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Revision as of 10:56, 26 June 2011 by Uskat (talk | contribs) (Secondary Structure Mutation Analysis)

General Information

SNP-id rs61731240
Codon 179
Mutation Codon His -> Asp
Mutation Triplet CAT -> GAT

Pysicochemical Properities

First of all, we explored the amino acid properties and compared them for the original and the mutated amino acid. Therefore we created the possible effect that the mutation could have on the protein.

His Asp consequences
aromatic, positive charged, polar, hydrophilic negative charged, small, polar, hydrophilic On the one side, both amino acids are polar, but on the other side, His is positively charged, while Asp is negatively charged, which is an essential difference between these both amino acids. Therefore it is very likely, that this change causes big changes in the structure of the protein and the protein therefore will probably not work any longer. Furthermore, the structure of the two amino acids is very different, because of the aromatic ring of the His.

Visualisation of the Mutation

In the next step, we created the visualization of the muation with PyMol. Therefore we created a picture for the original amino acid, for the new mutated amino acid and finally for both together in one picture whereas the mutation is white colored. The following pictures display that the mutated amino acid Aspartate looks very different to Histidine. Histidine has an aromatical ring. Contrary, Aspartate is smaller and forks at the end of the rest. Furthermore, it is also orientated in a completly different direction. This shows that the amino acids have huge structural differences which will probably cause drastical effects on protein structure and function.

picture original aa picture mutated aa combined picture
Amino acid Histidine
Amino acid Aspartate
Picture which visualize the mutation

Subsitution Matrices Values

PAM 1 Pam 250 BLOSOUM 62
value aa most frequent substitution rarest substitution value aa most frequent substitution rarest substitution value aa most frequent substitution rarest substitution
3 20 (Gln) 0 (Ile, Met) 4 7 (Gln) 2 (Ala, Cys, Gly, Ile, Leu, Met, Phe, Thr, Trp, Val) -1 2 (Tyr) -3 (Cys, Ile, Leu, Val)

PSSM analysis

self-information expected self-information
His 9 65
Asp -3 0

Conservation analysis with Multiple Alignments

As a next step we created a multiple alignment which contains the HEXA sequence and 9 other mammalian homologous sequences from uniprot. Afterwards we looked at the position of the different mutations and looked at the conservation level on this position. The regarded mutation is presented by the colored column. Here we can see, that the all other mammalians have on this Position the amino acid Histidine. Therefore, the mutation on this position is highly conserved and a mutation on there will cause probably huge structural and functional changes for the protein.

Mutation in the multiple alignment

Secondary Structure Mutation Analysis

As a next step we compared the different results of the secondary structure prediction tools JPred and PsiPred. Afterwards we can examine in which secondary structure element and where therein the mutation takes place. This can give an overview of how drastical the mutation can be. In this case both tools agree and predict at the position of the mutation a coil. This has a result, that the mutation at this position would not destroy or split a secondary structure element. It will probably only changes the coil between two secondary structure elements, but this can sometimes also cause a change of the the following secondary structure. We think that a drastical change of the protein structure and its function is unlikly because the mutation does not affect a secondary struture element. The change of the coil will probably only take places between two secondary structure elements which will not change.


Comparison with the real structure:

Mutation at position 179
Mutation at position 179 - detailed view

SNAP Prediction

Substitution Prediction Reliability Index Expected Accuracy
D Non-neutral 6 93%

A detailed list of all possible substitutions can be found [here]

SIFT Prediction

SIFT Matrix:
Each entry contains the score at a particular position (row) for an amino acid substitution (column). Substitutions predicted to be intolerant are highlighted in red.

Sift legend.png
179 sift.png.png

SIFT Table
Threshold for intolerance is 0.05.
Amino acid color code: nonpolar, uncharged polar, basic, acidic.
Capital letters indicate amino acids appearing in the alignment, lower case letters result from prediction.

Predict Not ToleratedPositionSeq RepPredict Tolerated

Polyphen2 Prediction

HumDiv prediction
HumVar prediction