Homology Modelling GLA

^{by Benjamin Drexler and Fabian Grandke}

Calculation of Models

Available Homologous Structures

The HHpred search from Task1 output the following sequences(Top 10):

PDB-ID	Name	Probability	E-value	P-value	Identity
> 60% sequence identity
3hg3_A	Alpha-galactosidase A	1.0	0	0	97%
> 40% sequence identity
1ktb_A	Alpha-N-acetylgalactosaminidase	1.0	0	0	53%
< 40% sequence identity
1uas_A	Alpha-galactosidase	1.0	0	0	39%
3lrk_A	Alpha-galactosidase 1	1.0	0	0	32%
3a5v_A	Alpha-galactosidase	1.0	0	0	35%
1szn_A	Alpha-galactosidase	1.0	0	0	34%
3a21_A	Putative secreted alpha-galactosidase	1.0	0	0	34%
3cc1_A	BH1870 protein	1.0	0	0	26%
3a24_A	Alpha-galactosidase	1.0	0	0	14%
1zy9_A	Alpha-galactosidase	1.0	2.2E-37	8.8E-42	14%

MODELLER

We used the MODELLER as described in the tutorial Using Modeller for TASK 4.

PDB-ID	Unsupervised	Supervised	Identity	Comment
3LX9_A			99%
3GXP_A			99%
3H53_A			99%
3HG3_A			97%
3IGU_A			54%
1KTB_A			53%
1UAS_A			39%
3LRK_A			34%	Was removed due to little sequence identity. Caused huge gaps in alignment.
3CC1_A			28%	Was removed due to little sequence identity. Caused huge gaps in alignment.

iTasser

Figure 1 shows, that iTasser takes an amino acid sequence as input and tries to retrieve template proteins from PDB. In the next step fragments from the the templates are reassembled to a complete model. In the last step, the model is reassembled by taking energy calculations into account. Additionally biological function prediction is done, but that was not of interest of this task.<ref name=itasser1>http://zhanglab.ccmb.med.umich.edu/I-TASSER/about.html</ref>

Figure 1: A schematic representation of the I-TASSER protocol for protein structure and function predictions. The protein chains are colored from blue at the N-terminus to red at the C-terminus.<ref name=itasser2>Roy et al., I-TASSER: a unified platform for automated protein structure and function prediction, Nature Protocols, 2007</ref>

SWISS-MODEL

Following sequences have been selected:

3hg3_A					1ktb_A					3cc1_A
	Automated Mode		Aligned Mode			Automated Mode		Aligned Mode			Automated Mode		Aligned Mode
Identity	Z-score	Model	Z-score	Model	Identity	Z-score	Model	Z-score	Model	Identity	Z-score	Model	Z-score	Model
97%	0		-0.415		53%	0		-2.261		26%	0		Error¹	NA

¹The sequences are to different to create a useful model from the alignment. In the automated mode the template itself has been used as model, what is useless, because the sequences have only 26% identity.

Aborting: too many unfruitful attempts to rebuild a loop. This is likely to indicate a misalignment in this region Use Swiss-PdbViewer to adjust your alignment in this region and resubmit an optimise mode modelling request.

References

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