Aggrescan3D: example_2D4F_dynamic

Project name: example_2D4F_dynamic_mode

Status: done

submitted: 2014-12-23 00:32:28, status changed: 2014-12-23 02:49:13

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

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Show buried residues

Minimal score value: -3.8048
Maximal score value: 1.8693
Average score: -0.8944
Total score value: -87.6522

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
0	M	A	1.7599
1	I	A	1.8693
2	Q	A	-0.2740
3	R	A	-1.0071
4	T	A	-0.9535
5	P	A	-1.0368
6	K	A	-1.3154
7	I	A	-0.5290
8	Q	A	-0.4010
9	V	A	0.0000
10	Y	A	0.2543
11	S	A	-0.6954
12	R	A	-1.6405
13	H	A	-2.1948
14	P	A	-2.0060
15	A	A	-2.2739
16	E	A	-2.9929
17	N	A	-2.6719
18	G	A	-2.7083
19	K	A	-2.8450
20	S	A	-2.1391
21	N	A	0.0000
22	F	A	-0.4358
23	L	A	0.0000
24	N	A	0.0000
25	C	A	0.0000
26	Y	A	0.3682
27	V	A	0.0000
28	S	A	0.0000
29	G	A	0.0000
30	F	A	-0.1371
31	H	A	-0.8747
32	P	A	-1.2654
33	S	A	0.0000
34	D	A	-1.6769
35	I	A	-1.3861
36	E	A	-1.9310
37	V	A	-0.9084
38	D	A	0.0000
39	L	A	0.0000
40	L	A	-2.3730
41	K	A	-2.6729
42	N	A	-3.0831
43	G	A	-2.4978
44	E	A	-3.6302
45	R	A	-3.8048
46	I	A	0.0000
47	E	A	-3.1574
48	K	A	-2.9430
49	V	A	-1.6178
50	E	A	-1.8636
51	H	A	-1.9306
52	S	A	-1.0911
53	D	A	-1.1006
54	L	A	0.7074
55	S	A	0.8855
56	F	A	1.3751
57	S	A	-0.2662
58	K	A	-1.9795
59	D	A	-2.1736
60	W	A	-0.5545
61	S	A	0.0567
62	F	A	0.0000
63	Y	A	1.3007
64	L	A	1.0899
65	L	A	0.3300
66	Y	A	0.1895
67	Y	A	-0.2197
68	T	A	0.0000
69	E	A	-1.7713
70	F	A	-0.7817
71	T	A	-0.6360
72	P	A	-1.0234
73	T	A	-1.8490
74	E	A	-2.6721
75	K	A	-2.9432
76	D	A	0.0000
77	E	A	-2.6418
78	Y	A	0.0000
79	A	A	-1.1131
80	C	A	0.0000
81	R	A	-0.8525
82	V	A	0.0000
83	N	A	-1.0749
84	H	A	0.0000
85	V	A	0.2708
86	T	A	0.4027
87	L	A	0.7830
88	S	A	0.1001
89	Q	A	-0.6928
90	P	A	-0.8005
91	K	A	-0.7476
92	I	A	0.5076
93	V	A	0.0589
94	K	A	-1.3872
95	W	A	-1.1063
96	D	A	-2.6856
97	R	A	-1.9234

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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, -0.8944 in this case) is selected and presented in A3D results.