Difference between revisions of "Structure-based mutation analysis (PKU)"

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(Mutations)
(GLN172HIS)
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=== GLN172HIS ===
 
=== GLN172HIS ===
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<figure id="fig:ARG158GLNmutation">
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[[File:GLN172HISmutation.png|thumb|300px|left|<caption> The bindingsites are colored according to the overview picture above the mutation is colored in red, and the sticks for this residue as well as for the binding residues are shown as well.</caption>]]
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</figure>In <xr id="fig:ARG158GLNmutation" /> one can see the big distance between the binding sites and the mutation location. Since we know that this is harmless, one would tend to say, that its clear, due to the distance, but as we know, that we also have mutations in a big distance which cause the disease, we are bound to say we do not know the mechanism.
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=== ARG243GLN ===
 
=== ARG243GLN ===
 
=== LEU255SER ===
 
=== LEU255SER ===

Revision as of 16:52, 20 June 2012

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="tab:uniprotresult">

Table with results from UNIProt with r-Value inserted
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="tab: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="fig:1J8Uwhole">
Rendering of the overall 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
</figure>
<figure id="fig:1J8Uclose">
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
</figure>

<figure id="fig:structuremoving">

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)

</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 changed them to mutations, which we think are interesting from a structural view. 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
Unknown.jpeg
GLN172HIS non-disease
Unknown.jpeg
ARG243GLN disease causing
Unknown.jpeg
LEU255SER disease causing
Unknown.jpeg
MET276VAL non-disease
Unknown.jpeg
ARG297CYS disease causing
Unknown.jpeg
New.jpeg
ALA322GLY hyperphenylalaninemia
Unknown.jpeg
GLU330ASP disease causing
Unknown.jpeg
New.jpeg
GLY337VAL disease causing
Unknown.jpeg
ARG408TRP disease causing
Unknown.jpeg

ARG158GLN

<figure id="fig:ARG158GLNmutation">

The bindingsites are colored according to the overview picture above the mutation is colored in red, and the sticks for this residue as well as for the binding residues are shown as well.

</figure>This mutation, which is diseasecausing is in a moderate distance to the important binding sites (<xr id="fig:ARG158GLNmutation" />). A clear explanation, why this has an effect on the protein can not be found from the structure alone. But even with the results from last weeks Task, we just had to rely on the clashes which occurred when we estimated the structure.

GLN172HIS

<figure id="fig:ARG158GLNmutation">

The bindingsites are colored according to the overview picture above the mutation is colored in red, and the sticks for this residue as well as for the binding residues are shown as well.

</figure>In <xr id="fig:ARG158GLNmutation" /> one can see the big distance between the binding sites and the mutation location. Since we know that this is harmless, one would tend to say, that its clear, due to the distance, but as we know, that we also have mutations in a big distance which cause the disease, we are bound to say we do not know the mechanism.

ARG243GLN

LEU255SER

MET276VAL

ARG297CYS

ALA322GLY

GLU330AS P

ARG408TRP