Difference between revisions of "Canavan Task 6 - Sequence-based mutation analysis"
(→E285A) |
(→Physico-chemical effects) |
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− | <td style=" |
+ | <td style="border-bottom:solid;border-right:solid" rowspan=2>E285A</td> |
<td style="border-right:solid">Glutamic Acid</td> |
<td style="border-right:solid">Glutamic Acid</td> |
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<td>-3.5 (polar)</td> |
<td>-3.5 (polar)</td> |
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− | <td style=" |
+ | <td style="border-bottom:solid;border-right:solid" rowspan=2>A305E</td> |
<td style="border-right:solid">Alanine</td> |
<td style="border-right:solid">Alanine</td> |
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<td>1.8 (nonpolar)</td> |
<td>1.8 (nonpolar)</td> |
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− | <td style=" |
+ | <td style="border-bottom:solid;border-right:solid" rowspan=2>G123E</td> |
<td style="border-right:solid">Glycine</td> |
<td style="border-right:solid">Glycine</td> |
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<td>-0.4 (nonpolar)</td> |
<td>-0.4 (nonpolar)</td> |
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− | <td style="color:red;border-bottom:solid;border-right:solid" rowspan=2>R71H</td> |
+ | <td style="color:red;border-color:black;border-bottom:solid;border-right:solid" rowspan=2>R71H</td> |
<td style="border-right:solid">Arginine</td> |
<td style="border-right:solid">Arginine</td> |
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<td>-4.5 (polar)</td> |
<td>-4.5 (polar)</td> |
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− | <td style="border-bottom:solid;border-right:solid" rowspan=2>R71K</td> |
+ | <td style="color:red;border-color:black;border-bottom:solid;border-right:solid" rowspan=2>R71K</td> |
<td style="border-right:solid">Arginine</td> |
<td style="border-right:solid">Arginine</td> |
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<td>-4.5 (polar)</td> |
<td>-4.5 (polar)</td> |
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− | <td style="border-bottom:solid;border-right:solid" rowspan=2>K213E</td> |
+ | <td style="color:red;border-color:black;border-bottom:solid;border-right:solid" rowspan=2>K213E</td> |
<td style="border-right:solid">Lysine</td> |
<td style="border-right:solid">Lysine</td> |
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<td>-3.9 (polar)</td> |
<td>-3.9 (polar)</td> |
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− | <td style="border-bottom:solid;border-right:solid" rowspan=2>V278M</td> |
+ | <td style="color:red;border-color:black;border-bottom:solid;border-right:solid" rowspan=2>V278M</td> |
<td style="border-right:solid">Valine</td> |
<td style="border-right:solid">Valine</td> |
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<td>4.2 (nonpolar)</td> |
<td>4.2 (nonpolar)</td> |
Revision as of 15:32, 13 June 2012
Contents
Protocol
Further information can be found in the protocol.
Choosing mutations
mutant | E285A | A305E | G123E | R71H | R71K | K213E | V278M | A93A | T277T | P280P |
known effect | 1% activity in Ashkenazi Jews | 0% activity in non-Ashkenazi | 25% | Canavan Disease | not disease related | Canavan Disease | not disease related | synonymous SNPs - not disease related | synonymous SNPs - not disease related | synonymous SNPs - not disease related |
structural location | helix - binding pocket | loop C-terminus | beta-sheet | active site | active site | loop region | loop region | outer helix | outer loop | outer loop |
Physico-chemical effects
TODO: Valine - Glutamic Acid - small-bulky-issue
mutation | Amino acid | Hydrophobicity (and diff.) | Volume [Å3] (and diff.) | Isoelectric point pI(Charge) | Grantham Score | |||
E285A | Glutamic Acid | -3.5 (polar) | 5.3 | 138.4 (bulky) | 49.8 | 3.2 (negative) | 2.8 | 107 |
Alanine | 1.8 (nonpolar) | 88.6 (tiny) | 6.0 (neutral) | |||||
A305E | Alanine | 1.8 (nonpolar) | 5.3 | 88.6 (tiny) | 49.8 | 6.0 (neutral) | 2.8 | 107 |
Glutamic Acid | -3.5 (polar) | 138.4 (bulky) | 3.2 (negative) | |||||
G123E | Glycine | -0.4 (nonpolar) | 3.1 | 60.1 (tiny) | 78.3 | 6.0 (neutral) | 2.8 | 98 |
Glutamic Acid | -3.5 (polar) | 138.4 (bulky) | 3.2 (negative) | |||||
R71H | Arginine | -4.5 (polar) | 1.3 | 173.4 (bulky) | 20.2 | 10.8 (positive) | 3.2 | 29 |
Histidine | -3.2 (polar) | 153.2 (bulky) | 7.6 (neutral) | |||||
R71K | Arginine | -4.5 (polar) | 0.6 | 173.4 (bulky) | 4.8 | 10.8 (positive) | 1.1 | 26 |
Lysine | -3.9 (polar) | 168.6 (bulky) | 9.7 (positive) | |||||
K213E | Lysine | -3.9 (polar) | 0.4 | 168.6 (bulky) | 30.2 | 9.7 (positive) | 6.5 | 26 |
Glutamic Acid | -3.5 (polar) | 138.4 (bulky) | 3.2 (negative) | |||||
V278M | Valine | 4.2 (nonpolar) | 2.3 | 140.0 (small) | 22.9 | 6.0 (neutral) | 0.3 | 21 |
Methionine | 1.9 (nonpolar) | 162.9 (bulky) | 5.7 (neutral) |
conservative (0-50), moderately conservative (51-100), moderately radical (101-150), or radical (≥151) according to the classification proposed by
E285A
Location
This amino acid is located at the end of helix in the binding pocket. Yet is it not involved in substrate binding. DSSP does not assign a state to E285.
physico-chemical properties
Glutamic acid and Alanine have different physico-chemical properties, which is represented in a moderate Grantham Score of 107. Whereas glutamic acid is negatively charged, alanine has no charge or polarity. Furthermore Alanine is much smaller than glutamic acid.
substitution matrices
In Blosum62 the substitution E --> A is scored -1. The lowest score in Blosum64, that represents a really unlikely mutation event is -4 and the highest score, that represents a likely mutation is 11. This means, that a substitution from E to A is very unlikely.
In PAM1 the substitution E --> A is scored 17 which means a muation probability of 0.17%. The worst score in Blosum62 is 0 for 0% mutation probability and the highest score is 56 for 0.56% mutation probability.
A score in PAM1 expresses how probable a mutation from A to B will be, assuming the two proteins are 99% similar (1% AA mutations in both sequences).
As we are just considering variations of the same protein within a family, this mutation is very unlikely.
PSSM
A305E
G123E
R71H
R71C
K213E
V278M
A93A
T277T
P280P
References
Henikoff, S. & Henikoff, J.G. (1992) "Amino acid substitution matrices from
protein blocks." Proc. Natl. Acad. Sci. USA 89:10915-10919.