Project name: jana

Status: done

submitted: 2018-10-10 11:35:16, status changed: 2018-11-24 16:04:05
Settings
Chain sequence(s) A: MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
Distance of aggregation 10 Å
Dynamic mode Yes
Show buried residues

Minimal score value
-4.0743
Maximal score value
1.0829
Average score
-1.1958
Total score value
-90.8792

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 -2.1159
2 Q A -2.3133
3 I A 0.0000
4 F A -0.4944
5 V A 0.0000
6 K A -0.8012
7 T A 0.0000
8 L A 1.0829
9 T A -0.2259
10 G A -1.2456
11 K A -1.8964
12 T A -1.1774
13 I A 0.0000
14 T A -0.7597
15 L A 0.0000
16 E A -2.5088
17 V A 0.0000
18 E A -2.5896
19 P A -2.0572
20 S A -1.8350
21 D A -2.4980
22 T A 0.0000
23 I A 0.0000
24 E A -2.2883
25 N A -2.5437
26 V A 0.0000
27 K A -2.0314
28 A A -2.2134
29 K A -3.3164
30 I A 0.0000
31 Q A -3.4907
32 D A -4.0743
33 K A -3.8699
34 E A -3.7917
35 G A -1.8321
36 I A -1.2088
37 P A -0.8674
38 P A -1.2351
39 D A -2.0131
40 Q A -1.4114
41 Q A 0.0000
42 R A -1.0661
43 L A 0.0000
44 I A -0.0604
45 F A 0.0000
46 A A -0.3196
47 G A -0.7040
48 K A -0.8419
49 Q A -1.4812
50 L A 0.0000
51 E A -1.8374
52 D A -2.0845
53 G A -1.9751
54 R A -2.9123
55 T A 0.0000
56 L A 0.0000
57 S A -1.8931
58 D A -2.0268
59 Y A -0.4433
60 N A -1.5664
61 I A -1.2700
62 Q A -2.1575
63 K A -3.0945
64 E A -2.8492
65 S A 0.0000
66 T A -0.5740
67 L A 0.0000
68 H A -0.1951
69 L A 0.0000
70 V A 0.8548
71 L A 0.1933
72 R A -0.6837
73 L A -0.0778
74 R A -1.7872
75 G A -1.3320
76 G A -1.0710

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, -1.1958 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015