Difference between revisions of "Gaucher Disease: Task 08 - Sequence-based mutation analysis"

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Revision as of 16:44, 31 August 2013

LabJournal

Mutation Set

<figtable id="sele">

Mutations
mRNA Protein
Reference Sequence Position Codon change Codon Number Amino Acid change One letter code
rs368786234 656 AGC ⇒ AGA 77 Ser ⇒ Arg S77R
rs374003673 847 AAT ⇒ AGT 141 Asn ⇒ Ser N141S
CM880035 - CGG ⇒ CAG 159 Arg ⇒ Gln R159Q
rs374591570 1062 CTC ⇒ TTC 213 Leu ⇒ Phe L213F
CM992894 - GGA ⇒ GAA 241 Gly ⇒ Glu G241E
rs371083513 1470 GTA ⇒ ATA 349 Val ⇒ Ile V349I
CM960697 - ACG ⇒ ATG 408 Thr ⇒ Met T408M
CM880036 - AAC ⇒ AGC 409 Asn ⇒ Ser N409S
CM870010 - CTG ⇒ CCG 483 Leu ⇒ Pro L483P
CM057072 - AAC ⇒ AGC 501 Asn ⇒ Ser N501S
Information about 10 randomly selected mutations for glucocerebrosidase taken from HGMD (CM...) and dbSNP (rs...).

</figtable>

Mutation Analysis

In our analysis we looked closer to the amino acid properties and their changing characteristics by mutation. We analysed the structural difference between wild type (WT) and mutation. We also considered their secondary structure and distinguished between helix (H), sheet (E) and loop (C). We also took two different substitution matrices into account, BLOSUM62 and PAM250. Point Accepted Mutation matrix has only positiv integer values as scores and is not symmetric. The score reflects the probability of a amino acid to mutate into another. In contrast the BLOcks SUbstitution Matrix has also negativ integers and is symmetric. A positive score indicates that a substitution occurs more than random. While a score of 0 shows that the substitution occurs randomly, a negative one points to a mutation less frequent than a random mutation. In case one of our selected mutations has the worst possible substitution score for this amino acids we highlighted the score red in <xr id="ana"/>. To consider also evolutionary information we created different PSSM matrices. These position specific scoring matrices are based on alignments. Just as BLOSUM, the PSSM has positive and negative integer values as scores. A positve value shows that the substitution occurs more often than expected. Critical functional residues, like active site residues, have high positive scores. One PSSM was created with a PsiBlast search. The other one is based on an alignment consisting of all mammalian homologous sequences.


<figtable id="ana">

Mutation Analysis
Changes of Physiochemical Properties Structural Properties Conservation Interpretation
Mutation From To Pymol Visualization Secondary Structure BLOSUM62 score PAM250 score PSSM score PSSM WT frequency PSSM mutatant frequency MSA WT frequency MSA mutant frequency
S77R polar, neutral charge, sulfur-containing polar, positive, basic
Mutation of serine (blue) to arginine (orange) on position 77.
E -1 6 1 11% 9% 64% 2%
N141S polar, neutral charge, acidic polar, neutral, sulfur-containing
Mutation of asparagine (blue) to serine (orange) on position 141.
H 1 5 0 10% 7% 55% 3%
R159Q polar, positive charge, basic polar, neutral, acidic
Mutation of arginine (blue) to glutamine (orange) on position 159.
E 1 5 -4 83% 0% 86% 0%
L213F nonpolar, neutral charge, aliphatic, hydrophobic nonpolar, neutral, aromatic, hydrophobic
Mutation of leucine (blue) to phenylalanine (orange) on position 213.
E 0 13 3 22% 13% 100% 0%
G241E nonpolar, neutral charge, aliphatic polar, negative, acidic
Mutation of glycine (blue) to glutamic acid (orange) on position 241.
C -2 9 -1 10% 3% 83% 0%
V349I nonpolar, neutral charge, aliphatic, hydrophobic nonpolar, neutral, aliphatic, hydrophobic
Mutation of valine (blue) to isoleucine (orange) on position 349.
E 3 4 0 14% 5% 97% 3%
T408M polar, neutral charge, hydroxyl-containing nonpolar, neutral, sulfur-containing
Mutation of threonine (blue) to methionine (orange) on position 408.
H -1 5 -1 4% 2% 82% 0%
N409S polar, neutral charge, acidic polar, neutral, sulfur-containing
Mutation of asparagine (blue) to serine (orange) on position 409.
H 1 5 1 10% 9% 76% 2%
L483P nonpolar, neutral charge, aliphatic, hydrophobic nonpolar, neutral, cyclic
Mutation of serine (blue) to arginine (orange) on position 483
E -3 5 -3 29% 1% 100% 0%
N501S polar, neutral charge, acidic polar, neutral, sulfur-containing
Mutation of asparagine (blue) to serine (orange) on position 501.
E 1 5 -2 87% 3% 86% 1%
Analysis of the chosen mutations of <xr id="sele"/> in the field of their properties, secondary structure and conservation. The secondary structure can be classified as helix (H), sheet (E) and loop (C). In case a mutations is the worst possible subsitution for this amino acid, the substitution matrix score is coloured red.

</figtable>

Comparison of different approaches

<figtable id="app">

Summary of different prediction approaches
Mutation Analysis of <xr id="ana"/> SIFT Polyphen2 MutationTaster SNAP Validation
S77R 0.46
N141S
R159Q
L213F
G241E
V349I
T408M
N409S
L483P
N501S
Information about selected from different predictors of amino acid substitution effects as well as our own interpretation based on our data of the previous exercises of task8. We divide between three different kind of effects: disease causing, possibly damaging and non-disease causing. The predictions are colored acording to this.

</figtable>

References

http://en.wikipedia.org/wiki/Amino_acid

hgmd

[GENE%20AND%20%22human%22[ORGN]%20AND%20%22snp%22[SNP_CLASS]%20&cmd=DetailsSearch dbSNP]