Difference between revisions of "Homology modelling Gaucher Disease"

From Bioinformatikpedia
Line 40: Line 40:
 
| 28 || 1egz_A || 12.0 || 113-387 || 97.4
 
| 28 || 1egz_A || 12.0 || 113-387 || 97.4
 
|}
 
|}
  +
<caption>Homologs found by HHsearch. Bold: selected templated used for the following modelling.</caption>
 
</figtable>
 
</figtable>
   
 
== Modeller ==
 
== 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.
+
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 they can be built by modeller itself. We created models for our target protein by (1) using a single template and employing Modeller to compute 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 ===
 
=== Single-template modeling ===
  +
<xr id="tab:modeller-single-models"/> shows the resulting models. 2wnw_A produced the best looking model: all major secondary structure elements coincided with the native structure 1ogs_A (red). Only the target range 1-31 which was not covered by template (cf. table <xr id="tab:templates"/> resulted in some deviating loop regions (at the top right corner). Although 2y24_A is less conserved than 2wnw_A, the model came close to the native structure. 3nco_A shares the same TIM beta/alpha-barrel domain (the tube at the center) than 1ogs_A but is missing the Glycosyl hydrolase domain (the sheets at the right side) such that the model was less well structured in this region.
   
  +
<figtable id="tab:modeller-single-models">
{|
 
  +
{|style="border-style:solid; border-width: 1px"
 
|[[File:modeller-1ogs_A-2wnw_A.png|thumb|150px|2wnw_A]]
 
|[[File:modeller-1ogs_A-2wnw_A.png|thumb|150px|2wnw_A]]
 
|[[File:modeller-1ogs_A-2y24_A.png|thumb|150px|2y24_A]]
 
|[[File:modeller-1ogs_A-2y24_A.png|thumb|150px|2y24_A]]
Line 53: Line 56:
 
|[[File:modeller-single-dope.png|thumb|200px|Dope score per residue.]]
 
|[[File:modeller-single-dope.png|thumb|200px|Dope score per residue.]]
 
|}
 
|}
  +
<caption>Models built by Modeller using single templates and alignments computed by Modeller itself. Red: 1ogs_A.</caption>
  +
</figtable>
  +
  +
asdasd
   
<figtable id="tab:modeller_results">
+
<figtable id="tab:modeller-single-eval">
 
{| style="border-collapse: separate; border-style: solid; border-spacing: 0; border-width: 2px 0 2px 0; text-align:right" width="700px"
 
{| style="border-collapse: separate; border-style: solid; border-spacing: 0; border-width: 2px 0 2px 0; text-align:right" width="700px"
 
|- style="background-color: lightgrey; height=0"
 
|- style="background-color: lightgrey; height=0"

Revision as of 20:45, 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.

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

Homologs found by HHsearch. Bold: selected templated used for the following modelling. </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 they can be built by modeller itself. We created models for our target protein by (1) using a single template and employing Modeller to compute 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

<xr id="tab:modeller-single-models"/> shows the resulting models. 2wnw_A produced the best looking model: all major secondary structure elements coincided with the native structure 1ogs_A (red). Only the target range 1-31 which was not covered by template (cf. table <xr id="tab:templates"/> resulted in some deviating loop regions (at the top right corner). Although 2y24_A is less conserved than 2wnw_A, the model came close to the native structure. 3nco_A shares the same TIM beta/alpha-barrel domain (the tube at the center) than 1ogs_A but is missing the Glycosyl hydrolase domain (the sheets at the right side) such that the model was less well structured in this region.

<figtable id="tab:modeller-single-models">

2wnw_A
2y24_A
3nco_A
Dope score per residue.

Models built by Modeller using single templates and alignments computed by Modeller itself. Red: 1ogs_A. </figtable>

asdasd

<figtable id="tab:modeller-single-eval">

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

2wnw_A-2y24_A-3kl0_A
2wnw_A-3nco_A
3ik2_A-3nco_A-1egz_A
Dope score per residue.

<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

2wnw_A
2y24_A
3nco_A
2wnw_A
2y24_A
3nco_A
Dope score per residue.

<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

2wnw_A
2y24_A
3nco_A
Dope score per residue.

<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

2wnw_A
2y24_A
3nco_A
Dope score per residue.

<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

2wnw_A
2y24_A
3nco_A
Dope score per residue.

<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>