Difference between revisions of "Gaucher Disease: Task 04 - Lab Journal"

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==Exploring Structural Alignments==
 
==Exploring Structural Alignments==
   
The structure of the pyridoxal kinase (2F7K) is not from our set, because we did not have any hits with sequence identity <30% to our reference protein. So we extracted 2F7K randomly from COPS entries with a different L30 group.
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The structure of the pyridoxal kinase (2F7K) is not from our set, because we did not have any hits with sequence identity <30% to our reference protein. So we extracted 2F7K randomly from COPS entries with a different L30 group. The Sequence identity to the reference structure 1ogs_A is determined by CATH (SSAP).
   
   

Revision as of 15:01, 17 August 2013

Exploring Structural Alignments

The structure of the pyridoxal kinase (2F7K) is not from our set, because we did not have any hits with sequence identity <30% to our reference protein. So we extracted 2F7K randomly from COPS entries with a different L30 group. The Sequence identity to the reference structure 1ogs_A is determined by CATH (SSAP).


LGA

LGA On the LGA server the pdb IDs of the proteins were used. The method automatically chosed chain A. 1. default parameters:

-4 -o2 -gdc

2. with aligned CA atoms:

-4 -o2 -gdc -atom:CA -lga_m

3. with aligned all atoms

-4 -o2 -gdc -ah:0 -lga_m

In the end we decided to use the default parameters (1.), as this results to better RMSD values than the other paramteres (2. und 3.).

Pymol

In Pymol we aligned each structure of our set, shown in table1, to our disease causing protein structure. For this we only used chain A, as we also used only chain A for calculating the rmsd with other methods. On the other hand the steric configuration of both identical chains are aranged different than two chains of another structure. So, even if each chain has a low RMSD to one chain of our protein, the steric configuration can lead to a high RMSD anyway.

To align all atoms:

align 1ogs_A and resi 1-496, structure2 and resi 1-n

To align all C alpha atoms:

align 1ogs_A and resi 1-496 and name ca, structure2 and resi 1-n and name ca

whereas n is the sequence length of structure2.

SSAP

SSAP is the structural alignment method used by CATH. The structures were entered via their PDB ID. In case of several chains, we always used Chain A.

TopMatch

For TopMatch, only the chains "A" of the structures were aligned. As can be seen, for the first three sequences, which have a high similarity to the target 1OGS_A, the length of the alignment (L) is high and the RMSD (E_r) is low (below 1). For the remaining five sequences, which have a much lower sequence similarity to the target, the RMSD becomes higher and the number of superposed residues drastically lower.

SAP

For SAP, structural alignments the SAP webservice was used with the second option - uploading the PDB files (because entering the PDB IDs did not work).

Evaluation of structural alignments and sequence alignments