Team:TU Darmstadt/modelling/Structure

All these steps are performed to every template used for the modeling approach. For our project we set the maximum amount of templates to 20. Every derived structure is evaluated using an average per-residue quality Z-scores. At last a hybrid model is built containing the best regions of all predictions. This procedure make prediction’s accurate and thus more realistic. For the evaluation we used the Yasara Z-scores.A Z-score describes how many standard deviations the model quality is away from the average high-resolution X-ray structure. Negative values indicate that the homology model looks worse than a high-resolution X-ray structure. The overall Z-scores for all models have been calculated as the weighted averages of the individual Z-scores using the formula Overall = 0.145*Dihedrals + 0.390*Packing1D + 0.465*Packing3D [7].

Parameters
We used the Yasara script hm_build.mcr for the model creation with the following parameters:

Modeling speed (slow = best): Slow

Number of PSI-BLAST iterations in template search (PsiBLASTs): 3

Maximum allowed PSI-BLAST E-value to consider template (EValue Max): 0.5

Maximum number of templates to be used (Templates Total): 20

Maximum number of templates with same sequence (Templates SameSeq): 1

Maximum oligomerization state (OligoState): 4 (tetrameric)

Maximum number of alignment variations per template: (Alignments): 5

Maximum number of conformations tried per loop (LoopSamples): 50

Maximum number of residues added to the termini (TermExtension): 10

LssmOrange - first modelling

Here we show our hybrid homology model of our protein, LssmOrange in ribbon representation. Furthermore we illustrate the average quality z-score as a function of residue number. Nevertheless it was subjected to a final round of simulated annealing minimization in explicit solvent and obtained the following quality Z-scores:

Check Type	Quality Z-score	Comment
Dihedrals	WERT	BLA
Packing 1D	WERT	BLA
Packing 3D	WERT	BLA
Overall	WERT	BLA

LssmOrange - second modelling

Check Type	Quality Z-score	Comment
Dihedrals	WERT	BLA
Packing 1D	WERT	BLA
Packing 3D	WERT	BLA
Overall	WERT	BLA

LssmOrange - third modelling (dimer)

Check Type	Quality Z-score	Comment
Dihedrals	WERT	BLA
Packing 1D	WERT	BLA
Packing 3D	WERT	BLA
Overall	WERT	BLA

References

[1] E. Krieger, G. Koraimann, and G. Vriend, “Increasing the precision of comparative models with YASARA NOVA--a self-parameterizing force field.,” Proteins, vol. 47, no. 3, pp. 393–402, 2002.
[2] S. F. Altschul, T. L. Madden, A. A. Schäffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman, “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.,” Nucleic Acids Res, vol. 25, no. 17, pp. 3389–3402, Sep. 1997.
[3] R. W. Hooft, G. Vriend, C. Sander, and E. E. Abola, “Errors in protein structures.,” Nature, vol. 381, no. 6580. Nature Publishing Group, p. 272, 1996.
[4] D. T. Jones, “Protein secondary structure prediction based on position-specific scoring matrices,” Journal of Molecular Biology, vol. 292, no. 2, pp. 195–202, 1999.
[5] A. A. Canutescu, A. A. Shelenkov, and R. L. Dunbrack, “A graph-theory algorithm for rapid protein side-chain prediction.,” Protein Science, vol. 12, no. 9, pp. 2001–2014, 2003.
[6] E. Krieger, K. Joo, J. Lee, J. Lee, S. Raman, J. Thompson, M. Tyka, D. Baker, and K. Karplus, “Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8.,” Proteins, vol. 77 Suppl 9, no. June, pp. 114–122, 2009.
[7] http://www.yasara.org/homologymodeling.htm