Rs121907967

From Bioinformatikpedia
Revision as of 10:59, 30 June 2011 by Uskat (talk | contribs) (SCWRL Prediction)

General Information

SNP-id rs121907967
Codon 329
Mutation Codon Trp -> TER
Mutation Triplet TGG -> TAG

Back to [Sequence-based mutation analysis]

Sequence-based Mutation Analysis

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.

Trp TER consequences
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.

Back to [Sequence-based mutation analysis]


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
Amino acid Tryptophan
Visualization of the mutated protein

Back to [Sequence-based mutation analysis]


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)

Back to [Sequence-based mutation analysis]


PSSM Analysis

Besides, we looked additional at the position specific scoring matrix (PSSM) for ouer sequence. In contrast to PAM and BLOSOUM, the PSSM contains a specific substitution rate for each position in the sequence. Therefore, the PSSM is more position specific than PAM or BLOSOUM. We extracted the substitution value for the underlying mutation, the value for the most frequent substitution 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.


PSSM
value aa most frequent substitution rarest substitution
X 12 -5

Back to [Sequence-based mutation analysis]


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.

Mutation in the multiple alignment

Back to [Sequence-based mutation analysis]


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 normally has as a result, that the mutation at this position would not destroy or split a secondary structure element which would have no drastical changes for the protein. In this special case with a substitution to a stop codon there will be anyway structural changes followed by functional loose.

JPred:
...CCCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEECC...
PsiPred:
...CCCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEECC...

Comparison with the real Structure:

Afterwards we also visualize the position of the muation (red) in the real 3D-structure of PDB and compare it with the predicted secondary structure. The visualisation can therefore like above the predicted secondary structure display if the mutation is in a secondary structure element or in some other regions.

Here in this case the mutationposition does not agree with the position of the predicted secondary structure and is within a alpha helix. Normally, this means that the mutation will probably destroy or split the helix which has structural and functional changes of the protein as result. In this special case with a substitution to a stop codon there will be anyway structural changes followed by functional loose.

Mutation at position 329
Mutation at position 329 - detailed view

Back to [Sequence-based mutation analysis]


SNAP Prediction

No prediction available, because the protein ends here. However, in this special case with a substitution to a stop codon there will be anyway a drastical protein structure change which is followed by the the functional loose of the protein.

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

Back to [Sequence-based mutation analysis]


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
329 sift.png.png



Back to [Sequence-based mutation analysis]


PolyPhen2 Prediction

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 affect a function of the protein hardly and probably the protein is useless afterwards.

Back to [Sequence-based mutation analysis]


Structure-based Mutation Analysis

SCWRL Prediction

n this case the mutation is from Tryptophan to a stop codon. Therefore, we made no SCREWL prediction, because it is clear that it will cause a damage of the 3D-structure of the protein. Furthermore, it will of course affect a function of the protein hardly and probably the protein is useless afterwards.

Back to [Structure-based mutation analysis]