Aggrescan3D: Road To Nobel

Project name: Road To Nobel

Status: done

submitted: 2018-12-14 07:48:15, status changed: 2018-12-14 10:00:32

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Chain sequence(s)	A: MTYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTE
Distance of aggregation	10 Å
Dynamic mode	Yes

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Show buried residues

Minimal score value: -2.93
Maximal score value: 0.7562
Average score: -1.1992
Total score value: -67.1578

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	0.7044
2	T	A	-0.3471
3	Y	A	0.0000
4	K	A	-1.9963
5	L	A	0.0000
6	I	A	-0.9706
7	L	A	0.0000
8	N	A	-1.9787
9	G	A	-1.9646
10	K	A	-2.2496
11	T	A	-1.0211
12	L	A	-0.9219
13	K	A	-2.1965
14	G	A	-1.8006
15	E	A	-2.3537
16	T	A	-1.4859
17	T	A	-1.4077
18	T	A	-1.0004
19	E	A	-1.4293
20	A	A	-0.1669
21	V	A	0.7562
22	D	A	-0.8443
23	A	A	-0.5784
24	A	A	-0.7019
25	T	A	-0.5590
26	A	A	0.0000
27	E	A	-1.4949
28	K	A	-1.9635
29	V	A	-0.3294
30	F	A	0.0000
31	K	A	-2.9300
32	Q	A	-2.5273
33	Y	A	-1.5427
34	A	A	0.0000
35	N	A	-2.4601
36	D	A	-2.8338
37	N	A	-2.1616
38	G	A	-1.2224
39	V	A	-0.8226
40	D	A	-2.4249
41	G	A	-2.1833
42	E	A	-2.0110
43	W	A	-0.3328
44	T	A	-0.0552
45	Y	A	-0.2350
46	D	A	-2.2240
47	D	A	-2.4912
48	A	A	-1.5076
49	T	A	-0.9317
50	K	A	-1.3126
51	T	A	-1.3320
52	F	A	0.0000
53	T	A	-0.8261
54	V	A	0.0000
55	T	A	-1.9075
56	E	A	-2.5807

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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, -1.1992 in this case) is selected and presented in A3D results.