From Bioinformatikpedia
Revision as of 13:56, 26 June 2011 by Uskat (talk | contribs) (PolyPhen2 Prediction)

General Information

SNP-id rs1054374
Codon 293
Mutation Codon Ser -> Ile
Mutation Triplet AGT -> ATT

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.

Ser Ile consequences
polar, tiny, hydrophilic, neutral aliphatic, hydrophobic, neutra Ile is much bigger than Ser and also is branched, because it is an aliphatic amino acid. Therefore the structure of both amino acids is really different and Ile is to big for the position where Ser was. Therefore, there has to be a big change in the 3D structure of the protein and the protein probably will loose its 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 that the original amino acid Serine looks different to Isoleucine. Serine is very small whereas Isoleucine is bigger and has two spreadin chains. The first part of the rest agrees in both amino acids. In this case the difference is not so heavy, but can also cause some structural changes which can have affects on the protein function. All in all, the mutation will probably have no structural or functional changes.

picture original aa picture mutated aa combined picture
Amino acid Serine
Amino acid Isoleucine
Picture which visualize the mutation

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, the substitution of Serine to Isoleucine acid has very low value that is nearer to the values for the rarest subsitution for PAM1. Contrary, for PAM250 the value for the amino acid subsitution Histidine to Aspartic acid is average. This means the most frequent subsitution value is almost as far as the rarerest subsitution from the the underlying value. The difference between the two PAMs can be ascribed to the different preparations of these two kind of substitutions matrices. For the PAM1-matrice the substitution rate is 1% which means the prabability that one amino acid changes is 1% and that there is 99% similarity. Contrary, PAM250 means that 250 mutations have been fixed per 100 residues which has as result only similarity about 20%. A possible reason that PAM250 has a better value for the amino acid substitution is that the similarity is low and the amino acids are probably dissimilar. BLOSOUM62 has like PAM1 for this substitution a very low value that is nearer to the values for the rarest subsitution. Therefore, according to PAM1 and BLOSOUM62 a mutation at this position will almost certainly cause structural changes which can affect functional changes. The value from PAM250 is not realy significant and therefore we are not able to determine effects on the protein.

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
2 38 (Thr) 1 (Leu) 5 9 (Ala, Gly, Pro, Thr) 3 (Phe) -2 1 (Ala, Asn, Thr) -3 (Trp)

PSSM analysis

self-information expected self-information
Ser 1 10
Ile 1 7

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 the many other mammalians have on this position another amino acid. Only four other mammalian agrees and have at this position a Serine. Therefore, the mutation on this position is not highly conserved and a mutation there will cause probably no structural and functional changes for the protein.

Mutation in the multiple alignment

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 has a result, that the mutation at this position would not destroy or split a secondary structure element. It will probably only changes the coil between two secondary structure elements, but this can sometimes also cause a change of the the following secondary structure. We think that a drastical change of the protein structure and its function is unlikly because the mutation does not affect a secondary struture element. The change of the coil will probably only take places between two secondary structure elements which will probably not changes the protein.


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 almost agree with the position of the predicted secondary structure and is within a coil. Like explained above this means a mutation will probably not destroy a secondary structure element which affects no drastical structural change. Otherwise it can cause a change of the position of the two nearest secondary structure element which can has a functional loose as a consequence. We think that a structural change is unlikely, because it is not within a secondary structure element and will therefore not cause extrem changes of the protein.

Mutation at position 293
Mutation at position 293 - detailed view

SNAP Prediction

Next, we looked at the result of the SNAP prediction. For this prediction we took the amino acid of the certain position and checked every possible amino acid mutation. Afterwards we extract the result for Isoleucine which is the real mutation in this case. SNAP has a result that the exhange from Serine to Isoleucine at this position is neutral with a relative high accuracy. This means that this certain mutation on this position cause very likely no structural and functional changes of the protein.

Substitution Prediction Reliability Index Expected Accuracy
I Neutral 2 69%

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
293 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

PolyPhen2 Prediction

Finally, we also regarded the PolyPhen2 prediction for this muation. This prediction visualizes have strongly demaging the mutation probably will be. Therefore it gives the result for two possible cases: HumDiv and HumVar. HumDiv is a prefered model for evaluation rare allels, dense mapping of regions identified by genome-wide assiociation studies and analysis of neutral selection. In contrast, HumVar is a prefered model for diagnostic of Mendelian diseases which require distinguishing mutations with drastic effects from all remaining human variations including abundant mildly deleterious allels. We decided to look at both possible models, which are agrees in the most cases.

In this case both models predict that the mutation is benign. This means that the mutation is neutral and will probably not damage the structure and the function of the protein.

HumDiv prediction
HumVar prediction