Task 4: Structural Alignments

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lab journal task 4

PDB structures selection

We first selected a set of structures that span different ranges of sequence identity to the reference structure (1A6Z). The domain A of the reference structure has the CATH annotation 3.30.500.10.9 (Murine Class I Major Histocompatibility Complex H2-DB subunit A domain 1) and the domain b 2.60.40.10 (immunoglobulins). We decided to take the domain A as template and only searched for structures with a similar annotation to 3.30.500.10.9, since the immunglobulin domain is only bound to the protein and not directly connected. Also, because the disease causing mutations are all located in the MHC domain. <xr id="selected structures"/> list the structures, their CATH numbers and percent sequence idenity to the reference. Unfortunately, we could not find a structure with a sequence identity over 60%. The most similar structure we could find was 1qvo with 39% identity.

<figtable id="selected structures">

Table 1: Table of the selected pdb structures, the chain, the CATH annotation, their sequence identity to the refeerence 1A6Z_A and the protein type.

category	ID	chain	domain	CATH number	Sequence identity (%)	protein (organism)
reference	1A6Z	A	1	3.30.500.10	-	HFE (Homo sapiens)
identical sequence	1DE4	A	1	3.30.500.10	100	HFE (Homo sapiens)
> 30% SeqID	1QVO	A	01	3.30.500.10	39	HLA class I histocompatibility antigen, A-11 alpha chain (Homo sapiens)
< 30% SeqID	1S7X	A	00	3.30.500.10	29	H-2 class I histocompatibility antigen, D-B alpha chain (Mus musculus)
CAT	2IA1	A	01	3.30.500.20	11.1	BH3703 protein (Bacillus halodurans)
CA	3NCI	A	01	3.30.342.10	5.8	DNA polymerase (Enterobacteria phage RB69)
C	1VZY	A	01	3.55.30.10	2.8	33 KDA CHAPERONIN (Bacillus subtilis)
different CATH	1MUS	A	01	1.10.246.40	12.6	Tn5 transposase (Escherichia coli)

<\figtable>

The pairwise sequence alignments for computing the pairwise sequence identity were constructed with Emboss Needle http://www.ebi.ac.uk/Tools/psa/emboss_needle/ using default parameters.

Results

Differenct structural alignments were applied to superimpose the reference structure to all other structures. The resulting alignments scores are specified in <xr id="score results"/>. The numbers in bracket after the RMSD values indicate the number of aligned residues that were used to compute the corresponding value.

<figtable id="score results">

Table 2: Results of the structural alignments of the selected proteins to the template 1A6Z_A. The different alignment scores are listed for each method and the numbers of equivalen residues are stated in brackets after the RMSD.

PDB ID	Seq. identity (%)	Pymol		LGA		SSAP		TopMatch			CE
		RMSD (only C_alpha)	RMSD (all atom)	RMSD	LGA_S	RMSD	SSAP_Score	RMSD	S	S_r	RMSD	Score
1DE4_A	100	0.675 (237)	0.767 (1836)	1.14 (267)	95.77	1.60 (272)	93.07	1.08	260	1.03	1.19 (267)	543
1QVO_A	39	2.165 (233)	2.279 (1565)	2.29 (259)	67.86	2.58 (268)	86.39	2.62	228	2.50	2.44 (266)	432
1S7X_A	29	1.889 (233)	2.049 (1557)	2.12 (256)	71.90	2.36 (267)	86.25	2.66	227	2.56	2.29 (265)	342
2IA1_A	11.1	18.132 (74)	18.283 (501)	2.83 (86)	19.44	15.85 (140)	56.19	2.91	76	2.82	3.93 (93)	300
3NCI_A	5.8	16.561 (26)	17.329 (178)	3.11 (84)	17.19	14.54 (168)	30.18	3.05	53	2.94	4.47 (75)	333
1VZY_A	2.8	6.260 (29)	6.951 (168)	3.25 (63)	13.44	26.34 (208)	58.01	2.61	68	2.53	5.80 (91)	245
1MUS_A	12.6	23.521 (180)	23.891 (1143)	2.82 (69)	16.02	18.53 (215)	46.30	3.58	69	3.43	6.61 (78)	379

<\figtable>

<figtable id="pymol str. al.">

Table 3: Visualisation of the pariwise structural alignments of all selected proteins to the template 1A6Z_A. The template is shown in green and the target in red.

	1DE4_A	1QVO_A	1S7X_A	2IA1_A	3NCI_A	1VZY_A	1MUS_A

</figtable>

• Pymol only uses a subset of atoms for the computation of the RMSD.
• LGA computes the RMSD from all atoms under distance cutoff. It therfore uses more atoms than Pymol if the proteins are similar, but few if the structures are more divergent.
• SSAP
• TopMatch
• CE