Aggrescan3D: 76-30f [mutate: FA30G]

Project name: 76-30f [mutate: FA30G]

Status: done

submitted: 2020-06-16 17:11:42, status changed: 2020-06-20 15:24:05

Settings

Chain sequence(s)	A: MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKNEYACRVNHVTLSQPKIVKWDRDM
Distance of aggregation	10 Å
Dynamic mode	Yes
Mutated residues	FA30G
Energy difference between WT (input) and mutated protein (by FoldX)	5.00812 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.

Drag cursor over the plot to display residue labels.

Show buried residues

Minimal score value: -3.2868
Maximal score value: 1.9679
Average score: -0.746
Total score value: -74.6045

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	1.0231
1	I	A	1.5102
2	Q	A	-0.4075
3	R	A	-0.7677
4	T	A	-1.0565
5	P	A	-1.0736
6	K	A	-1.5259
7	I	A	-0.3739
8	Q	A	-0.3495
9	V	A	-0.5004
10	Y	A	-0.7505
11	S	A	0.0000
12	R	A	-1.5129
13	H	A	-1.7784
14	P	A	-1.5624
15	A	A	-1.8959
16	E	A	-2.9619
17	N	A	-3.1000
18	G	A	-2.5706
19	K	A	-3.0981
20	S	A	-2.0521
21	N	A	0.0000
22	F	A	-0.8578
23	L	A	0.0000
24	N	A	0.0000
25	C	A	0.0000
26	Y	A	0.1810
27	V	A	0.0000
28	S	A	-0.1422
29	G	A	0.0000
30	G	A	0.0000	mutated: FA30G
31	H	A	0.0000
32	P	A	-0.0966
33	S	A	-0.1022
34	D	A	0.0000
35	I	A	-0.4240
36	E	A	-1.3507
37	V	A	0.0000
38	D	A	0.0000
39	L	A	0.0000
40	L	A	-1.4125
41	K	A	-2.0000
42	N	A	-2.3672
43	G	A	-2.2699
44	E	A	-3.0423
45	R	A	-2.5108
46	I	A	-1.5797
47	E	A	-2.3016
48	K	A	-2.4540
49	V	A	-1.6703
50	E	A	-2.5209
51	H	A	-1.7365
52	S	A	-1.0600
53	D	A	-0.3425
54	L	A	1.6507
55	S	A	1.4239
56	F	A	1.9679
57	S	A	0.2725
58	K	A	-1.6016
59	D	A	-0.8436
60	W	A	0.3150
61	S	A	0.6277
62	F	A	1.3736
63	Y	A	1.2366
64	L	A	0.9786
65	L	A	0.3765
66	Y	A	0.0000
67	Y	A	-0.7216
68	T	A	0.0000
69	E	A	-1.8400
70	F	A	-0.6250
71	T	A	-1.3213
72	P	A	-2.1271
73	T	A	-1.7486
74	E	A	-3.1565
75	K	A	-3.0636
76	N	A	-2.2819
77	E	A	-2.1045
78	Y	A	0.0000
79	A	A	-0.8662
80	C	A	0.0000
81	R	A	-0.6577
82	V	A	0.0000
83	N	A	-0.7529
84	H	A	0.0000
85	V	A	1.7269
86	T	A	1.2544
87	L	A	1.6955
88	S	A	0.7573
89	Q	A	-0.0205
90	P	A	-0.5409
91	K	A	-0.6299
92	I	A	0.8990
93	V	A	-0.2031
94	K	A	-1.7707
95	W	A	0.0000
96	D	A	-2.9427
97	R	A	-3.2868
98	D	A	-2.6443
99	M	A	-0.5444

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, -0.746 in this case) is selected and presented in A3D results.