Difference between revisions of "Rs61747114"

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=== Conservation Analysis with Multiple Alignments ===
 
=== Conservation Analysis with Multiple Alignments ===
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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 second colored column. Here we can see, that the all other mammalians have also on this position the amino acid Leucine. Therefore, the mutation on this position is highly conserved and a mutation there will cause probably huge structural and functional changes for the protein.
   
 
[[Image:mut_5.png|thumb|center|600px|Mutation in the multiple alignment]]
 
[[Image:mut_5.png|thumb|center|600px|Mutation in the multiple alignment]]

Revision as of 10:45, 26 June 2011

General Information

SNP-id rs61747114
Codon 248
Mutation Codon Leu -> Phe
Mutation Triplet CTT -> TTT

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.

Leu Phe consequences
aliphatic, hydrophobic, neutral aromatic, hydrophobic, neutral Leu is an aliphatic amino acid, wheras Phe is an aromatic amino acid. This means, that Phe has an aromatic ring in its structure. But both amino acids are relatively big and so it is possible, that the exchange of this amino acids do not change the structure of the protein that much. Therefore, we suggest it is possible, that the protein will work.

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 Phenylalanine looks very different to Leucine. Leucine forks at the end of the rest whereas Phenylalanine has an huge aromatical ring. The only thing that agrees is the orientation and the length of the res before the fork or the aromativ ring. All in all the difference probably prevails the agreement and therefore the mutation will probably caus changes in protein structure and function.

picture original aa picture mutated aa combined picture
Amino acid Leucine
Amino acid Phenylalanine
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
13 45 (Met) 0 (Asp, Cys) 13 20 (Met) 2 (Cys) 0 2 (Ile, Met) -4 (Asp, Gly)

PSSM analysis

self-information expected self-information
Leu 1 13
Phe -3 1

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 second colored column. Here we can see, that the all other mammalians have also on this position the amino acid Leucine. Therefore, the mutation on this position is highly conserved and a mutation there will cause probably huge structural and functional changes for the protein.

Mutation in the multiple alignment

Secondary Structure Mutation Analysis

JPred:
...HHHHHHHHCCCEEEECCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC...
PsiPred:
...HHHHHHHHCCCEEEECCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCH...

Comparison with the real structure:

Mutation at position 248
Mutation at position 248 - detailed view

SNAP Prediction

Substitution Prediction Reliability Index Expected Accuracy
F Neutral 3 78%

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
248 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
cwpenkgrsthaQ248L1.00YIDVFML




PolyPhen2 Prediction

HumDiv prediction
HumVar prediction