Homology based structure predictions BCKDHA

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:
-1w85_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

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:
-1w85_A -> P21873
< 40% sequence identity (ideally go towards 20%) :
-2r8o_A -> P27302

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]

Protocol Modeller

SWISS-MODEL

SWISS-MODEL server page

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
1w85_A	1w85_A
2r8o_A	2r8o_A

iTasser

1w85_A

1w85_A

Prediction for 1w85_A

Sequ GVKTFQFPFAEQLEKVAEQFPTFQILNEEGEVVNEEAMPELSDEQLKELMRRMVYTRILDQRSISLNRQGRLGFYAPTAGQEASQIASHFALEKEDFILP
Pred CCCCCCCCCHHHCCCCCCCCCSSSSSCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCCSSSC
Conf 9988678803312122677876989899998888756799999999999999999999999999999678854562888879999999986799898980

Sequ GYRDVPQIIWHGLPLYQAFLFSRGHFHGNQIPEGVNVLPPQIIIGAQYIQAAGVALGLKMRGKKAVAITYTGDGGTSQGDFYEGINFAGAFKAPAIFVVQ
Pred CCHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHCCHHHHHHHHHHHHHCCCCCSSSSSSCCCCCCCHHHHHHHHHHHHHCCCSSSSSS
Conf 6226899998699899999973687767878999865377730415555899999999964989889999347621101599999999996799899982

Sequ NNRFAISTPVEKQTVAKTLAQKAVAAGIPGIQVDGMDPLAVYAAVKAARERAINGEGPTLIETLCFRYGPHTMSGDDPTRYRSKELENEWAKKDPLVRFR
Pred CCCSSCCCCHHHHHCCCCHHHHHHCCCCCSSSSCCCCHHHHHHHHHHHHHHHHCCCCCSSSSSSSSSSCCCCCCCCCCCCCCCHHHHHHHHHCCCHHHHH
Conf 7972403229877479878986221799858987957999999999999999828998899999976158657889975678999999988379099999

Sequ KFLEAKGLWSEEEENNVIEQAKEEIKEAIKKADETPKQKVTDLISIMFEELPFNLKEQYEIYKEKESK
Pred HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHCC
Conf 99998799999999999999999999999999858998999998451038998799999999998549

2.Evaluation of models

Swissmodel

Numeric evaluation

QMEAN4 global scores

QMEANscore4

1w85_A	2r8o_A
0.596	0.271

QMEAN Z-Score

1w85_A	2r8o_A
-2.872	-6.943
Z-Score plot1 1w85_A	Z-Score plot1 2r8o_A
Z-Score plot2 1w85_A	Z-Score plot2 2r8o_A

Score components

1w85_A	2r8o_A
score components 1w85_A	score components 2r8o_A

Local scores

1w85_A	2r8o_A
Coloring by residue error 1w85_A	Coloring by residue error 2r8o_A
Residue error plot 1w85_A	Residue error plot 2r8o_A

Global scores: QMEAN4:

	1w85_A		2r8o_A
Scoring function term	Raw score	Z-score	Raw score	Z-score
C_beta interaction energy	-152.10	0.11	-47.91	-1.49
All-atom pairwise energy	-9145.04	-0.55	-2558.65	-1.98
Solvation energy	-14.56	-2.14	10.53	-4.08
Torsion angle energy	-57.90	-2.03	18.95	-4.99
QMEAN4 score	0.596	-2.87	0.271	-6.94

Local Model Quality Estimation

1w85_A	2r8o_A
Local Model Quality Estimation 1w85_A	Local Model Quality Estimation 2r8o_A