Homology based structure predictions BCKDHA
Contents
1.Calculation of models
To find similar structures to BCKDHA we ran HHsearch:
hhsearch -i query -d database -o output
It found the following 10 hits in the pdb70 database.
| No | Hit | Prob | E-value | P-value | Score | SS | Cols | Query HMM | Template HMM | Identity |
|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 2bfd_A 2-oxoisovalerate dehydr | 1.0 | 1 | 1 | 791.3 | 0.0 | 400 | 1-400 | 1-400 (400) | 99% |
| 2 | 1qs0_A 2-oxoisovalerate dehydr | 1.0 | 1 | 1 | 571.5 | 0.0 | 349 | 32-382 | 52-407 (407) | 39% |
| 3 | 1w85_A Pyruvate dehydrogenase | 1.0 | 1 | 1 | 530.8 | 0.0 | 356 | 8-382 | 6-362 (368) | 34% |
| 4 | 1umd_A E1-alpha, 2-OXO acid de | 1.0 | 1 | 1 | 521.8 | 0.0 | 351 | 34-386 | 16-367 (367) | 37% |
| 5 | 2ozl_A PDHE1-A type I, pyruvat | 1.0 | 1 | 1 | 482.7 | 0.0 | 331 | 46-380 | 25-356 (365) | 27% |
| 6 | 3l84_A Transketolase; TKT, str | 1.0 | 1 | 1 | 85.4 | 0.0 | 133 | 161-297 | 113-252 (632) | 21% |
| 7 | 2r8o_A Transketolase 1, TK 1; | 1.0 | 1 | 1 | 74.5 | 0.0 | 121 | 161-285 | 113-245 (669) | 33% |
| 8 | 2o1x_A 1-deoxy-D-xylulose-5-ph | 1.0 | 1 | 1 | 74.2 | 0.0 | 127 | 161-287 | 122-254 (629) | 18% |
| 9 | 1gpu_A Transketolase; transfer | 1.0 | 1 | 1 | 74.2 | 0.0 | 140 | 161-302 | 115-265 (680) | 22% |
| 10 | 3m49_A Transketolase; alpha-be | 1.0 | 1 | 1 | 68.8 | 0.0 | 121 | 161-285 | 139-271 (690) | 31% |
> 60% sequence identity:
-2bfd_A
> 40% sequence identity:
< 40% sequence identity (ideally go towards 20%) :
-1qs0_A, 1umd_A, 1w85_A, 2r8o_A, 3m49_A, 2ozl_A, 1gpu_A, 3l84_A, 2o1x_A, -1w85_A
HHSearch has only hits with an identity higher than 60% or lower than 40%.
These are the templates we will work with:
> 60% sequence identity:
-2bfd_A
< 40% sequence identity (ideally go towards 20%) :
-2r8o_A
Modeller
MODELLER is used for homology or comparative modeling of protein three-dimensional structures.It calculates a model containing all non-hydrogen atoms. There are also many other tasks provided by MODELLER like de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc.[1]
A tutorial is provided on [2] and on [3]
To run modeller with more than one target we use the targets:
-1DTW:A 95%
-2BFE:A 94%
-2BFB:A 99%
-2bfd:A 99%
-3m49:A 31%
-1gpu:A 22%
-2o1x:A 18%
SWISS-MODEL
To find protein structure homology models SWISS-MODEL can be used. As input it needs a protein sequence or a UniProt AC Code. Optional the template PDB-Id and the chain or a template file can be assigned.
SWISS-MODEL is a fully automated protein structure homology-modeling server. It is accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer).
SWISS-MODEL
SWISS-MODEL server:
| ID | link |
|---|---|
| 2bfd_A | 2bfd_A |
| 2r8o_A | 2r8o_A |
iTasser
| 2bfd_A |
| 2bfd_A |
Prediction for 2bfd_A
This prediction is based on several templates fount by iTasser itself.
2.Evaluation of models
As we want to compare the predicted models to the existing PDB entry we need the PDB file for 1U5B. Here only chain A is important, as the sequence for chain A was used to create the models. Therefore chain B has to be removed from the PDB file. Herefore we used a program names ExtractChains.pl provided by <ref>http://www.rosettacommons.org/guide/PDB+Manipulation+Scripts</ref>.
Swissmodel
Numeric evaluation
QMEAN4 global scores
QMEANscore4
| 2bfd_A | 2r8o_A |
|---|---|
| 0.67 | 0.271 |
QMEAN Z-Score
| 2bfd_A | 2r8o_A |
|---|---|
| -1.604 | -6.943 |
Score components
| 2bfd_A | 2r8o_A |
|---|---|
Local scores
| 2bfd_A | 2r8o_A |
|---|---|
Global scores: QMEAN4:
| 2bfd_A | 2r8o_A | |||
|---|---|---|---|---|
| Scoring function term | Raw score | Z-score | Raw score | Z-score |
| C_beta interaction energy | -162.66 | 0.54 | -47.91 | -1.49 |
| All-atom pairwise energy | -10811.93 | 0.35 | -2558.65 | -1.98 |
| Solvation energy | -27.04 | -1.02 | 10.53 | -4.08 |
| Torsion angle energy | -75.78 | -1.45 | 18.95 | -4.99 |
| QMEAN4 score | 0.670 | -1.60 | 0.271 | -6.94 |
Local Model Quality Estimation
| 2bfd_A | 2r8o_A |
|---|---|
