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

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(→‎Structure selection)
(→‎Structure selection)
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! style="background:#32CD32;" | Coverage %
  
! style="background:#32CD32;" | Coverage %
 
|-
  
|-
−
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=1DMW 1DMW] || X-ray || 2.00 || 0.20 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B118-424%5D 118-424] || x
 +
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=1DMW 1DMW] || X-ray || 2.00 || 0.20 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B118-424%5D 118-424] || 67,92
 
|-
  
|-
−
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=1J8T 1J8T] || X-ray || 1.70 || 0.20 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427] || x
+
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=1J8T 1J8T] || X-ray || 1.70 || 0.20 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427] || 71.90
 
|- style="background-color: #D8BFD8"
  
|- style="background-color: #D8BFD8"
−
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=1J8U 1J8U] || X-ray || '''1.50''' || '''0.16''' || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427] || x
+
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=1J8U 1J8U] || X-ray || '''1.50''' || '''0.16''' || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427] || 71.90
 
|-
  
|-
−
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=1KW0 1KW0] || X-ray || 2.50 || 0.22 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427] || x
+
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=1KW0 1KW0] || X-ray || 2.50 || 0.22 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427] || 71.90
 
|-
  
|-
−
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=1LRM 1LRM] || X-ray || 2.10 || 0.21 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427] || x
+
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=1LRM 1LRM] || X-ray || 2.10 || 0.21 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427] || 71.90
 
|-
  
|-
−
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=1MMK 1MMK] || X-ray || 2.00 || 0.20 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B103-427%5D%5D 103-427] || x
+
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=1MMK 1MMK] || X-ray || 2.00 || 0.20 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B103-427%5D%5D 103-427] || 71.90
 
|-
  
|-
−
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=1MMT 1MMT] || X-ray || 2.00 || 0.21 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427] || x
+
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=1MMT 1MMT] || X-ray || 2.00 || 0.21 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B103-427%5D 103-427] || 71.90
 
|-
  
|-
−
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=1PAH 1PAH] || X-ray || 2.00 || 0.18 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424] || x
+
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=1PAH 1PAH] || X-ray || 2.00 || 0.18 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424] || 68.14
 
|-
  
|-
−
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=1TDW 1TDW] || X-ray || 2.10 || 0.21 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424] || x
+
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=1TDW 1TDW] || X-ray || 2.10 || 0.21 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424] || 68.14
 
|-
  
|-
−
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=1TG2 1TG2] || X-ray || 2.20 || 0.21 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424] || x
+
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=1TG2 1TG2] || X-ray || 2.20 || 0.21 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424] || 68.14
 
|-
  
|-
−
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=2PAH 2PAH] || X-ray || 3.10 || 0.25 || '''7.00''' || 136LEU-143ASP || '''A/B''' || [http://www.uniprot.org/blast/?about=P00439%5B118-452%5D '''118-452'''] || x
 +
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=2PAH 2PAH] || X-ray || 3.10 || 0.25 || '''7.00''' || 136LEU-143ASP || '''A/B''' || [http://www.uniprot.org/blast/?about=P00439%5B118-452%5D '''118-452'''] || 74.12
 
|-
  
|-
−
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=3PAH 3PAH] || X-ray || 2.00 || 0.18 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424] || x
+
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=3PAH 3PAH] || X-ray || 2.00 || 0.18 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424] || 68.14
 
|-
  
|-
−
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=4ANP 1ANP] || X-ray || 2.11 || 0.20 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B104-427%5D 104-427] || x
+
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=4ANP 1ANP] || X-ray || 2.11 || 0.20 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B104-427%5D 104-427] || 68.81
 
|-
  
|-
−
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=4PAH 4PAH] || X-ray || 2.00 || 0.17 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424] || x
 +
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=4PAH 4PAH] || X-ray || 2.00 || 0.17 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424] || 68.14
 
|-
  
|-
−
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=5PAH 5PAH] || X-ray || 2.10 || '''0.16''' || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424] || x
+
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=5PAH 5PAH] || X-ray || 2.10 || '''0.16''' || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424] || 68.14
 
|-
  
|-
−
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=6PAH 6PAH] || X-ray || 2.15 || 0.17 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424] || x
+
| [http://www.pdb.org/pdb/explore/explore.do?pdbId=6PAH 6PAH] || X-ray || 2.15 || 0.17 || 6.80 || - || A || [http://www.uniprot.org/blast/?about=P00439%5B117-424%5D 117-424] || 68.14
 
|}
  
|}
 
<small><center>'''<caption>''' ...</caption></center></small>
  
<small><center>'''<caption>''' ...</caption></center></small>

Revision as of 12:34, 11 August 2013

Page still under construction!!!

Summary

In Task 8 the sequence of PAH was used for finding mutational effects, now the structure will be taken for these analysis. But how to find out, if a mutation changes the structure? Therefore, one calculates the energy of all atoms for the wildtype and the mutated structure and compares the results for changes. There are two different methods for this calculations given: Quantum Mechanics (QM) and Molecular Mechanics (MM). In QM the energy of all electrons in a protein is calculated. It is one of the most accurated methods, but it is very time consuming. In MM the energy of a system is calculated as a function of nuclear positions. It is very fast and easy to calculate, but it ignores electronic motions and is not as accurate as QM. Since QM is too time intensive and the results of MM are nearly as good as the ones calculated with QM, we use MM for the further analysis. Molecular Mechanics uses force fields for the energy calculation, which is defined as a sum of terms. The terms are non-bonded (electrostatic and Van-der-Waals) and bonded (Bond stretching, Angle stretching, bond rotation) interactions. For the structure based mutation analysis the SCWRL and FoldX webserver were used.

Structure selection

Lab journal

In some Tasks before, we used the protein structure of 2PAH as reference, but now we have to check some more constraints for the protein structure selection:

  • 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 check which protein structure to use for further analysis, we compared the constraint data for all sequences given in the PAH (P00439) Uniprot entry. <figtable id="pro-struc">

Protein Method Resolution(Å) R-factor pH Gaps Chain Positions Coverage %
1DMW X-ray 2.00 0.20 6.80 - A 118-424 67,92
1J8T X-ray 1.70 0.20 6.80 - A 103-427 71.90
1J8U X-ray 1.50 0.16 6.80 - A 103-427 71.90
1KW0 X-ray 2.50 0.22 6.80 - A 103-427 71.90
1LRM X-ray 2.10 0.21 6.80 - A 103-427 71.90
1MMK X-ray 2.00 0.20 6.80 - A 103-427 71.90
1MMT X-ray 2.00 0.21 6.80 - A 103-427 71.90
1PAH X-ray 2.00 0.18 6.80 - A 117-424 68.14
1TDW X-ray 2.10 0.21 6.80 - A 117-424 68.14
1TG2 X-ray 2.20 0.21 6.80 - A 117-424 68.14
2PAH X-ray 3.10 0.25 7.00 136LEU-143ASP A/B 118-452 74.12
3PAH X-ray 2.00 0.18 6.80 - A 117-424 68.14
1ANP X-ray 2.11 0.20 6.80 - A 104-427 68.81
4PAH X-ray 2.00 0.17 6.80 - A 117-424 68.14
5PAH X-ray 2.10 0.16 6.80 - A 117-424 68.14
6PAH X-ray 2.15 0.17 6.80 - A 117-424 68.14
...

</figtable> All proteins were found with the X-ray diffraction method. In <xr id="pro-struc"/> we can see, that the protein 1J8U has a better resolution value as well as R-factor than the other proteins...

Visualisation of used mutations

Following five mutations are mapped to the crystal structure:

Substitution Prediction Database
Gln172His neutral dbSNP
Ala259Val non-neutral HGMD
Thr266Ala non-neutral dbSNP
Phe392Ser non-neutral dbSNP
Pro416Gln non-neutral HGMD


Gly103Ser
...

Gln172His
...

Ala259Val
...

Thr266Ala
...

Phe392Ser
...

Pro416Gln
...

Mutated structure creation

SCWRL

...

FoldX

...

Energy comparisons

...

Minimise

...

References

<references/>

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