Difference between revisions of "Sequence-based mutation analysis HEXA"

From Bioinformatikpedia
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(rs1054374: Ser -> Ile)
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'''Conservation analysis with multiple alignments'''
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[[Image:mut_6.png|thumb|center|600px|Mutation in the multiple alignment]]
   
 
===rs121907967: Trp -> TER ===
 
===rs121907967: Trp -> TER ===

Revision as of 12:14, 23 June 2011

Mutations

SNP-id codon number mutation codon mutation triplet
rs4777505 29 Asn -> Ser AAC -> AGC
rs121907979 39 Leu -> Arg CTT -> CGT
rs61731240 179 His -> Asp CAT -> GAT
rs121907974 211 Phe -> Ser TTC -> TCC
rs61747114 248 Leu -> Phe CTT -> TTT
rs1054374 293 Ser -> Ile AGT -> ATT
rs121907967 329 Trp -> TER TGG -> TAG
rs1800430 399 Asn -> Asp AAC -> GAC
rs121907982 436 Ile -> Val ATA -> GTA
rs121907968 485 Trp -> Arg gTGG -> CGG

Analysis of the mutations

rs4777505: Asn -> Ser

pysicochemical properities

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

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)

Conservation analysis with multiple alignments

Mutation in the multiple alignment

rs121907979: Leu -> Arg

pysicochemical properities

Leu Arg consequences
aliphatic, hydrophobic, neutral positive charged, polar, hydrophilic Leucine is smaller and without a positive charge. Therefore, Arg is too big for the position of Leu, therefore, the change of Leu with Arg has to cause changes in the 3D structure of the protein. Furthermore, Leu is a hydrophobic amino acid, whereas Arg is hydrophilic. This is the complete contrary and therefore we suggest, that the protein will not function any longer.

Visualisation of the mutation

picture original aa picture mutated aa combined picture
Amino acid Leucine
Amino acid Arginine
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
1 22 (Ile) 0 (Asp, Cys) 4 20 (Met) 2 (Cys) -2 0 (Phe) -4 (Asp, Gly)

Conservation analysis with multiple alignments

Mutation in the multiple alignment

rs61731240: His -> Asp

pysicochemical properities

His Asp consequences
aromatic, positive charged, polar, hydrophilic negative charged, small, polar, hydrophilic On the one side, both amino acids are polar, but on the other side, His is positively charged, while Asp is negatively charged, which is an essential difference between these both amino acids. Therefore it is very likely, that this change causes big changes in the structure of the protein and the protein therefore will probably not work any longer. Furthermore, the structure of the two amino acids is very different, because of the aromatic ring of the His.

Visualisation of the mutation

picture original aa picture mutated aa combined picture
Amino acid Histidine
Amino acid Aspartate
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
3 20 (Gln) 0 (Ile, Met) 4 7 (Gln) 2 (Ala, Cys, Gly, Ile, Leu, Met, Phe, Thr, Trp, Val) -1 2 (Tyr) -3 (Cys, Ile, Leu, Val)

Conservation analysis with multiple alignments

Mutation in the multiple alignment

rs121907974: Phe -> Ser

pysicochemical properities

Phe Ser consequences
polar, tiny, hydrophilic, neutral aliphatic, hydrophobic, neutral 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

picture original aa picture mutated aa combined picture
Amino acid Phenylalanine
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
2 28 (Tyr) 0 (Asp, Cys, Glu, Lys, Pro, Val) 2 20 (Tyr) 1 (Arg, Asp, Cys, Gln, Glu, Gly, Lys, Pro) -2 3 (Tyr) -4 (Pro)

Conservation analysis with multiple alignments

Mutation in the multiple alignment

rs61747114: Leu -> Phe

pysicochemical properities

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

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)

Conservation analysis with multiple alignments

Mutation in the multiple alignment

rs1054374: Ser -> Ile

pysicochemical properities

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

picture original aa picture mutated aa combined picture
Amino acid Serine
Amino acid Isoleucine
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
2 38 (Thr) 1 (Leu) 5 9 (Ala, Gly, Pro, Thr) 3 (Phe) -2 1 (Ala, Asn, Thr) -3 (Trp)

Conservation analysis with multiple alignments

Mutation in the multiple alignment

rs121907967: Trp -> TER

pysicochemical properities

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.


Visualisation of the mutation

picture original aa picture mutated aa combined picture
Amino acid Tryptophan
Visualization of the mutated protein

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
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)


rs1800430: Asn -> Asp

pysicochemical properities

Asn Asp consequences
polar, small, hydrophilic, negatively charged polar, small, hydrophilic, negatively charged Both amino acids have the same properities and therefore we suggest that an exchange of these two amino acids do not destroy the protein structure and function

Visualisation of the mutation

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


rs121907982: Ile -> Val

pysicochemical properities

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

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)


rs121907968: Trp -> Arg

pysicochemical properities

Trp Arg consequences
aromatic, polar, hydrophobic, neutral positive charged, polar, hydrophilic Trp is very big, because of two aromatic rings in its structure. Furthermore, it is hydrophobic, whereas, Arg is a hydrophilic amino acid. Therefore, the changes in the 3D structure might be extreme and delete the function of the protein.

Visualisation of the mutation

picture original aa picture mutated aa combined picture
Amino acid Tryptophan
Amino acid Arginine
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
2 2 (Arg) 0 (all, except Arg, Phe, Ser, Tyr) 2 2 (Arg) 0 (all, except Arg, His, Leu, Phe, Ser, Tyr) -3 2 (Tyr) -4 (Asn, Asp, Pro)

Summary page

[Here] you can find all results of the different analysis in one table.