Difference between revisions of "Rs121907967"

From Bioinformatikpedia
(Visualisation of the Mutation)
(Conservation Analysis with Multiple Alignments)
 
(22 intermediate revisions by 2 users not shown)
Line 1: Line 1:
=== General Information ===
+
== General Information ==
   
 
{| border="1" style="text-align:center; border-spacing:0;"
 
{| border="1" style="text-align:center; border-spacing:0;"
Line 16: Line 16:
 
|}
 
|}
   
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA Sequence-based mutation analysis]]
----
 
  +
  +
== Sequence-based Mutation Analysis ==
   
=== Pysicochemical Properities ===
+
=== Pysicochemical Properties ===
   
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.
+
First of all, we explored the amino acid properties and compared them for the original and the mutated amino acid. Therefore we thought about the possible effects that the mutation could have on the protein.
   
 
{| border="1" style="text-align:center; border-spacing:0;"
 
{| border="1" style="text-align:center; border-spacing:0;"
Line 33: Line 35:
 
|}
 
|}
   
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA Sequence-based mutation analysis]]
 
----
 
----
   
=== Visualisation of the Mutation ===
+
=== Visualization 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.
 
   
  +
In the next step, we created the visualization of the mutation with PyMol. Therefore we created two pictures: one which displays the original amino acid (Figure 1) and one that displays the consequence of the resulting termination (Figure 2). 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 completely other way. Therefore, this mutation will have engraving effects on the protein. The protein will probably loss its whole function and is not usable anymore.
   
 
{| border="1" style="text-align:center; border-spacing:0;"
 
{| border="1" style="text-align:center; border-spacing:0;"
|picture original aa
+
|picture original amino acid
 
|consequence for the whole protein
 
|consequence for the whole protein
 
|-
 
|-
|[[Image:W329.png|thumb|150px|Amino acid Tryptophan]]
+
|[[Image:W329.png|thumb|150px|Figure 1: Amino acid Tryptophan]]
|[[Image:prot_ter.png|thumb|150px|Visualization of the mutated protein]]
+
|[[Image:prot_ter.png|thumb|150px|Figure 2: Visualization of the mutated protein]]
 
|-
 
|-
 
|}
 
|}
   
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA Sequence-based mutation analysis]]
 
----
 
----
   
=== Subsitution Matrices Values ===
+
=== Substitution 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 according amino acid substitution, the most frequent value for the substitution of the examined amino acid and the rarest substitution.
  +
  +
In this case, we get no informations because there is no entry for the substitution of Tryptophan to a stop codon. Therefore we can not say what the possible consequences for the protein are only by looking at the substitution matrices. However, a stop codon will if course always have a drastic effect on the protein and its function.
   
 
{| border="1" style="text-align:center; border-spacing:0;"
 
{| border="1" style="text-align:center; border-spacing:0;"
Line 61: Line 65:
 
|colspan="3" | BLOSOUM 62
 
|colspan="3" | BLOSOUM 62
 
|-
 
|-
|value aa
+
|value amino acid
 
|most frequent substitution
 
|most frequent substitution
 
|rarest substitution
 
|rarest substitution
|value aa
+
|value amino acid
 
|most frequent substitution
 
|most frequent substitution
 
|rarest substitution
 
|rarest substitution
|value aa
+
|value amino acid
 
|most frequent substitution
 
|most frequent substitution
 
|rarest substitution
 
|rarest substitution
Line 83: Line 87:
 
|}
 
|}
   
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA Sequence-based mutation analysis]]
 
----
 
----
   
=== PSSM analysis ===
+
=== PSSM Analysis ===
  +
  +
Besides, we looked additional at the position specific scoring matrix (PSSM) for our sequence. In contrast to PAM and BLOSOUM, the PSSM contains a specific substitution rate for each position in the sequence. Therefore, the PSSM is more position specific than PAM or BLOSOUM. We extracted the substitution value for the underlying mutation, the value for the most frequent substitution and the rarest substitution.
  +
  +
In this case, we got no information because there is no entry for the substitution of Tryptophan to a stop codon. Therefore we can not say what the possible consequences for the protein are by only looking at the substitution matrices. However, a stop codon will if course always have a drastic effect on the protein and its function.
  +
   
 
{| border="1" style="text-align:center; border-spacing:0;"
 
{| border="1" style="text-align:center; border-spacing:0;"
  +
|colspan="3" | PSSM
|
 
|self-information
 
|expected self-information
 
 
|-
 
|-
  +
|value amino acid
|Trp
 
  +
|most frequent substitution
|12
 
  +
|rarest substitution
|78
 
  +
|-
  +
| X
  +
| 12
  +
| -5
 
|-
 
|-
 
|}
 
|}
   
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA Sequence-based mutation analysis]]
 
----
 
----
   
 
=== Conservation Analysis with Multiple Alignments ===
 
=== Conservation Analysis with Multiple Alignments ===
[[Image:mut_6.png|thumb|center|600px|Mutation in the multiple alignment]]
 
   
  +
As a next step we created a multiple alignment which contains the HEXA sequence and 9 other mammalian homologous sequences from [[http://www.uniprot.org 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 on Figure 3.
  +
Here we can see, that all other mammalians have at this position the same amino acid. Therefore, the mutation at this position is highly conserved and in a normal case this would be a indication for structural and functional changes. In this special case it will cause anyway structural and functional changes, because it is a substitution with a stop codon and therefore only a part of the protein will be translated.
  +
  +
[[Image:mut_7.png|thumb|center|600px|Figure 3: Mutation in the multiple alignment]]
  +
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA Sequence-based mutation analysis]]
 
----
 
----
   
 
=== Secondary Structure Mutation Analysis ===
 
=== 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 drastic the mutation can be.
  +
In this case both tools agree and predict at the position of the mutation a coil. This normally has as a result, that the mutation at this position would not destroy or split a secondary structure element which would have no drastic changes for the protein.
  +
In this special case with a substitution to a stop codon there will be anyway structural changes followed by functional loss.
   
 
JPred:
 
JPred:
Line 112: Line 134:
 
...CCCCCCCCC<font color="red">C</font>CCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEECC...
 
...CCCCCCCCC<font color="red">C</font>CCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEECC...
   
Comparison with the real structure:
+
''' Comparison with the real Structure: '''
  +
  +
Afterwards we also visualize the position of the mutation (red) in the real 3D-structure of [[http://www.pdb.org PDB]] and compare it with the predicted secondary structure. The visualization 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 mutation position does not agree with the position of the predicted secondary structure and is within a alpha helix (Figure 4 and Figure 5). Normally, this means that the mutation will probably destroy or split the helix which has structural and functional changes of the protein as result. In this special case with a substitution to a stop codon there will be anyway structural changes followed by functional loose.
  +
 
{|
 
{|
| [[Image:329_mut.png|thumb|250px|Mutation at position 329]]
+
| [[Image:329_mut.png|thumb|250px|Figure 4: Mutation at position 329]]
| [[Image:329_mut_detail.png|thumb|250px|Mutation at position 329 - detailed view]]
+
| [[Image:329_mut_detail.png|thumb|250px|Figure 5: Mutation at position 329 - detailed view]]
 
|}
 
|}
   
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA Sequence-based mutation analysis]]
 
----
 
----
   
 
=== SNAP Prediction ===
 
=== SNAP Prediction ===
   
No prediction available, because the protein ends here.
+
No prediction available, because the protein ends here. However, in this special case with a substitution to a stop codon there will be anyway a drastic protein structure change which is followed by the the functional loose of the protein.
   
 
A detailed list of all possible substitutions can be found [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/rs121907967_SNAP here]]
 
A detailed list of all possible substitutions can be found [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/rs121907967_SNAP here]]
   
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA Sequence-based mutation analysis]]
 
----
 
----
   
Line 131: Line 160:
   
 
SIFT Matrix:<br>
 
SIFT Matrix:<br>
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.
+
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 (Figure 7).
   
 
{|
 
{|
| [[Image:sift_legend.png|center]]
+
| [[Image:sift_legend.png|center|thumb|800px|Figure 6: Legend]]
 
|-
 
|-
| [[Image:329_sift.png.png|center]]
+
| [[Image:329_sift.png.png|center|thumb|800px|Figure 7: Shift Matrix]]
 
|}
 
|}
 
<br><br>
 
<br><br>
   
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA Sequence-based mutation analysis]]
 
----
 
----
   
 
=== PolyPhen2 Prediction ===
 
=== 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 .....
+
In this case the substitution 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 affect a function of the protein hardly and probably the protein is useless afterwards.
  +
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Sequence-based_mutation_analysis_HEXA Sequence-based mutation analysis]]
  +
  +
  +
== Structure-based Mutation Analysis ==
  +
  +
=== Mapping onto Crystal Structure ===
  +
  +
In Figure 8 you can see the mapping of the functional residues onto the crystal structure of the protein.
  +
  +
[[Image:mut329_active.png|thumb|center|400px|Figure 8: Visualization of the mutation and important functional sites<br>Color declaration: <br>
  +
* <font color=red>red</font>: position of mutation<br>
  +
* <font color=magenta >magenta</font>: maintained protein<br>
  +
* <font color=green>green</font>: position of active side<br>
  +
* <font color=yellow>yellow</font>: position of glycolysation<br>
  +
* <font color=cyan>cyan</font>: position of Cysteine]]
  +
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Structure-based_mutation_analysis_HEXA Structure-based mutation analysis]]
  +
----
  +
  +
=== SCWRL Prediction ===
  +
  +
In this case the mutation is from Tryptophan to a stop codon. Therefore, we made no SCREWL prediction, because it is clear that it will cause a damage of the 3D-structure of the protein. Furthermore, it will of course affect a function of the protein hardly and probably the protein is useless afterwards.
  +
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Structure-based_mutation_analysis_HEXA Structure-based mutation analysis]]
  +
----
  +
  +
=== FoldX Energy Comparison ===
  +
  +
It was not possible to calculate the energy of the mutated protein, because the mutation leads to a stop codon in the sequence. Therefore, we know surly, that the protein is damaged, but we can not calculate any energy values for this structure.
  +
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Structure-based_mutation_analysis_HEXA Structure-based mutation analysis]]
  +
----
  +
  +
=== Minimise Energy Comparison ===
  +
  +
It was not possible to calculate the energy of the mutated protein, because the mutation leads to a stop codon in the sequence. Therefore, we know surly, that the protein is damaged, but we can not calculate any energy values for this structure.
  +
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Structure-based_mutation_analysis_HEXA Structure-based mutation analysis]]
  +
----
  +
  +
=== Gromacs Energy Comparison ===
  +
  +
It was not possible to calculate the energy of the mutated protein, because the mutation leads to a stop codon in the sequence. Therefore, we know surly, that the protein is damaged, but we can not calculate any energy values for this structure.
  +
  +
Back to [[http://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php/Structure-based_mutation_analysis_HEXA Structure-based mutation analysis]]
  +
----

Latest revision as of 18:14, 31 August 2011

General Information

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

Back to [Sequence-based mutation analysis]

Sequence-based Mutation Analysis

Pysicochemical Properties

First of all, we explored the amino acid properties and compared them for the original and the mutated amino acid. Therefore we thought about the possible effects 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.

Back to [Sequence-based mutation analysis]


Visualization of the Mutation

In the next step, we created the visualization of the mutation with PyMol. Therefore we created two pictures: one which displays the original amino acid (Figure 1) and one that displays the consequence of the resulting termination (Figure 2). 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 completely other way. Therefore, this mutation will have engraving effects on the protein. The protein will probably loss its whole function and is not usable anymore.

picture original amino acid consequence for the whole protein
Figure 1: Amino acid Tryptophan
Figure 2: Visualization of the mutated protein

Back to [Sequence-based mutation analysis]


Substitution 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 according amino acid substitution, the most frequent value for the substitution of the examined amino acid and the rarest substitution.

In this case, we get no informations because there is no entry for the substitution of Tryptophan to a stop codon. Therefore we can not say what the possible consequences for the protein are only by looking at the substitution matrices. However, a stop codon will if course always have a drastic effect on the protein and its function.

PAM 1 Pam 250 BLOSOUM 62
value amino acid most frequent substitution rarest substitution value amino acid most frequent substitution rarest substitution value amino acid 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)

Back to [Sequence-based mutation analysis]


PSSM Analysis

Besides, we looked additional at the position specific scoring matrix (PSSM) for our sequence. In contrast to PAM and BLOSOUM, the PSSM contains a specific substitution rate for each position in the sequence. Therefore, the PSSM is more position specific than PAM or BLOSOUM. We extracted the substitution value for the underlying mutation, the value for the most frequent substitution and the rarest substitution.

In this case, we got no information because there is no entry for the substitution of Tryptophan to a stop codon. Therefore we can not say what the possible consequences for the protein are by only looking at the substitution matrices. However, a stop codon will if course always have a drastic effect on the protein and its function.


PSSM
value amino acid most frequent substitution rarest substitution
X 12 -5

Back to [Sequence-based mutation analysis]


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 on Figure 3. Here we can see, that all other mammalians have at this position the same amino acid. Therefore, the mutation at this position is highly conserved and in a normal case this would be a indication for structural and functional changes. In this special case it will cause anyway structural and functional changes, because it is a substitution with a stop codon and therefore only a part of the protein will be translated.

Figure 3: Mutation in the multiple alignment

Back to [Sequence-based mutation analysis]


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 drastic the mutation can be. In this case both tools agree and predict at the position of the mutation a coil. This normally has as a result, that the mutation at this position would not destroy or split a secondary structure element which would have no drastic changes for the protein. In this special case with a substitution to a stop codon there will be anyway structural changes followed by functional loss.

JPred:
...CCCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEECC...
PsiPred:
...CCCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEECC...

Comparison with the real Structure:

Afterwards we also visualize the position of the mutation (red) in the real 3D-structure of [PDB] and compare it with the predicted secondary structure. The visualization 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 mutation position does not agree with the position of the predicted secondary structure and is within a alpha helix (Figure 4 and Figure 5). Normally, this means that the mutation will probably destroy or split the helix which has structural and functional changes of the protein as result. In this special case with a substitution to a stop codon there will be anyway structural changes followed by functional loose.

Figure 4: Mutation at position 329
Figure 5: Mutation at position 329 - detailed view

Back to [Sequence-based mutation analysis]


SNAP Prediction

No prediction available, because the protein ends here. However, in this special case with a substitution to a stop codon there will be anyway a drastic protein structure change which is followed by the the functional loose of the protein.

A detailed list of all possible substitutions can be found [here]

Back to [Sequence-based mutation analysis]


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 (Figure 7).

Figure 6: Legend
Figure 7: Shift Matrix



Back to [Sequence-based mutation analysis]


PolyPhen2 Prediction

In this case the substitution 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 affect a function of the protein hardly and probably the protein is useless afterwards.

Back to [Sequence-based mutation analysis]


Structure-based Mutation Analysis

Mapping onto Crystal Structure

In Figure 8 you can see the mapping of the functional residues onto the crystal structure of the protein.

Figure 8: Visualization of the mutation and important functional sites
Color declaration:
* red: position of mutation
* magenta: maintained protein
* green: position of active side
* yellow: position of glycolysation
* cyan: position of Cysteine

Back to [Structure-based mutation analysis]


SCWRL Prediction

In this case the mutation is from Tryptophan to a stop codon. Therefore, we made no SCREWL prediction, because it is clear that it will cause a damage of the 3D-structure of the protein. Furthermore, it will of course affect a function of the protein hardly and probably the protein is useless afterwards.

Back to [Structure-based mutation analysis]


FoldX Energy Comparison

It was not possible to calculate the energy of the mutated protein, because the mutation leads to a stop codon in the sequence. Therefore, we know surly, that the protein is damaged, but we can not calculate any energy values for this structure.

Back to [Structure-based mutation analysis]


Minimise Energy Comparison

It was not possible to calculate the energy of the mutated protein, because the mutation leads to a stop codon in the sequence. Therefore, we know surly, that the protein is damaged, but we can not calculate any energy values for this structure.

Back to [Structure-based mutation analysis]


Gromacs Energy Comparison

It was not possible to calculate the energy of the mutated protein, because the mutation leads to a stop codon in the sequence. Therefore, we know surly, that the protein is damaged, but we can not calculate any energy values for this structure.

Back to [Structure-based mutation analysis]