Project name: polqQ [mutate: QA31E]

Status: done

submitted: 2017-03-17 09:25:45, status changed: 2017-03-17 11:44:17
Settings
Chain sequence(s) A: MYPYDVPDYAQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQHHHHHH
Distance of aggregation 10 Å
Dynamic mode Yes
Mutated residues QA31E
Energy difference between WD and mutated (by FoldX) 0.0739618 kcal/mol
Show buried residues

Minimal score value
-5.4479
Maximal score value
2.0739
Average score
-3.7694
Total score value
-290.2447

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
1 M A 1.8786
2 Y A 2.0739
3 P A 1.4937
4 Y A 1.8143
5 D A 1.0314
6 V A 1.5552
7 P A 0.1827
8 D A -0.6563
9 Y A 0.1556
10 A A -0.9016
11 Q A -2.5033
12 Q A -2.5491
13 Q A -2.9792
14 Q A -3.6162
15 Q A -3.8423
16 Q A -4.3646
17 Q A -4.6654
18 Q A -4.6985
19 Q A -5.0244
20 Q A -4.7973
21 Q A -5.0712
22 Q A -5.1283
23 Q A -5.0167
24 Q A -5.0037
25 Q A -5.0493
26 Q A -4.9702
27 Q A -5.0529
28 Q A -4.9447
29 Q A -4.9940
30 Q A -5.1969
31 E A -5.4479 mutated: QA31E
32 Q A -5.0844
33 Q A -4.9552
34 Q A -4.9086
35 Q A -4.8946
36 Q A -4.6220
37 Q A -4.6192
38 Q A -4.6852
39 Q A -4.6235
40 Q A -4.6554
41 Q A -4.6285
42 Q A -4.8075
43 Q A -4.8671
44 Q A -4.9252
45 Q A -4.8974
46 Q A -4.8511
47 Q A -4.9766
48 Q A -4.9634
49 Q A -4.8939
50 Q A -4.8065
51 Q A -4.8863
52 Q A -4.8783
53 Q A -4.7608
54 Q A -4.7844
55 Q A -4.9372
56 Q A -4.9914
57 Q A -5.1446
58 Q A -4.9836
59 Q A -5.0271
60 Q A -4.9169
61 Q A -4.8140
62 Q A -4.6503
63 Q A -4.4762
64 Q A -4.0257
65 Q A -4.0226
66 Q A -4.1344
67 Q A -3.7852
68 Q A -3.5458
69 Q A -3.4269
70 Q A -3.4601
71 Q A -3.5450
72 H A -3.7801
73 H A -3.4546
74 H A -3.4620
75 H A -3.0777
76 H A -2.9231
77 H A -2.3965

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, -3.7694 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015