Project name: Jaimebd1 [mutate: FB19D, WB23D]

Status: done

submitted: 2018-04-14 10:19:19, status changed: 2018-04-16 02:23:38
Settings
Chain sequence(s) B: LSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGP
Distance of aggregation 10 Å
Dynamic mode Yes
Mutated residues FB19D, WB23D
Energy difference between WT (input) and mutated protein (by FoldX) 3.98913 kcal/mol

CAUTION: Your mutation/s can destabilize the protein structure

Show buried residues

Minimal score value
-3.2025
Maximal score value
1.9757
Average score
-0.939
Total score value
-44.1348

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
14 L B 0.3383
15 S B -1.1227
16 Q B -2.2866
17 E B -2.7141
18 T B -2.1670
19 D B -2.4890 mutated: FB19D
20 S B -2.4114
21 D B -2.1340
22 L B -0.8022
23 D B -1.9328 mutated: WB23D
24 K B -1.9854
25 L B 0.5637
26 L B 0.5833
27 P B -1.0826
28 E B -2.3977
29 N B -2.1446
30 N B -1.1665
31 V B -0.0663
32 L B 0.4505
33 S B -0.6754
34 P B -0.1000
35 L B 0.3997
36 P B -0.1267
37 S B -0.5355
38 Q B -1.0267
39 A B 0.1799
40 M B 1.1497
41 D B 0.2565
42 D B 0.5062
43 L B 1.9079
44 M B 1.9757
45 L B 0.8077
46 S B -0.2959
47 P B -1.5004
48 D B -3.2025
49 D B -3.1322
50 I B -1.5464
51 E B -2.9621
52 Q B -2.7185
53 W B -1.3584
54 F B -0.2247
55 T B -1.3334
56 E B -2.1861
57 D B -1.5872
58 P B -0.8893
59 G B -0.4495
60 P B -0.5001

Above is the comparison between the input structure and the most aggregation prone model (predicted in the flexibility simulations, download both models in the PDB file format , download table with rmsd values ). The picture presents the most aggregation prone model (in blue) superimposed on the input structure (in red). The plot shows rmsd profile (distances between residues of the superimposed structures).

Dynamic mode uses CABS-flex simulations of protein structure fluctuations. The structure fluctuations may have impact on the size and extent of aggregation "hot-spots" on the protein surface. The dynamic mode uses the following pipeline: (1) based on the input structure, CABS-flex predicts a set of different models reflecting protein dynamics in solution; (2) for each of these models A3D score is calculated; (3) finally, the most aggregation prone model (the model with the highest A3D score, -0.939 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015