Difference between revisions of "Rs121907982"

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(Pysicochemical Properities)
(Visualisation of the Mutation)
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=== Visualisation of the Mutation ===
 
=== Visualisation of the Mutation ===
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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 the mutation from Isoleucine to Valine. Isoleucine is longer than Valine and one part spreads in the other direction than this of Valine. Valine is small and forks at its end. All in all, the differencesof both amino acids is not so drastical and therefore the protein will probably not have a strutural and functional change.
   
 
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Revision as of 20:30, 25 June 2011

General Information

SNP-id rs121907982
Codon 436
Mutation Codon Ile -> Val
Mutation Triplt ATA -> GTA

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.

Ile Val consequences
aliphatic, hydrophobic, neutra aliphatic, hydrophobic, neutral In this case, the pysicochemical properties are equal. Furthermore, they almost agree in their size. Therefore, we suggest, that there is no big effect on the 3D structure of the protein and therefore, also no big effect on the protein function.

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 the mutation from Isoleucine to Valine. Isoleucine is longer than Valine and one part spreads in the other direction than this of Valine. Valine is small and forks at its end. All in all, the differencesof both amino acids is not so drastical and therefore the protein will probably not have a strutural and functional change.

picture original aa picture mutated aa combined picture
Amino acid Isoleucine
Amino acid Valin
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
33 33 (Val) 0 (Gly, Pro, Trp) 9 9 (Val) 1 (Trp) 3 3 (Val) -4 (Gly)

PSSM analysis

self-information expected self-information
Ile -4 1
Val -3 1

Conservation Analysis with Multiple Alignments

Mutation in the multiple alignment

Secondary Structure Mutation Analysis

JPred:
...HHHHHHHHCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEE...
PsiPred:
...HHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHCCCCCE...

Comparison with the real structure:

Mutation at position 436
Mutation at position 436 - detailed view

SNAP Prediction

Substitution Prediction Reliability Index Expected Accuracy
V Neutral 0 53%

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
436 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
wc436I1.00fYHMpIVgLnTQDRASEK




PolyPhen2 Prediction

HumDiv prediction
HumVar prediction