Difference between revisions of "Homology modelling Gaucher Disease"
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− | The object of this task was to apply homology modelling for predicting the tertiary structure of glycosylceramidase given its [[https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Gaucher_Disease#Sequence sequence]]. For this, we first selected different templates which were than used to derive the structure of glycosylceramidase using three different homology modeling tools, namely Modeller, SWISS-MODEL, and the I-TASSER server. The resulting models were evaluated using both quality assessment scores and the native crystal structure [http://www.rcsb.org/pdb/explore/explore.do?structureId=1OGS 1ogs]. Technical details are reported in our [[task04_protocol |
+ | The object of this task was to apply homology modelling for predicting the tertiary structure of glycosylceramidase given its [[https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Gaucher_Disease#Sequence sequence]]. For this, we first selected different templates which were than used to derive the structure of glycosylceramidase using three different homology modeling tools, namely Modeller, SWISS-MODEL, and the I-TASSER server. The resulting models were evaluated using both quality assessment scores and the native crystal structure [http://www.rcsb.org/pdb/explore/explore.do?structureId=1OGS 1ogs]. Technical details are reported in our [[task04_protocol|protocol]]. |
== Template selection == |
== Template selection == |
||
− | We used HHsearch for searching the PDB for homologous templates. <xr id="templates"/> lists some of the top-ranking templates. 2nt0_A is identical to the target 1ogs_A and was therefore excluded. Although all listed hits are homologous to the target (HHsearch probability > |
+ | We used HHsearch for searching the PDB for homologous templates. <xr id="tab:templates"/> lists some of the top-ranking templates. 2nt0_A is identical to the target 1ogs_A and was therefore excluded. Although all listed hits are homologous to the target (HHsearch probability > 97%), their sequence identity was below 30%. We therefore selected 2wnw_A (blue) as a close homolog, 2y24_A (green) as an intermediate homolog, and 3nco_A (yellow) as a more distant homolog. Note that the latter two templates to not cover the complete target which makes the homology modeling process harder. |
<figtable id="tab:templates"> |
<figtable id="tab:templates"> |
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== Modeller == |
== Modeller == |
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+ | Modeller is a popular tools for building models by the satisfaction of spatial restrains which are derived, for instance, from one or several target-template alignments. The alignments can come from any alignment or homology search tool, or it can be built by modeller itself. We built a model for our target protein by (1) using a single template and employing Modeller to built the alignment, (2) using a single template and the alignment from HHsearch, and (3) using multiple templates. The Model quality was assessed via the DOPE and DOPE z-score reported by Modeller as well as the QMEAN6 score from the SWISS-MODEL workspace. We compared the resulting models to the crystal structure 1ogs_A via the weighted all-atom RMSD score computed by SAP, as well as the TM-score, GDT_TS, and GTD_HA score which we computed by the program TMscore. |
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=== Single-template modeling === |
=== Single-template modeling === |
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+ | |||
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|[[File:modeller-1ogs_A-2wnw_A.png|thumb|150px|2wnw_A]] |
|[[File:modeller-1ogs_A-2wnw_A.png|thumb|150px|2wnw_A]] |
Revision as of 20:15, 29 May 2012
The object of this task was to apply homology modelling for predicting the tertiary structure of glycosylceramidase given its [sequence]. For this, we first selected different templates which were than used to derive the structure of glycosylceramidase using three different homology modeling tools, namely Modeller, SWISS-MODEL, and the I-TASSER server. The resulting models were evaluated using both quality assessment scores and the native crystal structure 1ogs. Technical details are reported in our protocol.
Contents
Template selection
We used HHsearch for searching the PDB for homologous templates. <xr id="tab:templates"/> lists some of the top-ranking templates. 2nt0_A is identical to the target 1ogs_A and was therefore excluded. Although all listed hits are homologous to the target (HHsearch probability > 97%), their sequence identity was below 30%. We therefore selected 2wnw_A (blue) as a close homolog, 2y24_A (green) as an intermediate homolog, and 3nco_A (yellow) as a more distant homolog. Note that the latter two templates to not cover the complete target which makes the homology modeling process harder. <figtable id="tab:templates">
Hit Nr | Template | Identity | Query HMM | Prob |
---|---|---|---|---|
> 80% sequence identity | ||||
1 | 2nt0_A | 100.0 | 1-497 | 100.0 |
40% - 80% sequence identity | ||||
< 30% sequence identity | ||||
2 | 2wnw_A | 28.0 | 36-496 | 100.0 |
3 | 3clw_A | 14.0 | 64-495 | 100.0 |
4 | 2y24_A | 18.0 | 66-495 | 100.0 |
5 | 3kl0_A | 19.0 | 65-495 | 100.0 |
6 | 3zr5_A | 17.0 | 65-494 | 100.0 |
7 | 3ik2_A | 14.0 | 65-495 | 99.2 |
22 | 3nco_A | 11.0 | 113-384 | 97.7 |
28 | 1egz_A | 12.0 | 113-387 | 97.4 |
</figtable>
Modeller
Modeller is a popular tools for building models by the satisfaction of spatial restrains which are derived, for instance, from one or several target-template alignments. The alignments can come from any alignment or homology search tool, or it can be built by modeller itself. We built a model for our target protein by (1) using a single template and employing Modeller to built the alignment, (2) using a single template and the alignment from HHsearch, and (3) using multiple templates. The Model quality was assessed via the DOPE and DOPE z-score reported by Modeller as well as the QMEAN6 score from the SWISS-MODEL workspace. We compared the resulting models to the crystal structure 1ogs_A via the weighted all-atom RMSD score computed by SAP, as well as the TM-score, GDT_TS, and GTD_HA score which we computed by the program TMscore.
Single-template modeling
<figtable id="tab:modeller_results">
Template | DOPE | DOPE z-score | QMEAN6 | RMSD | TM-score | GDT_TS | GTD_HA |
---|---|---|---|---|---|---|---|
2wnw_A | -55925 | -0.471 | 0.689 | 1.006 | 0.824 | 0.661 | 0.479 |
2y24_A | -47194 | 0.777 | 0.376 | 1.222 | 0.550 | 0.294 | 0.223 |
3nco_A | -44033 | 1.224 | 0.139 | 2.158 | 0.252 | 0.093 | 0.043 |
</figtable>
Multiple-template modeling
<figtable id="tab:modeller_results">
Template | DOPE | DOPE z-score | QMEAN6 | RMSD | TM-score | GDT_TS | GTD_HA |
---|---|---|---|---|---|---|---|
2wnw_A-2y24_A-3kl0 | -39084 | 1.930 | 0.314 | 1.987 | 0.465 | 0.277 | 0.179 |
2wnw_A-3nco_A | -46962 | 0.807 | 0.556 | 1.256 | 0.778 | 0.593 | 0.409 |
3ik2_A-3nco_A-1egz_A | -25391 | 0.3881 | 0.101 | 6.607 | 0.241 | 0.062 | 0.029 |
</figtable>
Using global HHsearch alignments
<figtable id="tab:modeller-hhsearch-results">
Template | DOPE | DOPE z-score | QMEAN6 | RMSD | TM-score | GDT_TS | GTD_HA |
---|---|---|---|---|---|---|---|
2wnw_A | -54695 | -0.295 | 0.726 | 1.079 | 0.869 | 0.732 | 0.538 |
2y24_A | -47256 | 0.765 | 0.566 | 1.640 | 0.722 | 0.553 | 0.386 |
3nco_A | -32577 | 2.857 | 0.272 | 9.757 | 0.398 | 0.235 | 0.131 |
</figtable>
Using local HHsearch alignments
<figtable id="tab:modeller-hhsearch-local-results">
Template | DOPE | DOPE z-score | QMEAN6 | RMSD | TM-score | GDT_TS | GTD_HA |
---|---|---|---|---|---|---|---|
2wnw_A | -53593 | -0.744 | 0.749 | 1.003 | 0.866 | 0.731 | 0.532 |
2y24_A | -46290 | -0.030 | 0.564 | 1.162 | 0.724 | 0.563 | 0.381 |
3nco_A | -25047 | 0.886 | 0.451 | 1.827 | 0.402 | 0.245 | 0.138 |
</figtable>
SWISS-MODEL
Automated mode
<figtable id="tab:modeller_results">
Template | DOPE | DOPE z-score | QMEAN6 | RMSD | TM-score | GDT_TS | GTD_HA |
---|---|---|---|---|---|---|---|
2wnw_A | -53863 | -0.786 | 0.530 | 1.003 | 0.858 | 0.723 | 0.540 |
2y24_A | -42674 | 0.565 | 0.430 | 1.100 | 0.712 | 0.539 | 0.382 |
3nco_A | -27101 | 2.109 | 0.270 | 2.158 | 0.422 | 0.252 | 0.138 |
</figtable>
Alignment mode
<figtable id="tab:modeller_results">
Template | DOPE | DOPE z-score | QMEAN6 | RMSD | TM-score | GDT_TS | GTD_HA |
---|---|---|---|---|---|---|---|
2wnw_A | -53963 | -0.788 | 0.540 | 1.011 | 0.859 | 0.722 | 0.536 |
2y24_A | -40131 | 1.055 | 0.360 | 1.222 | 0.510 | 0.238 | 0.067 |
3nco_A | -30244 | 0.689 | 0.240 | 2.001 | 0.426 | 0.247 | 0.135 |
</figtable>