|Mutation Codon||Trp -> TER|
|Mutation Triplet||TGG -> TAG|
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.
|aromatic, polar, hydrophobic||TER||By this change, the protein is not complete, therefore it is not possible for the protein to fold and to function.|
Visualisation of the Mutation
In the next step, we created the visualization of the muation with PyMol. Therefore we created two pictures: one which displays the original amino acid and one that displays the consequence of the resulting termination. The grey and the red parts of 3D-structure are the original protein whereas the red part shows the remaining protein if there is an exchange of Tryptophan to a stop codon. Here we can see that the remaining red part has only the half size of the protein. Furthermore, the missing part can have an effect on the folding of the remaining part, which this one can fold in a complety other way. Therefore, this muation will have engraving effects on the protein. The protein will probably loose its whole function and is not usable anymore.
|picture original aa||consequence for the whole protein|
Subsitution Matrices Values
Afterwards, we looked at the values of the substitution matrices PAM1, PAM250 and BLOSSUM62. Therefore we looked detailed at the three values: the value for accoding amino acid substitution, the most frequent value for the substitution of the examined amino acid and the rarest substitution.
In this case, we get no informations because there is no entry for the substitution of Tryptophan to a stop codon. Therefore we can not say what the possible consequences for the protein are only by looking at the substitution matrices. However,a stop codon will if course always have a drastical effect on the protein and its function.
|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|
|X||2 (Arg)||0 (all, except Arg, Phe, Ser, Tyr)||X||2 (Arg)||0 (all, except Arg, His, Leu, Phe, Ser, Tyr)||X||2 (Tyr)||-4 (Asn, Asp, Pro)|
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 all other mammalians have on this Position the same amino acid. Therefore, the mutation on this position is highly conserved and in a normal case this would be a indication for structural and functional changes. In this special case it will cause anyway structural and functional changes, because it is a substitution with a stop codon and therefore only a part of the protein will be translated.
Secondary Structure Mutation Analysis
JPred: ...CCCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEECC... PsiPred: ...CCCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEECC...
Comparison with the real structure:
No prediction available, because the protein ends here.
A detailed list of all possible substitutions can be found [here]
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.
In this case the mutation is from Tryptophan to a stop codon. Therefore, we made no PolyPhen2 prediction, because it is clear that it will cause a damage of the 3D-structure of the protein. Furthermore, it will of course .....