Difference between revisions of "Structural Alignments (Phenylketonuria)"

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(→‎Modelling scores)
(→‎Evaluate sequence alignments)
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== Evaluate sequence alignments ==
  
== Evaluate sequence alignments ==
 
[[Lab Journal - Task 4 (PAH) #Evaluate sequence alignments|Lab journal]] <br>
  
[[Lab Journal - Task 4 (PAH) #Evaluate sequence alignments|Lab journal]] <br>
  +
<figtable id="model_rmsd">
−
...
  
  +
{| border="1" cellpadding="5" cellspacing="0" align="center"
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|-
  +
! colspan="8" style="background:#32CD32;" | RMSD results
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|-
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! style="background:#90EE90;" align="center" | pdb
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! style="background:#90EE90;" align="center" | RMSD
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! style="background:#90EE90;" align="center" | LGA_S
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! style="background:#90EE90;" align="center" | LGA_Q
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! style="background:#90EE90;" align="center" | Seq_id
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|-
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| 1phz || 0.83 || 90.65 || 32.44 || 99.34
  +
|-
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| 1j8u || 0.73 || 90.29 || 35.83 || 99.67
  +
|-
  +
| 2v27 || 1.70 || 62.77 || 12.55 || 96.02
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|-
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| 2qmx || 3.18 || 7.46 || 1.25 || 4.88
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|-
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| 3luy || 2.82 || 7.17 || 1.24 || 13.89
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|-
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| 1qey || 0.64 || 3.65 || 1.63 || 0.00
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|-
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| 1wyp || 2.67 || 8.43 || 1.37 || 0.00
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|-
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| 1a6s || 3.15 || 6.93 || 1.08 || 11.43
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|-
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|}
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<center><small>'''<caption>'' ... </caption></small></center>
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</figtable>
   
 
== References ==
  
== References ==

Revision as of 15:01, 1 June 2013

Summary

...

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

...

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

...

Evaluate sequence alignments

Lab journal
<figtable id="model_rmsd">

RMSD results
pdb RMSD LGA_S LGA_Q Seq_id
1phz 0.83 90.65 32.44 99.34
1j8u 0.73 90.29 35.83 99.67
2v27 1.70 62.77 12.55 96.02
2qmx 3.18 7.46 1.25 4.88
3luy 2.82 7.17 1.24 13.89
1qey 0.64 3.65 1.63 0.00
1wyp 2.67 8.43 1.37 0.00
1a6s 3.15 6.93 1.08 11.43
' ...

</figtable>

References

<references/>

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