Gaucher Disease: Task 05 - Homology Modelling

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Calculation of models

Structures from task 04

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 from PDB 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 Swissmodel to align the sequences, 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

Modeller - multiple target modeling

In multiple target modeling Modeller first aligns the user selected templates, then adds the target to the MSA, which is finally used for modeling. We tried the following template combinations:

  • close homologues (> 60% sequence identity): all four (3KE0_A, 2XWD_A, 2WKL_A and 2NSX_A)
  • distant homologues (< 30% sequence identity): all three (2WNW_A, 1VFF_A and 3II1_A)
  • one close and one distant homologues: 2XWD_A and 2WNW_A
  • several close and distant homologues: all

Swissmodel

Model for 2GEP could not be created, because the alignment quality between target and specified template (2GEP) is too low and they could not be aligned with BLAST or HHsearch.

iTasser

The run with 2xwd as template is still running on the server.

For details how we executed the programs please see the lab journal.

Evaluation of models

Modeller

Swissmodel

iTasser