Aggrescan3D: survivor [mutate: VC51E]

Project name: survivor [mutate: VC51E]

Status: done

submitted: 2019-10-07 06:23:59, status changed: 2019-10-07 19:48:45

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Chain sequence(s)	C: LKFNQLKFRKKKLKFCKSHIHDWGLFAMEPIAADEMVIEYVGQNIRQVIADMREKRYEDEGIGSSYMFRVDHDTIIDATKCGNFARFINHSCNPNCYAKVITVESQKKIVIYSKQHINVNEEITYDYKFPIEDVKIPCLCGSENCRGTLN
Distance of aggregation	10 Å
Dynamic mode	Yes
Mutated residues	VC51E
Energy difference between WT (input) and mutated protein (by FoldX)	-0.48131 kcal/mol 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: -4.4337
Maximal score value: 2.3951
Average score: -0.8563
Total score value: -128.4469

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
4	L	C	0.3654
5	K	C	-1.5531
6	F	C	-0.1608
7	N	C	-1.0529
8	Q	C	-1.5829
9	L	C	0.0000
10	K	C	-1.8951
11	F	C	-0.2672
12	R	C	-1.8513
13	K	C	-2.5564
14	K	C	-2.2538
15	K	C	-2.0384
16	L	C	-0.6254
17	K	C	-0.1011
18	F	C	1.3117
19	C	C	-0.0095
20	K	C	-1.6325
21	S	C	-1.1381
22	H	C	-1.3049
23	I	C	-0.3058
24	H	C	-0.6616
25	D	C	-1.8885
26	W	C	-0.8232
27	G	C	-0.4479
28	L	C	0.0000
29	F	C	0.7015
30	A	C	0.0000
31	M	C	0.0837
32	E	C	0.0000
33	P	C	1.5762
34	I	C	2.3951
35	A	C	0.4810
36	A	C	-0.7923
37	D	C	-2.4461
38	E	C	0.0000
39	M	C	0.0000
40	V	C	0.0000
41	I	C	-0.5158
42	E	C	0.0000
43	Y	C	0.0573
44	V	C	0.0000
45	G	C	-1.7058
46	Q	C	-2.1467
47	N	C	-2.3378
48	I	C	0.0000
49	R	C	-3.0341
50	Q	C	-2.5164
51	E	C	-2.1048	mutated: VC51E
52	I	C	-0.3489
53	A	C	0.0000
54	D	C	-2.0458
55	M	C	-1.0720
56	R	C	-1.7574
57	E	C	-3.0660
58	K	C	-4.3607
59	R	C	-4.2233
60	Y	C	-2.7600
61	E	C	-4.3635
62	D	C	-4.4337
63	E	C	-3.2372
64	G	C	-1.9412
65	I	C	0.0726
66	G	C	-0.9232
67	S	C	-0.2773
68	S	C	-0.5192
69	Y	C	0.0000
70	M	C	-0.3227
71	F	C	0.0000
72	R	C	-1.9052
73	V	C	0.0000
74	D	C	-1.9524
75	H	C	-2.4674
76	D	C	-3.5111
77	T	C	-2.7482
78	I	C	0.0000
79	I	C	0.0000
80	D	C	0.0000
81	A	C	0.0000
82	T	C	-1.1217
83	K	C	-1.8420
84	C	C	-1.3151
85	G	C	-1.3907
86	N	C	-1.4052
87	F	C	0.0000
88	A	C	-0.5074
89	R	C	0.0000
90	F	C	0.0000
91	I	C	0.0000
92	N	C	-0.8678
93	H	C	-0.7168
94	S	C	0.0000
95	C	C	-0.8194
96	N	C	-1.2923
97	P	C	-1.4524
98	N	C	-1.6366
99	C	C	0.0000
100	Y	C	0.1902
101	A	C	0.0000
102	K	C	-0.5203
103	V	C	0.0000
104	I	C	0.2565
105	T	C	-0.3962
106	V	C	-0.6629
107	E	C	-1.9101
108	S	C	-1.4675
109	Q	C	-1.4603
110	K	C	-1.0262
111	K	C	-0.3096
112	I	C	0.0000
113	V	C	0.0000
114	I	C	0.0000
115	Y	C	-0.0391
116	S	C	0.0000
117	K	C	-2.5145
118	Q	C	-1.9500
119	H	C	-0.1999
120	I	C	2.0956
121	N	C	1.0713
122	V	C	1.9843
123	N	C	0.7398
124	E	C	0.0000
125	E	C	-0.4215
126	I	C	0.0000
127	T	C	0.0000
128	Y	C	0.0000
129	D	C	-0.7568
130	Y	C	0.0000
131	K	C	-0.5636
132	F	C	-0.4193
133	P	C	-0.5392
134	I	C	-0.4309
135	E	C	-2.1001
136	D	C	-2.0410
137	V	C	-0.6069
138	K	C	-1.7299
139	I	C	-0.6789
140	P	C	-0.3284
141	C	C	-0.2561
142	L	C	0.0884
143	C	C	0.0000
144	G	C	-1.2413
145	S	C	-1.5712
146	E	C	-2.3879
147	N	C	-2.3559
148	C	C	-1.3811
149	R	C	-2.0084
150	G	C	-1.1541
151	T	C	-0.6664
152	L	C	0.0000
153	N	C	-1.4680

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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, -0.8563 in this case) is selected and presented in A3D results.