Difference between revisions of "Task 4: Homology based structure predictions"
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| + | ! Template HMM |
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| + | ! Residues |
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| + | ! Sequence Identity |
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Revision as of 19:25, 2 June 2011
Task description
The full description of this task can be found here.
Calculation of models
Overview of available homologous structures
Search
We used hhsearch with the standard parameter to find homologous structures of our protein. The following command was executed:
- ./hhsearch -i reference_pah_aa.fasta -d pdb70.db -b 500 -o hhsearch.out
We received the following hits:
| No. | PDB ID | Description | Prob | E-Value | P-Value | Score | SS | Cols | Query HMM | Template HMM | Residues | Sequence Identity |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 1phz_A | Protein (phenylalanine | 1 | 1 | 1 | 1084.4 | 0 | 429 | 1-429 | 1-429 | (429) | 92% |
| 2 | 1j8u_A | Phenylalanine-4-hydroxy | 1 | 1 | 1 | 894.5 | 0 | 325 | 103-427 | 1-325 | (325) | 100% |
| 3 | 1toh_A | Tyroh tyrosine hydroxy | 1 | 1 | 1 | 890.7 | 0 | 342 | 111-452 | 2-343 | (343) | 60% |
| 4 | 1mlw_A | Tryptophan 5-monooxygen | 1 | 1 | 1 | 804.2 | 0 | 300 | 116-415 | 2-301 | (301) | 66% |
| 5 | 1ltz_A | Phenylalanine-4-hydroxy | 1 | 1 | 1 | 504.9 | 0 | 265 | 144-414 | 2-269 | (297) | 30% |
| 6 | 2v27_A | Phenylalanine hydroxyla | 1 | 1 | 1 | 471.1 | 0 | 254 | 167-424 | 4-271 | (275) | 30% |
| 7 | 2qmx_A | Prephenate dehydratase; | 1 | 1 | 1 | 70.0 | 0 | 53 | 33-85 | 199-251 | (283) | 40% |
| 8 | 2qmw_A | PDT prephenate dehydra | 1 | 1 | 1 | 66.1 | 0 | 51 | 35-85 | 190-240 | (267) | 37% |
| 9 | 3luy_A | Probable chorismate mut | 1 | 1 | 1 | 66.0 | 0 | 53 | 33-85 | 207-259 | (329) | 28% |
| 10 | 1y7p_A | Hypothetical protein AF | 1 | 1 | 1 | 19.9 | 0 | 38 | 36-73 | 6-43 | (223) | 16% |
Template structure selection
Homology modelling with Modeller
Homology modelling with Swissmodel
Homology modelling with iTasser
Evaluation of the calculated models
Selection of the reference structures
We had the following choice of reference structures for PAH:
| Entry | Method | Resolution (A) | Chain | Positions |
|---|---|---|---|---|
| 1DMW | X-Ray | 2.00 | A | 118-424 |
| 1J8T | X-Ray | 1.70 | A | 103-427 |
| 1J8U | X-Ray | 1.50 | A | 103-427 |
| 1KW0 | X-Ray | 2.50 | A | 103-427 |
| 1LRM | X-Ray | 2.10 | A | 103-427 |
| 1MMK | X-Ray | 2.00 | A | 103-427 |
| 1MMT | X-Ray | 2.00 | A | 103-427 |
| 1PAH | X-Ray | 2.00 | A | 117-424 |
| 1TDW | X-Ray | 2.10 | A | 117-424 |
| 1TG2 | X-Ray | 2.20 | A | 117-424 |
| 2PAH | X-Ray | 3.10 | A/B | 118-452 |
| 3PAH | X-Ray | 2.00 | A | 117-424 |
| 4PAH | X-Ray | 2.00 | A | 117-424 |
| 5PAH | X-Ray | 2.10 | A | 117-424 |
| 6PAH | X-Ray | 2.15 | A | 117-424 |
All these structures have in common that they did not solve the structure of the whole PAH protein. In addition, there is no complete true apo structure available either. All structures have at least a Fe2+ atom bound. So we defined these structures as our apo structure.
Finally, we decided to select 1J8T (apo) and 1J8U (complexed). As mentioned before our apo structure has complexed Fe2+ and our complexed structure is complexed with Fe2+ and BH4 (5,6,7,8-TETRAHYDROBIOPTERIN). The reason for our decision was that both structures are solved from the same group which somehow guaranties a more consistent methodology as if we had selected structures from two different groups. Another reason is the resolution, both structures are the two with the best resolved resolution which is 1.5 Angstrom and 1.7 Angstrom for 1J8U and 1J8T respectively. Finally for more easy comparison, both structures include the same range of amino acids which is from 103 to 427.
