Aggrescan3D: survivor [mutate: FC87N]

Project name: survivor [mutate: FC87N]

Status: done

submitted: 2019-10-11 13:19:42, status changed: 2019-10-11 15:45:49

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Chain sequence(s)	C: LKFNQLKFRKKKLKFCKSHIHDWGLFAMEPIAADEMVIEYVGQNIRQVIADMREKRYEDEGIGSSYMFRVDHDTIIDATKCGNFARFINHSCNPNCYAKVITVESQKKIVIYSKQHINVNEEITYDYKFPIEDVKIPCLCGSENCRGTLN
Distance of aggregation	10 Å
Dynamic mode	Yes
Mutated residues	FC87N
Energy difference between WT (input) and mutated protein (by FoldX)	0.55225 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: -4.3677
Maximal score value: 2.2537
Average score: -0.7245
Total score value: -108.6802

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	0.3053
5	K	C	-1.0656
6	F	C	0.0936
7	N	C	-1.4798
8	Q	C	-1.5672
9	L	C	0.0000
10	K	C	-1.7067
11	F	C	-0.3088
12	R	C	-0.9109
13	K	C	0.0000
14	K	C	-1.3543
15	K	C	-1.9629
16	L	C	-1.1527
17	K	C	-1.5203
18	F	C	-0.4214
19	C	C	-0.2897
20	K	C	-0.9571
21	S	C	-0.5864
22	H	C	-0.4993
23	I	C	0.9806
24	H	C	-0.2044
25	D	C	-0.6022
26	W	C	-0.2142
27	G	C	-0.5662
28	L	C	0.0000
29	F	C	-0.7513
30	A	C	0.0000
31	M	C	-0.6979
32	E	C	-0.1374
33	P	C	0.2381
34	I	C	0.2101
35	A	C	-0.1466
36	A	C	-1.1385
37	D	C	-1.4709
38	E	C	0.0000
39	M	C	0.0000
40	V	C	0.0000
41	I	C	0.5438
42	E	C	0.1343
43	Y	C	0.2550
44	V	C	0.0000
45	G	C	-1.5027
46	Q	C	-2.2072
47	N	C	-2.6629
48	I	C	-1.0962
49	R	C	-1.7182
50	Q	C	-0.4400
51	V	C	2.0800
52	I	C	2.2537
53	A	C	0.0000
54	D	C	-0.1093
55	M	C	0.4514
56	R	C	-0.9715
57	E	C	-1.9175
58	K	C	-3.4110
59	R	C	-3.5670
60	Y	C	-3.0201
61	E	C	-3.9669
62	D	C	-4.3677
63	E	C	-3.7234
64	G	C	-2.2167
65	I	C	-0.7883
66	G	C	-0.6007
67	S	C	-0.6805
68	S	C	0.0000
69	Y	C	0.0000
70	M	C	-0.5955
71	F	C	0.0000
72	R	C	-1.5885
73	V	C	0.0000
74	D	C	-2.8709
75	H	C	-2.8030
76	D	C	-2.2345
77	T	C	-2.1984
78	I	C	0.0000
79	I	C	0.0000
80	D	C	0.0000
81	A	C	0.0000
82	T	C	-1.1262
83	K	C	-1.8063
84	C	C	-0.4167
85	G	C	-0.8297
86	N	C	-1.1610
87	N	C	-1.2100	mutated: FC87N
88	A	C	-0.7322
89	R	C	-0.3778
90	F	C	0.0000
91	I	C	-0.0130
92	N	C	0.0000
93	H	C	-0.1734
94	S	C	-0.6081
95	C	C	-0.6842
96	N	C	-1.6225
97	P	C	-1.0434
98	N	C	-1.6046
99	C	C	0.0000
100	Y	C	0.2293
101	A	C	0.0000
102	K	C	-0.3562
103	V	C	0.0000
104	I	C	0.4304
105	T	C	-0.0114
106	V	C	0.5925
107	E	C	-1.6613
108	S	C	-1.6879
109	Q	C	-1.2864
110	K	C	0.0000
111	K	C	-0.0874
112	I	C	0.0000
113	V	C	0.0000
114	I	C	0.0000
115	Y	C	0.0456
116	S	C	0.0000
117	K	C	-2.4239
118	Q	C	-2.0527
119	H	C	-0.8685
120	I	C	1.0670
121	N	C	0.1129
122	V	C	1.1183
123	N	C	0.0583
124	E	C	0.0000
125	E	C	-1.7132
126	I	C	0.0000
127	T	C	-0.6187
128	Y	C	0.0000
129	D	C	0.0000
130	Y	C	0.0000
131	K	C	-0.4321
132	F	C	-0.4701
133	P	C	-0.6458
134	I	C	-1.0117
135	E	C	-2.7312
136	D	C	-2.8936
137	V	C	-2.2566
138	K	C	-2.5487
139	I	C	-0.9537
140	P	C	-0.1828
141	C	C	0.8265
142	L	C	1.7390
143	C	C	0.8607
144	G	C	-0.8097
145	S	C	-1.2950
146	E	C	-2.5439
147	N	C	-2.3664
148	C	C	-1.3728
149	R	C	-1.1299
150	G	C	0.0000
151	T	C	0.0000
152	L	C	0.1729
153	N	C	-0.6875

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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, -0.7245 in this case) is selected and presented in A3D results.