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Revision as of 20:08, 25 June 2011 by Uskat (talk | contribs) (Visualisation of the Mutation)

General Information

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

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.

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.

This shows that the amino acids have huge structural differences which will probably cause drastical effects on protein structure and function.

picture original aa consequence for the whole protein
Amino acid Tryptophan
Visualization of the mutated protein

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
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)

PSSM analysis

self-information expected self-information
Trp 12 78

Conservation Analysis with Multiple Alignments

Mutation in the multiple alignment

Secondary Structure Mutation Analysis


Comparison with the real structure:

Mutation at position 329
Mutation at position 329 - detailed view

SNAP Prediction

No prediction available, because the protein ends here.

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
329 sift.png.png

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 .....