Difference between revisions of "Structure-based mutation analysis (Phenylketonuria)"

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== Preparation ==
  
== Preparation ==
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[[Lab Journal - Task 9 (PAH) |Lab journal]] <br>
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In the further analysis we used the protein structure of [http://www.rcsb.org/pdb/explore/explore.do?structureId=2PAH 2PAH] for the analysis. Now, we will use [http://www.rcsb.org/pdb/explore/explore.do?structureId=1J8U 1J8U] since this structure got better results for the new constraints.
  
  +
  +
In the further analysis we used the protein structure of [http://www.rcsb.org/pdb/explore/explore.do?structureId=2PAH 2PAH] for the analysis. Now, we will use [http://www.rcsb.org/pdb/explore/explore.do?structureId=1J8U 1J8U] since this structure got better results for the following observed constraints:
  +
* Structure with the highest resolution (small Å value)
  +
* Smallest R-factor
  +
* Highest coverage
  +
* pH-value ideally near physiological pH of 7.4
  +
* No gaps (missing residues) included in the structure, so a consecutive numbering of residues should be given
  +
  +
To proof our statement, the results of the constraints of 2PAH and 1J8U are compared in the Table below.
  +
{|border="1" cellspacing="0" cellpadding="5" align="center" style="text-align:center"
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|-
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! style="background:#32CD32;" | Protein
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! style="background:#32CD32;" | Resolution(Å)
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! style="background:#32CD32;" | R-factor
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! style="background:#32CD32;" | pH
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! style="background:#32CD32;" | gaps
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! style="background:#32CD32;" | chain
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! style="background:#32CD32;" | Positions in [http://www.uniprot.org/uniprot/P00439 P00439]
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! style="background:#32CD32;" | Coverage %
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|-
  +
| 1DMW || 2.00 || 0.20 || 6.80 || x || A || 118-424 || x
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|-
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| 1J8T || 1.70 || 0.20 || 6.80 || x || A || 103-427 || x
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|-
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| 1J8U || <span style="background:#00FF00">1.50</span> || <span style="background:#00FF00">0.16</span> || 6.80 || 0 || A || 103-427 || 71.68
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|-
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| 1KW0 || 2.50 || 0.22 || 6.80 || x || A || 103-427 || x
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|-
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| 1LRM || 2.10 || 0.21 || 6.80 || x || A || 103-427 || x
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|-
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| 1MMK || 2.00 || 0.20 || 6.80 || x || A || 103-427 || x
  +
|-
  +
| 1MMT || 2.00 || 0.21 || 6.80 || x || A || 103-427 || x
  +
|-
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| 1PAH || 2.00 || 0.18 || 6.80 || x || A || 117-424 || x
  +
|-
  +
| 1TDW || 2.10 || 0.21 || 6.80 || x || A || 117-424 || x
  +
|-
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| 1TG2 || 2.20 || 0.21 || 6.80 || x || A || 117-424 || x
  +
|-
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| 2PAH || 3.10 || 0.25 || <span style="background:#00FF00">7.00</span> || x || A/B || 118-452 || 73.89
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|-
  +
| 3PAH || 2.00 || 0.18 || 6.80 || x || A || 117-424 || x
  +
|-
  +
| 4ANP || 2.11 || 0.20 || 6.80 || x || A || 104-427 || x
  +
|-
  +
| 4PAH || 2.00 || 0.17 || 6.80 || x || A || 117-424 || x
  +
|-
  +
| 5PAH || 2.10 || <span style="background:#00FF00">0.16</span> || 6.80 || x || A || 117-424 || x
  +
|-
  +
| 6PAH || 2.15 || 0.17 || 6.80 || x || A || 117-424 || x
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|}
   
 
== Energy comparisons ==
  
== Energy comparisons ==

Revision as of 17:43, 2 July 2013

Page still under construction!!!

Summary

...

Preparation

Lab journal

In the further analysis we used the protein structure of 2PAH for the analysis. Now, we will use 1J8U since this structure got better results for the following observed constraints:

  • Structure with the highest resolution (small Å value)
  • Smallest R-factor
  • Highest coverage
  • pH-value ideally near physiological pH of 7.4
  • No gaps (missing residues) included in the structure, so a consecutive numbering of residues should be given

To proof our statement, the results of the constraints of 2PAH and 1J8U are compared in the Table below.

Protein Resolution(Å) R-factor pH gaps chain Positions in P00439 Coverage %
1DMW 2.00 0.20 6.80 x A 118-424 x
1J8T 1.70 0.20 6.80 x A 103-427 x
1J8U 1.50 0.16 6.80 0 A 103-427 71.68
1KW0 2.50 0.22 6.80 x A 103-427 x
1LRM 2.10 0.21 6.80 x A 103-427 x
1MMK 2.00 0.20 6.80 x A 103-427 x
1MMT 2.00 0.21 6.80 x A 103-427 x
1PAH 2.00 0.18 6.80 x A 117-424 x
1TDW 2.10 0.21 6.80 x A 117-424 x
1TG2 2.20 0.21 6.80 x A 117-424 x
2PAH 3.10 0.25 7.00 x A/B 118-452 73.89
3PAH 2.00 0.18 6.80 x A 117-424 x
4ANP 2.11 0.20 6.80 x A 104-427 x
4PAH 2.00 0.17 6.80 x A 117-424 x
5PAH 2.10 0.16 6.80 x A 117-424 x
6PAH 2.15 0.17 6.80 x A 117-424 x

Energy comparisons

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FoldX

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Minimise

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References

<references/>

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