Aggrescan3D: survivor [mutate: IC120R]

Project name: survivor [mutate: IC120R]

Status: done

submitted: 2019-10-12 13:21:37, status changed: 2019-10-12 15:49:57

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Chain sequence(s)	C: LKFNQLKFRKKKLKFCKSHIHDWGLFAMEPIAADEMVIEYVGQNIRQVIADMREKRYEDEGIGSSYMFRVDHDTIIDATKCGNFARFINHSCNPNCYAKVITVESQKKIVIYSKQHINVNEEITYDYKFPIEDVKIPCLCGSENCRGTLN
Distance of aggregation	10 Å
Dynamic mode	Yes
Mutated residues	IC120R
Energy difference between WT (input) and mutated protein (by FoldX)	0.0151012 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: -3.843
Maximal score value: 1.6829
Average score: -0.7308
Total score value: -109.6253

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	1.1749
5	K	C	-0.0356
6	F	C	1.5532
7	N	C	0.5007
8	Q	C	0.0687
9	L	C	-0.0239
10	K	C	0.0000
11	F	C	-0.7998
12	R	C	-2.0209
13	K	C	-2.3988
14	K	C	-2.9202
15	K	C	-2.4311
16	L	C	-1.0403
17	K	C	-0.9337
18	F	C	0.9289
19	C	C	0.1714
20	K	C	-1.2719
21	S	C	-0.8645
22	H	C	-0.9550
23	I	C	0.8529
24	H	C	-0.5398
25	D	C	-1.0604
26	W	C	0.0000
27	G	C	0.0000
28	L	C	0.0000
29	F	C	0.1405
30	A	C	0.0000
31	M	C	-0.8165
32	E	C	-0.4408
33	P	C	-0.1036
34	I	C	0.2883
35	A	C	-0.5173
36	A	C	-1.3908
37	D	C	-2.0459
38	E	C	0.0000
39	M	C	0.2014
40	V	C	0.0000
41	I	C	0.0000
42	E	C	-1.0541
43	Y	C	0.0000
44	V	C	0.0000
45	G	C	-1.0665
46	Q	C	-1.1927
47	N	C	-0.8949
48	I	C	-0.0408
49	R	C	-0.7248
50	Q	C	-0.2442
51	V	C	1.6829
52	I	C	1.3733
53	A	C	0.0000
54	D	C	-1.2852
55	M	C	0.0067
56	R	C	-1.5242
57	E	C	-2.6213
58	K	C	-3.5514
59	R	C	-3.2716
60	Y	C	-2.1896
61	E	C	-3.5604
62	D	C	-3.8430
63	E	C	-2.8464
64	G	C	-1.5432
65	I	C	0.5841
66	G	C	-0.2013
67	S	C	0.1183
68	S	C	-0.3241
69	Y	C	0.0000
70	M	C	-0.1521
71	F	C	0.0000
72	R	C	-0.9575
73	V	C	0.0000
74	D	C	-2.2720
75	H	C	-2.3455
76	D	C	-1.5696
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	-1.0178
83	K	C	-1.8922
84	C	C	-0.8239
85	G	C	-1.1392
86	N	C	-1.2689
87	F	C	-0.4800
88	A	C	0.0000
89	R	C	-0.5315
90	F	C	0.0000
91	I	C	0.0000
92	N	C	-0.6589
93	H	C	-0.6000
94	S	C	-0.6576
95	C	C	-0.7984
96	N	C	-1.2403
97	P	C	-0.9418
98	N	C	-0.9907
99	C	C	0.0000
100	Y	C	-0.4104
101	A	C	0.0000
102	K	C	-1.0206
103	V	C	0.0000
104	I	C	0.1414
105	T	C	-0.2562
106	V	C	0.6406
107	E	C	-1.3150
108	S	C	-1.1848
109	Q	C	-1.3449
110	K	C	-1.0497
111	K	C	-0.8979
112	I	C	0.0000
113	V	C	0.0000
114	I	C	0.0000
115	Y	C	-0.4038
116	S	C	0.0000
117	K	C	-1.9445
118	Q	C	-2.0141
119	H	C	-2.1779
120	R	C	-1.7389	mutated: IC120R
121	N	C	-1.1067
122	V	C	0.6871
123	N	C	-0.4919
124	E	C	0.0000
125	E	C	-0.4542
126	I	C	0.0000
127	T	C	0.0000
128	Y	C	0.0000
129	D	C	-0.4913
130	Y	C	0.0000
131	K	C	-1.0127
132	F	C	-0.5781
133	P	C	-0.8373
134	I	C	-0.0830
135	E	C	-2.0545
136	D	C	-2.6859
137	V	C	-1.9288
138	K	C	-2.6802
139	I	C	0.0000
140	P	C	-0.9031
141	C	C	0.1174
142	L	C	0.9633
143	C	C	-0.3879
144	G	C	-1.0968
145	S	C	-1.8295
146	E	C	-2.8163
147	N	C	-2.5384
148	C	C	-1.7901
149	R	C	-2.1076
150	G	C	-1.0196
151	T	C	-0.1817
152	L	C	-0.5364
153	N	C	-1.5222

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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, -0.7308 in this case) is selected and presented in A3D results.