Homology modelling TSD

There will be no curiosity, no enjoyment of the process of life. All competing pleasures will be destroyed. But always — do not forget this, Winston — always there will be the intoxication of power, constantly increasing and constantly growing subtler. Always, at every moment, there will be the thrill of victory, the sensation of trampling on an enemy who is helpless. If you want a picture of the future, imagine a boot stamping on a human face — forever.

1984

protocol

Templates

Since similar sets were already collected for Task 2, the information was reused. In addition searches with HHpred on pdb70 and with COMA on pdb40 were performed. If two structures were mapped to the same Uniprot entry, only one, the 'most native' one, was used. The set of chosen templates is displayed in <xr id="tab:templates" />.
None of the searches revealed any structure with >80% sequence identity, other than the two already known structures 2gjx and 2gk1 which share 100% sequence identity. To still perform the task, 2gjx, which is the native structure <ref name="2gjxref">Lemieux,M. et al. (2006) Crystallographic Structure of Human beta-Hexosaminidase A: Interpretation of Tay-Sachs Mutations and Loss of GM2 Ganglioside Hydrolysis. Journal of molecular biology, 359, 913-29.</ref>, was chosen as reference and 2gk1, which has the inhibitor NGT bound, will be used as template. In the range between 40/80% sequence identity only one entry could be added from COMA. Most of the hits found by either COMA or HHpred turned out to have a sequence identity of lower than 25%.

<figtable id="tab:templates">

	PDB id	Sequence identity	Method
> 80% identity	2gk1 chain A	100%	Task2/HHpred/COMA
40% - 80% identity	1o7a chain D	56.6%	Task 2
	3lmy chain A	54%	COMA
< 30% identity	3nsm chain A	27.5%	Task 2
	3gh5 chain A	20.7%	Task 2

Table TODO: </figtable>

SWISS-MODEL

Default Modelling

2gjx chain E gets automatically assigned as template.

Low sequence identity

With the 3gh5 as template the automated SWISS-MODEL was not able to calculate a model structure for the Hex A subunit. Two alignments were produced, one with Blast and one with HHsearch. While the Blast alignment quality between target and template was too low to start with, the HHsearch alignment reached the next level and was sent to modelling but the building of a model was not successful.
The same occured for 3nsm which has a sequence identity about 7% higher than 3gh5. A sequence identity lower than 30% seems to be too low for modelling.

Evaluation

The QMEAN is a scoring function to describe the model quality. It is a linear combination of the 4 statistical potential terms C_beta interaction energy, all-atom pairwise energy, solvation energy and torsion angle energy. Hereby the QMEAN raw score ranges from 0 to 1 and indicates the reliability of the model. The QMEAN Z-score represents the absolute quality of the model by describing the likelihood that a given model is of comparable quality to experimental structures. Is calculated by comparison to reference structures and has a range of -4 to 4; the smaller the value the worse the model quality. For a more detailed explanation, see [1].

<figtable id="tab:swissOwneval">

	QMEAN raw score	QMEAN Z-score
2gjx	0.658	-1.63
2gk1	0.698	-0.96
1o7a	0.594	-2.73

Table TODO: Scores provided by SWISS-MODEL. </figtable>

<figtable id="tab:swisseval">

	Residues in common	Common residue RMSD	TM	GDT-TS	GDT-HA
2gjx	492	0.573	0.995	0.983	0.924
2gk1	492	0.213	0.999	1.000	0.999
1o7a	486	2.411	0.952	0.913	0.802

Table TODO: Calculated TM scores. </figtable>

<figtable id="tab:swissevalsap">

	Residues in common	Weighted RMSD	Unweighted RMSD	RMSD 6A around active site
2gjx	492	0.414	0.573
2gk1	491	0.189	0.212
1o7a	471	0.486	1.455

Table TODO: Calculated RMSD scores with SAP and Pymol. </figtable>

References

<references/>