Gaucher Disease: Task 04 - Lab Journal
Contents
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).
CATH description of different levels
- 3.20.20 TIM Barrel
- 3.20 Alpha-Beta Barrel
- 3 Alpha Beta
- 1 mostly Alpha
LGA
On the LGA server the PDB IDs of the proteins were used. The method automatically chose 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 led to better RMSD values than the other parameters (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, we used the TopMatch webservice. Only the chains A of the structures are aligned.
SAP
SAP is a pairwise protein structure alignment method which uses double dynamic programming. We used the SAP webservice with the second option: "uploading the PDB files". Other possibility is to enter the PDB IDs. There is no possibility to restrain the alignments to a specific chain, therefore the whole structures were used for superposition. However, because the two chains in each protein are identical, duplicate alignments were eliminated implicitly by the program.