Aggrescan3D: survivor [mutate: FC87S]

Project name: survivor [mutate: FC87S]

Status: done

submitted: 2019-10-12 02:58:58, status changed: 2019-10-12 05:26:05

Settings

Chain sequence(s)	C: LKFNQLKFRKKKLKFCKSHIHDWGLFAMEPIAADEMVIEYVGQNIRQVIADMREKRYEDEGIGSSYMFRVDHDTIIDATKCGNFARFINHSCNPNCYAKVITVESQKKIVIYSKQHINVNEEITYDYKFPIEDVKIPCLCGSENCRGTLN
Distance of aggregation	10 Å
Dynamic mode	Yes
Mutated residues	FC87S
Energy difference between WT (input) and mutated protein (by FoldX)	0.614084 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.

Drag cursor over the plot to display residue labels.

Show buried residues

Minimal score value: -4.251
Maximal score value: 2.304
Average score: -0.8109
Total score value: -121.6417

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	0.4172
5	K	C	-0.9759
6	F	C	0.2282
7	N	C	-1.0122
8	Q	C	-1.0140
9	L	C	-0.6453
10	K	C	-1.0240
11	F	C	0.1805
12	R	C	-0.8584
13	K	C	0.0000
14	K	C	-2.3580
15	K	C	-2.4491
16	L	C	-1.3803
17	K	C	-1.6776
18	F	C	-0.2321
19	C	C	-0.0349
20	K	C	-1.2656
21	S	C	-1.3391
22	H	C	-1.4846
23	I	C	-0.6066
24	H	C	-1.6554
25	D	C	-1.9348
26	W	C	0.0000
27	G	C	-0.9122
28	L	C	0.0000
29	F	C	-0.4313
30	A	C	0.0000
31	M	C	0.0318
32	E	C	0.1375
33	P	C	0.5460
34	I	C	0.0000
35	A	C	0.2454
36	A	C	-0.6570
37	D	C	-1.4002
38	E	C	0.0000
39	M	C	-0.2531
40	V	C	0.0000
41	I	C	0.0000
42	E	C	-0.9894
43	Y	C	-0.3086
44	V	C	0.0000
45	G	C	-1.0162
46	Q	C	-1.1145
47	N	C	-1.5966
48	I	C	-0.8923
49	R	C	-1.7861
50	Q	C	-0.3203
51	V	C	1.9957
52	I	C	2.3040
53	A	C	0.0000
54	D	C	-0.1791
55	M	C	0.6335
56	R	C	0.0000
57	E	C	-2.3222
58	K	C	-3.7133
59	R	C	-3.8484
60	Y	C	-2.9139
61	E	C	-3.9919
62	D	C	-4.2510
63	E	C	-3.4843
64	G	C	-2.0882
65	I	C	0.5867
66	G	C	-0.0219
67	S	C	0.2611
68	S	C	-0.0644
69	Y	C	0.0340
70	M	C	-0.2419
71	F	C	0.0000
72	R	C	-1.8789
73	V	C	-1.3901
74	D	C	-1.8768
75	H	C	-1.9824
76	D	C	-1.6431
77	T	C	0.0000
78	I	C	0.0000
79	I	C	0.0000
80	D	C	0.0000
81	A	C	0.0000
82	T	C	0.0000
83	K	C	-0.8109
84	C	C	-0.3410
85	G	C	-0.9657
86	N	C	-1.4559
87	S	C	-1.0311	mutated: FC87S
88	A	C	-0.8619
89	R	C	-0.5693
90	F	C	0.0000
91	I	C	0.0000
92	N	C	-0.7116
93	H	C	-0.7755
94	S	C	0.0000
95	C	C	-1.2604
96	N	C	-1.6998
97	P	C	-1.4074
98	N	C	-1.4565
99	C	C	0.0000
100	Y	C	-0.9115
101	A	C	0.0000
102	K	C	-1.0203
103	V	C	-0.1823
104	I	C	0.0138
105	T	C	-0.4468
106	V	C	-0.5878
107	E	C	-1.8922
108	S	C	-1.5406
109	Q	C	-1.8849
110	K	C	-1.3637
111	K	C	-1.2858
112	I	C	0.0000
113	V	C	0.0000
114	I	C	0.0000
115	Y	C	-0.5083
116	S	C	0.0000
117	K	C	-2.2494
118	Q	C	-1.8911
119	H	C	-0.6818
120	I	C	1.2704
121	N	C	0.8514
122	V	C	1.4874
123	N	C	-0.2193
124	E	C	0.0000
125	E	C	-1.8495
126	I	C	0.0000
127	T	C	0.0000
128	Y	C	0.0000
129	D	C	-1.2678
130	Y	C	0.0000
131	K	C	-1.6249
132	F	C	0.0000
133	P	C	-1.7346
134	I	C	-1.5724
135	E	C	-2.7761
136	D	C	-2.9329
137	V	C	-1.9377
138	K	C	-2.5044
139	I	C	-1.0342
140	P	C	-0.0649
141	C	C	0.5570
142	L	C	1.0823
143	C	C	-0.0365
144	G	C	-1.4295
145	S	C	-1.8372
146	E	C	-2.8344
147	N	C	-2.5258
148	C	C	-1.8089
149	R	C	-2.2504
150	G	C	-1.0707
151	T	C	-0.2023
152	L	C	0.0000
153	N	C	-1.6802

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, -0.8109 in this case) is selected and presented in A3D results.