Difference between revisions of "Structure-based mutation analysis (PKU)"
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<figure id="1J8Uclose">[[File:1J8Usitesclose.png|500px|thumb|left|<caption>Rendering of a close-up of the structures of 1J8U using PyMol. The protein is colored cyan overall, whereas the Fe-atom is colored red and the important residues are shown as sticks and colored in the element-based fashion. Binding is shown with yellow strokes, if the distance is bigger than 1.5 Å</caption>]] </figure> |
<figure id="1J8Uclose">[[File:1J8Usitesclose.png|500px|thumb|left|<caption>Rendering of a close-up of the structures of 1J8U using PyMol. The protein is colored cyan overall, whereas the Fe-atom is colored red and the important residues are shown as sticks and colored in the element-based fashion. Binding is shown with yellow strokes, if the distance is bigger than 1.5 Å</caption>]] </figure> |
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+ | <figure id="structuremoving"> |
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+ | [[File:1J8Umoving.gif|frame|center|<caption>Structure of 1J8U with both ligands Iron (red) and BH4 (element coded color) with their binding sites orange and yellow respectively. BH4-binding sites are van-der-Waal's based and hydrogen bond based, whereas iron is covalently bound (orange) <caption>]] |
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+ | </figure> |
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== Mutations == |
== Mutations == |
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As you probably know from [[Predicting_the_Effect_of_SNPs_(PKU)#Our dataset|last weeks dataset]] the first two mutations are located before residue 103 and therefore not contained in the structure. We will change them according to the premise, that the number of diseasecausing and non-diseasecausing mutations are equal.<br> |
As you probably know from [[Predicting_the_Effect_of_SNPs_(PKU)#Our dataset|last weeks dataset]] the first two mutations are located before residue 103 and therefore not contained in the structure. We will change them according to the premise, that the number of diseasecausing and non-diseasecausing mutations are equal.<br> |
Revision as of 14:22, 20 June 2012
Contents
Short task description
This week, we will introduce mutations in the known tertiary structure of our protein and calculate and compare the potential energy of mutant and wildtype protein with different methods. See the complete task description for details. Our journal might be found here at some time.
Finding the right structure
As proposed we searched the UNIProt entry for our protein and then selected the entry with the highest resolution and the lowest r-Value. In our case this is 1J8U which is the protein in a complex with its cosubstrate BH4. IN the following we will only use this structure, but we also list the results we found. <figtable id="uniprotresult">
Entry | Method | Resolution (Å) | r-Value | Chain | Positions | PDBsum |
---|---|---|---|---|---|---|
1DMW | X-ray | 2.00 | 0.200 | A | 118-424 | [»] |
1J8T | X-ray | 1.70 | 0.197 | A | 103-427 | [»] |
1J8U | X-ray | 1.50 | 0.157 | A | 103-427 | [»] |
1KW0 | X-ray | 2.50 | 0.220 | A | 103-427 | [»] |
1LRM | X-ray | 2.10 | 0.211 | A | 103-427 | [»] |
1MMK | X-ray | 2.00 | 0.199 | A | 103-427 | [»] |
1MMT | X-ray | 2.00 | 0.213 | A | 103-427 | [»] |
1PAH | X-ray | 2.00 | 0.176 | A | 117-424 | [»] |
1TDW | X-ray | 2.10 | 0.206 | A | 117-424 | [»] |
1TG2 | X-ray | 2.20 | 0.213 | A | 117-424 | [»] |
2PAH | X-ray | 3.10 | 0.251 | A/B | 118-452 | [»] |
3PAH | X-ray | 2.00 | 0.175 | A | 117-424 | [»] |
4ANP | X-ray | 2.11 | 0.204 | A | 104-427 | [»] |
4PAH | X-ray | 2.00 | 0.169 | A | 117-424 | [»] |
5PAH | X-ray | 2.10 | 0.163 | A | 117-424 | [»] |
6PAH | X-ray | 2.15 | 0.171 | A | 117-424 | [»] |
</figtable> In <xr id="uniprotresult"/> there are all results according to which we selected 1J8U to be our reference for this weeks task. The corresponding line is marked in yellow.
1J8U
In order to know the structure of the protein and its important residues, we have a look at its structure with PyMol and visualize the BH4 and the Fe-ion with the most important residues.
<figure id="structuremoving">
</figure>
Mutations
As you probably know from last weeks dataset the first two mutations are located before residue 103 and therefore not contained in the structure. We will change them according to the premise, that the number of diseasecausing and non-diseasecausing mutations are equal.
We propose the following dataset, chosen mostly from well known SNPs from OMIM. They include mutations causing no reported effect, the mild related hyperphenylalaninemia (reduced activity, but functional enzyme) and phenylketonuria.
SNP | effect | prediction | validation | |
---|---|---|---|---|
ARG158GLN | disease causing | |||
GLN172HIS | non-disease | |||
ARG243GLN | disease causing | |||
LEU255SER | disease causing | |||
MET276VAL | non-disease | |||
ARG297CYS | disease causing | |||
ALA322GLY | hyperphenylalaninemia | |||
GLU330ASP | disease causing | |||
GLY337VAL | disease causing | |||
ARG408TRP | disease causing |