Structural Alignments (Phenylketonuria)

Summary

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Explore structural alignments

Lab journal

Dataset generation

Our protein has the CATH Code: 1.10.800.10 (Phenylalanine Hydroxylase)

• reference structure of PAH: 2PAH (96,41% identity)
• identical sequence with filled binding site: 1LRM (--> pdb entry: looked at 3D structure and saw a filled binding site, two ligands: FE and HBI)
• identical sequence with unfilled binding site: not found anyone
• low sequence identity: 3LUY (32,2% - no pdb ID under 30%)
• high sequence identity: pdb ID: 2PHM (89,7%)
• CAT: 1J8U (CATH Code: 1.10.800.10) - there is no other category than 1.10.800.10 for CAT
• CA: 2B5U (CATH Code: 1.10.287.620)
• C: 3BQO (CATH Code: 1.25.40.210)
• other CATH category: 1V8H (CATH Code: 2.60.40.10)

Pymol

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LGA

LGA ...

SSAP / CATHEDRAL (used by CATH)

SSAP ...
uses Cβ

TopMatch

TopMatch ...
uses Cα

SAP or CE

SAP? ->Error!
->
CE
CE-PDB ...

Modelling scores

To compare the different models, the RMSDs (root-mean-square deviation) are compared. In TopMatch the same formular is taken but called Er (root-mean-square error). The RMSD gives the squared distance between corresponding positions of two superimposed proteins in Ångström. The results are shown in <xr id="rmsd"/>. <figtable id="rmsd">

RMSD results
Method	1lrm	3luy	2phm	1j8u	2b5u	3bqo	1vh8
LGA-RMSD	0.81	3.30	0.88	0.73	3.07	3.59	3.42
SSAP-RMSD	0.99	18.77	1.24	1.02	39.16	22.39	7.27
TopMatch-Er	0.60	1.98	0.81	0.63	1.21	1.12	3.25
CE-RMSD	0.65	5.13	0.95	0.68	4.06	4.68	5.92

Root-mean-square deviation/error in Ångström for the four protein structure alignment predictors LGA, SSAP, TopMatch and CE.

</figtable>

• lowest RMSDs: TopMatch
• LGA and CE sometimes the one sometimes the other is better. For very similar structures CE better, otherwise LGA???
• worst/highest RMSDs: SSAP, maybe the Cβ are more distant???

• careful about the sidechains: here always 2pah.A as query is taken and xx.A as target

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Evaluate sequence alignments

Lab journal
<figtable id="model_rmsd">

LGA and hhsearch results
	LGA				hhsearch
pdb	RMSD	LGA_S	LGA_Q	seq_id	probability	e-value	identities(%)
1phz	0.83	90.65	32.44	99.34	100.00	6.9e-165	92
1j8u	0.73	90.29	35.83	99.67	100.00	3.1e-135	100
2v27	1.70	62.77	12.55	96.02	100.00	3.6e-74	32
2qmx	3.18	7.46	1.25	4.88	98.20	1.1e-09	36
3luy	2.82	7.17	1.24	13.89	98.07	3.3e-09	22
1qey	0.64	3.65	1.63	0.00	54.00	3.4	67
1wyp	2.67	8.43	1.37	0.00	29.42	15	19
1a6s	3.15	6.93	1.08	11.43	20.59	29	36

...

</figtable>

• last two have a very low probability...

References

<references/>