Homology modelling Gaucher Disease

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 [[task04_protocol protocol].

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 > 95%), 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

Single-template modeling

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	-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>