Project name: polqQ [mutate: QA31E] [mutate: EA31Q]

Status: done

submitted: 2017-03-17 11:59:21, status changed: 2017-03-17 15:14:55
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Chain sequence(s) A: MYPYDVPDYAQQQQQQQQQQQQQQQQQQQQEQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQHHHHHH
Distance of aggregation 10 Å
Dynamic mode Yes
Mutated residues EA31Q
Energy difference between WD and mutated (by FoldX) -0.263608 kcal/mol
Show buried residues

Minimal score value
-5.0698
Maximal score value
1.8947
Average score
-3.6895
Total score value
-284.0921

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 1.8660
2 Y A 1.8947
3 P A 1.3900
4 Y A 1.7478
5 D A 0.7232
6 V A 1.4004
7 P A 0.2547
8 D A -0.5312
9 Y A 0.0961
10 A A -0.8991
11 Q A -2.4304
12 Q A -2.6393
13 Q A -2.4455
14 Q A -3.2585
15 Q A -3.8212
16 Q A -4.0295
17 Q A -4.2320
18 Q A -4.2999
19 Q A -4.4044
20 Q A -4.3400
21 Q A -4.5490
22 Q A -4.6872
23 Q A -4.6033
24 Q A -4.5771
25 Q A -4.5932
26 Q A -4.5547
27 Q A -4.5011
28 Q A -4.4913
29 Q A -4.4214
30 Q A -4.5545
31 Q A -4.5467 mutated: EA31Q
32 Q A -4.6387
33 Q A -4.5463
34 Q A -4.6463
35 Q A -4.6814
36 Q A -4.6087
37 Q A -4.8312
38 Q A -4.7374
39 Q A -4.6028
40 Q A -4.7599
41 Q A -4.7719
42 Q A -4.7338
43 Q A -4.7456
44 Q A -4.8480
45 Q A -4.8919
46 Q A -4.9537
47 Q A -4.8877
48 Q A -4.9267
49 Q A -5.0608
50 Q A -5.0425
51 Q A -5.0450
52 Q A -5.0698
53 Q A -5.0044
54 Q A -4.9607
55 Q A -4.8993
56 Q A -5.0005
57 Q A -4.9254
58 Q A -4.8203
59 Q A -4.7901
60 Q A -4.9253
61 Q A -4.8454
62 Q A -4.8265
63 Q A -4.8929
64 Q A -4.5627
65 Q A -4.5322
66 Q A -4.3641
67 Q A -4.1969
68 Q A -3.7776
69 Q A -3.6661
70 Q A -3.7984
71 Q A -3.4912
72 H A -3.6450
73 H A -3.6859
74 H A -3.2401
75 H A -3.0071
76 H A -2.8983
77 H A -2.2680

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, -3.6895 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015