Difference between revisions of "Rs4777505"

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(Visualisation of the Mutation)
(Visualisation of the Mutation)
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=== Visualisation of the Mutation ===
 
=== 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 Asparagine has a much smaller chain than Serine. Contrary Serine is longer and comes to a fork at the end of its rest. Furthermore, it is also orientated in a completly different direction. This shows that the amino acids have huge structural differences which will probably cause drastical effects on the protein structure and function.
+
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 Asparagine has a much smaller chain than Serine. Contrary Serine is longer and comes to a fork at the end of its rest. Furthermore, it is also orientated in a different direction. Otherwise comparing to other mutations this one is not extremly. Therefore, this exchange will probably not cause huge effects on the protein structure and function.
   
 
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Revision as of 20:19, 25 June 2011

General Information

SNP-ID Rs4777505
Codon Number 29
Mutation Codon Asn -> Ser
Mutation Triplet AAC -> AGC



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.

Asn Ser consequences
polar, small, hydrophilic, negatively charged polar, tiny, hydrophilic, neutral Both amino acids are polar and hydrophilic. Ser is tiny, Asn therefore is a small amino acid. The biggest difference between these two amino acid is, that Asn is negatively charged and Ser is neutral. But this is not that big difference and therefore we suggest, that this mutation do not delete the structure and function of the protein.



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 Asparagine has a much smaller chain than Serine. Contrary Serine is longer and comes to a fork at the end of its rest. Furthermore, it is also orientated in a different direction. Otherwise comparing to other mutations this one is not extremly. Therefore, this exchange will probably not cause huge effects on the protein structure and function.

picture original aa picture mutated aa combined picture
Amino acid Asparagine
Amino acid Serine
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
20 36 (Asp) 0 (Cys, Met) 5 7 (Asp) 2 (Cys, Leu, Phe, Trp) 1 1 (Asp, His, Ser) -4 (Trp)

PSSM analysis

self-information expexted self-information
Asn 1 5
Ser 3 24

Conservation Analysis with Multiple Alignments

Mutation in the multiple alignment

Secondary Structure Mutation Analysis

JPred:
CCHHHHHHHHHHHHHCCCCCCCEEEEEEEEEECCCEEEEECCCEEEEECCCCCCC...
PsiPred:
CHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCEEEEECCCEEEEECCCCCCC...

Comparison with the real structure:

Mutation at position 29
Mutation at position 29 - detailed view

SNAP Prediction

Substitution Prediction Reliability Index Expected Accuracy
S Neutral 8 96%

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
29 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
w29N0.78cfMHiYpVgLRNdQTASKE




PolyPhen2 Prediction

HumDiv prediction
HumVar prediction