Aggrescan3D: 76-93v [mutate: VA93G]

Project name: 76-93v [mutate: VA93G]

Status: done

submitted: 2020-06-16 17:13:11, status changed: 2020-06-20 16:58:23

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Chain sequence(s)	A: MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKNEYACRVNHVTLSQPKIVKWDRDM
Distance of aggregation	10 Å
Dynamic mode	Yes
Mutated residues	VA93G
Energy difference between WT (input) and mutated protein (by FoldX)	2.64316 kcal/mol CAUTION: Your mutation/s can destabilize the protein structure Changes in protein stability upon mutation are calculated using the FoldX forcefield. Computational prediction of protein stability is used with the intention of preventing the experimental characterization of proteins bearing mutations that significantly destabilize their structure. Mutations resulting in a predicted reduction in protein stability ≥ 1 kcal/mol are considered disruptive.

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Minimal score value: -3.4175
Maximal score value: 1.7522
Average score: -0.7069
Total score value: -70.6893

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	1.5895
1	I	A	1.7522
2	Q	A	-0.1887
3	R	A	-0.5100
4	T	A	-1.0681
5	P	A	-0.9246
6	K	A	-1.6765
7	I	A	-0.7412
8	Q	A	-0.8022
9	V	A	0.0000
10	Y	A	-0.4106
11	S	A	0.0000
12	R	A	-0.9167
13	H	A	-0.8173
14	P	A	-1.0128
15	A	A	-1.6064
16	E	A	-2.8309
17	N	A	-2.6355
18	G	A	-2.2354
19	K	A	-2.2322
20	S	A	-1.4188
21	N	A	0.0000
22	F	A	-0.0397
23	L	A	0.0000
24	N	A	0.0000
25	C	A	0.0000
26	Y	A	0.4681
27	V	A	0.0000
28	S	A	0.0000
29	G	A	-0.4807
30	F	A	0.0000
31	H	A	0.3621
32	P	A	-0.0462
33	S	A	-0.3881
34	D	A	-1.6592
35	I	A	-0.8893
36	E	A	-1.7905
37	V	A	0.0000
38	D	A	-1.5404
39	L	A	0.0000
40	L	A	0.0000
41	K	A	-2.4801
42	N	A	-2.9203
43	G	A	-2.4473
44	E	A	-3.4175
45	R	A	-3.2828
46	I	A	0.0000
47	E	A	-3.2358
48	K	A	-2.8098
49	V	A	-1.8135
50	E	A	-2.3774
51	H	A	-1.9178
52	S	A	-1.2200
53	D	A	-0.9782
54	L	A	1.2332
55	S	A	0.9696
56	F	A	1.1083
57	S	A	-0.2514
58	K	A	-1.8848
59	D	A	-1.8735
60	W	A	-0.0295
61	S	A	0.1697
62	F	A	0.9362
63	Y	A	1.3062
64	L	A	0.0000
65	L	A	0.1039
66	Y	A	0.0000
67	Y	A	0.0740
68	T	A	0.0000
69	E	A	-1.1545
70	F	A	-0.4553
71	T	A	-0.7198
72	P	A	-1.2544
73	T	A	-1.6298
74	E	A	-2.7825
75	K	A	-3.0224
76	N	A	0.0000
77	E	A	-2.1023
78	Y	A	0.0000
79	A	A	0.0000
80	C	A	0.0000
81	R	A	-0.9344
82	V	A	0.0000
83	N	A	-1.7828
84	H	A	0.0000
85	V	A	0.3640
86	T	A	0.8548
87	L	A	1.6326
88	S	A	0.4382
89	Q	A	-0.0728
90	P	A	-0.4962
91	K	A	-0.2208
92	I	A	0.8532
93	G	A	-0.2225	mutated: VA93G
94	K	A	-1.4924
95	W	A	-1.1132
96	D	A	-1.4977
97	R	A	-1.4936
98	D	A	-0.7796
99	M	A	0.1236

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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, -0.7069 in this case) is selected and presented in A3D results.