Aggrescan3D: Renee Maas

Project name: Renee Maas

Status: done

submitted: 2018-11-06 10:24:00, status changed: 2018-11-24 16:04:14

Settings

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

Drag cursor over the plot to display residue labels.

Show buried residues

Minimal score value: -2.0878
Maximal score value: 6.6813
Average score: 1.8865
Total score value: 98.0992

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	0.2604
2	D	A	-1.5367
3	K	A	-1.1213
4	V	A	0.6427
5	Q	A	-0.3888
6	Y	A	0.3965
7	L	A	1.2775
8	T	A	-0.0099
9	R	A	-1.2439
10	S	A	-0.4476
11	A	A	-0.2989
12	I	A	0.3797
13	R	A	-1.8498
14	R	A	-1.8920
15	A	A	-0.4061
16	S	A	-0.5204
17	T	A	-0.1509
18	I	A	1.1537
19	E	A	-0.6545
20	M	A	-0.2658
21	P	A	-1.1289
22	Q	A	-2.0731
23	Q	A	-2.0878
24	A	A	-1.6752
25	R	A	-2.0016
26	Q	A	-1.6499
27	N	A	-0.8001
28	L	A	1.0327
29	Q	A	0.5665
30	N	A	0.4945
31	L	A	2.8664
32	F	A	4.0681
33	I	A	3.8984
34	N	A	3.0450
35	F	A	5.0507
36	C	A	4.9186
37	L	A	5.7214
38	I	A	6.2469
39	L	A	5.7272
40	I	A	6.2058
41	F	A	6.6813
42	L	A	5.9160
43	L	A	6.1804
44	L	A	5.9342
45	I	A	5.4881
46	C	A	5.6123
47	I	A	5.9503
48	I	A	5.7997
49	V	A	5.4419
50	M	A	4.6878
51	L	A	4.5436
52	L	A	4.1141

Download PDB file

View in JSmol

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, 1.8865 in this case) is selected and presented in A3D results.