Difference between revisions of "Task 4: Homology based structure predictions"

From Bioinformatikpedia
(Overview of available homologous structures)
(Calculation of models)
Line 16: Line 16:
 
We received the following hits:
 
We received the following hits:
   
  +
{| border="1"
// INSERT TABLE
 
  +
|-
  +
| 1
  +
| 1phz_A
  +
| Protein (phenylalanine
  +
| 1
  +
| 1
  +
| 1
  +
| 1084.4
  +
| 0
  +
| 429
  +
| 1-429
  +
| 1-429
  +
| (429)
  +
|-
  +
| 2
  +
| 1j8u_A
  +
| Phenylalanine-4-hydroxy
  +
| 1
  +
| 1
  +
| 1
  +
| 894.5
  +
| 0
  +
| 325
  +
| 103-427
  +
| 1-325
  +
| (325)
  +
|-
  +
| 3
  +
| 1toh_A
  +
| Tyroh tyrosine hydroxy
  +
| 1
  +
| 1
  +
| 1
  +
| 890.7
  +
| 0
  +
| 342
  +
| 111-452
  +
| 2-343
  +
| (343)
  +
|-
  +
| 4
  +
| 1mlw_A
  +
| Tryptophan 5-monooxygen
  +
| 1
  +
| 1
  +
| 1
  +
| 804.2
  +
| 0
  +
| 300
  +
| 116-415
  +
| 2-301
  +
| (301)
  +
|-
  +
| 5
  +
| 1ltz_A
  +
| Phenylalanine-4-hydroxy
  +
| 1
  +
| 1
  +
| 1
  +
| 504.9
  +
| 0
  +
| 265
  +
| 144-414
  +
| 2-269
  +
| (297)
  +
|-
  +
| 6
  +
| 2v27_A
  +
| Phenylalanine hydroxyla
  +
| 1
  +
| 1
  +
| 1
  +
| 471.1
  +
| 0
  +
| 254
  +
| 167-424
  +
| 4-271
  +
| (275)
  +
|-
  +
| 7
  +
| 2qmx_A
  +
| Prephenate dehydratase;
  +
| 1
  +
| 1
  +
| 1
  +
| 70.0
  +
| 0
  +
| 53
  +
| 33-85
  +
| 199-251
  +
| (283)
  +
|-
  +
| 8
  +
| 2qmw_A
  +
| PDT prephenate dehydra
  +
| 1
  +
| 1
  +
| 1
  +
| 66.1
  +
| 0
  +
| 51
  +
| 35-85
  +
| 190-240
  +
| (267)
  +
|-
  +
| 9
  +
| 3luy_A
  +
| Probable chorismate mut
  +
| 1
  +
| 1
  +
| 1
  +
| 66.0
  +
| 0
  +
| 53
  +
| 33-85
  +
| 207-259
  +
| (329)
  +
|-
  +
| 10
  +
| 1y7p_A
  +
| Hypothetical protein AF
  +
| 1
  +
| 1
  +
| 1
  +
| 19.9
  +
| 0
  +
| 38
  +
| 36-73
  +
| 6-43
  +
| (223)
  +
|}
  +
   
   

Revision as of 18:22, 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:

1 1phz_A Protein (phenylalanine 1 1 1 1084.4 0 429 1-429 1-429 (429)
2 1j8u_A Phenylalanine-4-hydroxy 1 1 1 894.5 0 325 103-427 1-325 (325)
3 1toh_A Tyroh tyrosine hydroxy 1 1 1 890.7 0 342 111-452 2-343 (343)
4 1mlw_A Tryptophan 5-monooxygen 1 1 1 804.2 0 300 116-415 2-301 (301)
5 1ltz_A Phenylalanine-4-hydroxy 1 1 1 504.9 0 265 144-414 2-269 (297)
6 2v27_A Phenylalanine hydroxyla 1 1 1 471.1 0 254 167-424 4-271 (275)
7 2qmx_A Prephenate dehydratase; 1 1 1 70.0 0 53 33-85 199-251 (283)
8 2qmw_A PDT prephenate dehydra 1 1 1 66.1 0 51 35-85 190-240 (267)
9 3luy_A Probable chorismate mut 1 1 1 66.0 0 53 33-85 207-259 (329)
10 1y7p_A Hypothetical protein AF 1 1 1 19.9 0 38 36-73 6-43 (223)


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.

Numeric evaluation of the calculated models

Modeller

Swissmodel

iTasser

Comparison to experimental structure

Modeller

Swissmodel

iTasser

Discussion