Gaucher Disease: Task 05 - Lab Journal
This page is still under construction
Contents
Calculation of models
Structures set
We assembled the following structures in task 4, now we divide them into two groups: at > 60% and at < 30% sequence identity to our template protein, P04062 (536 aa long). PIDE was calculated as follows:
- first we aligned the two fasta sequences with ClustalW
- then calculated the PIDE (pairwise sequence identity) using SIAS with default options
Selected structures for single-template modelling are written in bold.
| Homologous structures to P04062 | ||
|---|---|---|
| PDB ID | PIDE with target (%) | Length (aa) |
| High PIDE | ||
| 2XWD_A | 91.51 | 505 |
| 2NSX_A | 92.53 | 497 |
| 2NT1_A | 92.53 | 497 |
| Low PIDE | ||
| 2GEP_A | 10.74 | 497 |
| 2F7K_A | 8.95 | 327 |
| 2QGU | 5.59 | 211 |
| 2ISB_A | 5.59 | 192 |
| 2DJF_A | 3.17 | 119 |
| 2DJF_B | 2.98 | 164 |
| 2DJF_C | 4.47 | 69 |
As the PIDE with P04062 in the low-PIDE group we have selected in task 4 is too low and 10.74% PIDE with 2GEP_A was not enough for Swiss-Model to align the sequences (with BLAST or HHsearch), we looked again at the found hit list in task 2 (HHblits, 2 iterations against Uniprot20 followed by one iteration against pdb_full with E-value cutoff 10E-10). The set of structures finally used is:
| Homologous structures to P04062 | ||||
|---|---|---|---|---|
| PDB ID | PIDE of alignment with target (%) | Length (aa) | Aligned columns (aa) | Query coverage |
| High PIDE | ||||
| 3KE0_A | 100 | 497 | 496 | 41-536 |
| 2XWD_A | 100 | 505 | 497 | 40-536 |
| 2WKL_A | 100 | 497 | 496 | 41-536 |
| 2NSX_A | 100 | 497 | 496 | 41-536 |
| Low PIDE | ||||
| 2WNW_A | 29 | 447 | 440 | 75-534 |
| 1VFF_A | 22 | 423 | 98 | 151-228 |
| 3II1_A | 20 | 535 | 84 | 452-514 |
TODO: brief execution explanation?
Modeller
TODO: execution scripts
Swiss-Model
We executed Swiss-Model online using the 'Automatic Modelling Mode'. In the advanced options, the specific template was specified.
iTasser
We also used iTasser from the web-server. In "Option I" a specific template was specified.
RMSD and GDT-score calculation
We used the TM-score tool from Zhang lab to calculate the RMSD and GDT-score. We also looked at the TM score. Execution:
TMscore <model> <native>
C_alpha RMSD calculation
We visualized all created models with Pymol. For this we aligned each model with the reference structures, 1OGS_A and 2V3E_B, and calculated the RMSD between the corresponding C_alpha atoms like in task 4:
align <native> and resi 1-497 and name ca, <model> and resi <from>-<to> and name ca
where "native" is the reference structure (1OGS_A or 2V3E_B) and "model" is the name of the model, "from" is its first residue and "to" its last residue.
