Difference between revisions of "Structure-based mutation analysis (PKU)"
|Line 261:||Line 261:|
== SCWRL ==
== SCWRL ==
=== preparations ===
We use the [[repairPDB]] script to extract the sequence from our model file. Afterwards we do some bashing to get the sequence in small letters but for the mutation, which is in capital.
$ repairPDB 1J8U.pdb -seq > 1J8U.seq
$ tr '[:upper:]' '[:lower:]' < 1J8U.seq > lower18JU.seq
Revision as of 11:29, 21 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">
</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.
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.
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.
</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.
</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.
</figure>This is the second mutation of this kind, which means a change from arginine to glycine. As the other mutation, this one is disease causing. But in difference to the other case, this one is rather close to the binding areas (see <xr id="fig:ARG243GLNmutation" /> )
</figure>When one compares this mutation ( in <xr id="fig:LEU255SERmutation" />) to the reference structure in <xr id="fig:structuremoving" /> one can see, that one of the yellow residues (BH4 binding site) is mutated. And as one would expect this mutation is harmful.
We use the repairPDB script to extract the sequence from our model file. Afterwards we do some bashing to get the sequence in small letters but for the mutation, which is in capital. <source lang="bash"> $ repairPDB 1J8U.pdb -seq > 1J8U.seq $ tr '[:upper:]' '[:lower:]' < 1J8U.seq > lower18JU.seq