protein [[Fabry_Disease#.CE.B1-galactosidase_A|α-galactosidase A]] with the programs MODELLER, SWISS-MODEL, iTasser and 3D-JIGSAW. Homology modelling relies on the following two assumptions. First, the structure of the protein is determined by its amino acid sequence. Second, the structure of a protein is more conserved than its amino acid sequence. Usually one performs homology modelling of a protein which structure is not known. In this case, we have several PDB structures of the α-galactosidase A available and hence we are able to evaluate the resulting models of the programs afterwards. |
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+ | =General= |
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=Calculation of Models= |
=Calculation of Models= |
Revision as of 22:23, 15 June 2011
by Benjamin Drexler and Fabian Grandke
Introduction
In this task, we performed homology modelling of the protein α-galactosidase A with the programs MODELLER, SWISS-MODEL, iTasser and 3D-JIGSAW. Homology modelling relies on the following two assumptions. First, the structure of the protein is determined by its amino acid sequence. Second, the structure of a protein is more conserved than its amino acid sequence. Usually one performs homology modelling of a protein which structure is not known. In this case, we have several PDB structures of the α-galactosidase A available and hence we are able to evaluate the resulting models of the programs afterwards.
General
Calculation of Models
Available Homologous Structures
The following table lists the best ten hits of the HHpred search of Task 1. We used 3HG3 (97% identity), 1KTB (53%) and 3CC1 (34%) as templates for the modelling process. This selection covers a wide range of sequence identity and hence we are able to evaluate how the sequence identity influence the quality of the models.
PDB-ID | Name | Probability | E-value | P-value | Identity | Template |
---|---|---|---|---|---|---|
> 60% sequence identity | ||||||
3hg3_A | Alpha-galactosidase A | 1.0 | 0 | 0 | 97% | x |
> 40% sequence identity | ||||||
1ktb_A | Alpha-N-acetylgalactosaminidase | 1.0 | 0 | 0 | 53% | x |
< 40% sequence identity | ||||||
1uas_A | Alpha-galactosidase | 1.0 | 0 | 0 | 39% | |
3lrk_A | Alpha-galactosidase 1 | 1.0 | 0 | 0 | 32% | |
3a5v_A | Alpha-galactosidase | 1.0 | 0 | 0 | 35% | |
1szn_A | Alpha-galactosidase | 1.0 | 0 | 0 | 34% | |
3a21_A | Putative secreted alpha-galactosidase | 1.0 | 0 | 0 | 34% | |
3cc1_A | BH1870 protein | 1.0 | 0 | 0 | 26% | x |
3a24_A | Alpha-galactosidase | 1.0 | 0 | 0 | 14% | |
1zy9_A | Alpha-galactosidase | 1.0 | 2.2E-37 | 8.8E-42 | 14% |
MODELLER
MODELLER is a program to produce three-dimensional protein structures based on homology or comparative modelling. The user has to provide the sequence of the protein to be modeled and the structure and sequence of at least one related protein that is used as a template. MODELLER uses all atoms of the template protein, but the hydrogen-atoms. We used MODELLER as described in the tutorial Using Modeller for TASK 4. Therefor we had to align both sequences and convert them into pir-format. This alignment is given as input together with the template pdb-file. Unfortunately the input file has to be provided as python file. Additionally to the pairwise approach we used a multiple alignment as template for the model. Therefor we created an alignment of the sequence, provided in the Multiple_Sequence_Alignments section of this page. Then we added the target sequence to the alignment and supervised it. The supervision showed, that the sequences aligned very well in general, but the sequences 3LRK_A and 3CC1_A. Thus, those were removed and the alignment was realigned. Both, the supervised and the unsupervised alignment have been used as input for MODELLER.<ref name=modeller>http://salilab.org/modeller/</ref>
Pairwise Alignments
In this section, we used a pairwise alignment between the template (i.e. 3HG3, 1KTB and 3CC1) and the target as the input for MODELLER.
Evaluation
![](/wiki/images/thumb/2/26/Fabry_disease_homology_modelling_modeller_combined.png/500px-Fabry_disease_homology_modelling_modeller_combined.png)
Apo (1R46) | Complexed (1R47) | |||||||
---|---|---|---|---|---|---|---|---|
Template | TMS (command line) | TMS (webserver) | RMSD | RMSD catalytic site | TMS (command line) | TMS (webserver) | RMSD | RMSD catalytic site |
3HG3 | 0.141 | 0.2743 | 0.498 | 0.326 | 0.1413 | 0.2746 | 0.512 | 0.366 |
1KTB | 0.140 | 0.2793 | 0.901 | 0.439 | 0.1413 | 0.2739 | 0.888 | 0.437 |
3CC1 | 0.1397 | 0.2670 | 2.864 | 3.436 | 0.1397 | 0.2665 | 2.853 | 3.405 |
Multiple Sequence Alignments
PDB-ID | Unsupervised | Supervised | Identity | Comment |
---|---|---|---|---|
3LX9_A | 99% | |||
3GXP_A | 99% | |||
3H53_A | 99% | |||
3HG3_A | 97% | |||
3IGU_A | 54% | |||
1KTB_A | 53% | |||
1UAS_A | 39% | |||
3LRK_A | 34% | Was removed due to little sequence identity. Caused huge gaps in alignment. | ||
3CC1_A | 28% | Was removed due to little sequence identity. Caused huge gaps in alignment. |
iTasser
Figure 1 shows, that iTasser takes an amino acid sequence as input and tries to retrieve template proteins from PDB. In the next step fragments from the the templates are reassembled to a complete model. In the last step, the model is reassembled by taking energy calculations into account. Additionally biological function prediction is done, but that was not of interest of this task.<ref name=itasser1>http://zhanglab.ccmb.med.umich.edu/I-TASSER/about.html</ref>
![](/wiki/images/thumb/0/08/GLA_Itasser.png/200px-GLA_Itasser.png)
We used the iTasser-server in two different ways:
- Standard parameters: the protein sequence is given as input and the program searches PDB for templates. The found proteins are used to create a template to predict the structure.
- PDB-ID as input: together with the amino acid sequence a template PDB-ID is given as input. The program takes all available information into account and uses them to calculate the structure.
As the iTasser server has very low capacities and only one job commitment at the same time is possible, the results of the second way are not yet present. The standalone version is no option, because it has a size of about 10GB and it does not work properly.
SWISS-MODEL
We used the swissmodel server with two different options:
- Automated Mode: A template sequence is given as input. As no further information are given, the model is directly created from the amino acid sequence. This method should only be used, if the sequence identity between target and template is greater than 50%.
- Aligned Mode: A pairwise alignment of template and target sequence is given as input. We created our alignments using online ClustalW2 from EBI.
Following sequences have been selected:
3hg3_A | 1ktb_A | 3cc1_A | ||||||
---|---|---|---|---|---|---|---|---|
Automated Mode | Aligned Mode | Automated Mode | Aligned Mode | Automated Mode | Aligned Mode | |||
Identity | Z-score | Z-score | Identity | Z-score | Z-score | Identity | Z-score | Z-score |
97% | 0 | -0.415 | 53% | -2.742 | -12.996 | 26% | Error¹ | -14.046 |
¹The sequences are to different to create a useful model(26%). In the automated mode sequence identity of at least 50% is recommended.
Evaluation of Models
MODELLER
Numeric Evaluation
Apo (1R46) | Complexed (1R47) | ||||||||
---|---|---|---|---|---|---|---|---|---|
Template | TMS | RMSD | RMSD catalytic site | TMS | RMSD | RMSD catalytic site | |||
3HG3 | 0.141 | 0.498 | 0.326 | 0.1413 | 0.512 | 0.366 | |||
1KTB | 0.140 | 0.901 | 0.439 | 0.1413 | 0.888 | 0.437 | |||
3CC1 | 0.1397 | 2.864 | 3.436 | 0.1397 | 2.853 | 3.405 |
Comparison to Experimental Structure
![](/wiki/images/thumb/2/26/Fabry_disease_homology_modelling_modeller_combined.png/500px-Fabry_disease_homology_modelling_modeller_combined.png)
iTasser
Numeric Evaluation
Comparison to Experimental Structure
SWISS-MODEL
Template 3HG3
Numeric Evaluation
Apo (1R46) | Complexed (1R47) | |||||||
---|---|---|---|---|---|---|---|---|
Mode | TMS (command line) | TMS (webserver) | RMSD | RMSD catalytic site | TMS (command line) | TMS (webserver) | RMSD | RMSD catalytic site |
Aligned | 0.1411 | 0.2729 | 0.485 | 0.279 | 0.1412 | 0.2731 | 0.489 | 0.290 |
Automated | 0.1411 | 0.2729 | 0.485 | 0.277 | 0.1412 | 0.2731 | 0.489 | 0.291 |
Comparison to Experimental Structure
![](/wiki/images/thumb/3/3e/Fabry_disease_homology_modelling_swissmodel_3hg3_combined.png/500px-Fabry_disease_homology_modelling_swissmodel_3hg3_combined.png)
Template 1KTB
Numeric Evaluation
Apo (1R46) | Complexed (1R47) | |||||||
---|---|---|---|---|---|---|---|---|
Mode | TMS (command line) | TMS (webserver) | RMSD | RMSD catalytic site | TMS (command line) | TMS (webserver) | RMSD | RMSD catalytic site |
Aligned | 0.1598 | 0.2638 | 0.943 | 5.073 | 0.1606 | 0.2636 | 0.932 | 6.409 |
Automated | 0.1361 | 0.2669 | 0.981 | 0.417 | 0.1368 | 0.2672 | 0.974 | 0.404 |
Comparison to Experimental Structure
![](/wiki/images/thumb/9/90/Fabry_disease_homology_modelling_swissmodel_1ktb_combined.png/500px-Fabry_disease_homology_modelling_swissmodel_1ktb_combined.png)
Template 3CC1
Numeric Evaluation
Apo (1R46) | Complexed (1R47) | |||||||
---|---|---|---|---|---|---|---|---|
Mode | TMS (command line) | TMS (webserver) | RMSD | RMSD catalytic site | TMS (command line) | TMS (webserver) | RMSD | RMSD catalytic site |
Aligned | 0.1302 | 0.2436 | 3.279 | 7.107 | 0.1300 | 0.2442 | 3.802 | 7.357 |
Automated | N/A | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
Comparison to Experimental Structure
![](/wiki/images/thumb/9/90/Fabry_disease_homology_modelling_swissmodel_3cc1.png/250px-Fabry_disease_homology_modelling_swissmodel_3cc1.png)
References
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