Aggrescan3D: survivor [mutate: IC120N]

Project name: survivor [mutate: IC120N]

Status: done

submitted: 2019-10-12 13:20:07, status changed: 2019-10-12 15:49:36

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Chain sequence(s)	C: LKFNQLKFRKKKLKFCKSHIHDWGLFAMEPIAADEMVIEYVGQNIRQVIADMREKRYEDEGIGSSYMFRVDHDTIIDATKCGNFARFINHSCNPNCYAKVITVESQKKIVIYSKQHINVNEEITYDYKFPIEDVKIPCLCGSENCRGTLN
Distance of aggregation	10 Å
Dynamic mode	Yes
Mutated residues	IC120N
Energy difference between WT (input) and mutated protein (by FoldX)	0.361127 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: -4.4902
Maximal score value: 1.9847
Average score: -0.7799
Total score value: -116.9778

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	0.3103
5	K	C	-1.2384
6	F	C	-0.2787
7	N	C	-1.7806
8	Q	C	-1.9764
9	L	C	0.0000
10	K	C	-2.0148
11	F	C	-0.6871
12	R	C	-2.2650
13	K	C	-1.8313
14	K	C	-1.8616
15	K	C	-1.5170
16	L	C	-0.1845
17	K	C	-0.3906
18	F	C	0.7064
19	C	C	-0.2679
20	K	C	-1.5515
21	S	C	-0.8114
22	H	C	-0.6798
23	I	C	0.8716
24	H	C	-0.2599
25	D	C	-0.3843
26	W	C	-0.4746
27	G	C	-0.5121
28	L	C	0.0000
29	F	C	0.0719
30	A	C	0.0000
31	M	C	-0.7323
32	E	C	-1.0445
33	P	C	-1.0148
34	I	C	0.0000
35	A	C	0.0000
36	A	C	-2.0571
37	D	C	-2.5734
38	E	C	0.0000
39	M	C	-0.3831
40	V	C	0.0000
41	I	C	0.0000
42	E	C	-1.1606
43	Y	C	0.0000
44	V	C	0.2563
45	G	C	0.0000
46	Q	C	-0.9150
47	N	C	-1.3483
48	I	C	-0.8521
49	R	C	-1.6146
50	Q	C	-0.7048
51	V	C	1.6595
52	I	C	1.9847
53	A	C	0.0000
54	D	C	-0.5144
55	M	C	0.2310
56	R	C	-1.0917
57	E	C	-2.1298
58	K	C	-3.7552
59	R	C	-4.1398
60	Y	C	-3.0317
61	E	C	-4.0634
62	D	C	-4.4902
63	E	C	-3.6889
64	G	C	-2.0676
65	I	C	0.1569
66	G	C	-0.0366
67	S	C	0.0233
68	S	C	-0.1596
69	Y	C	-0.2528
70	M	C	-0.1816
71	F	C	0.0000
72	R	C	-1.1061
73	V	C	0.0000
74	D	C	-1.0901
75	H	C	-2.0800
76	D	C	-2.7243
77	T	C	-1.9132
78	I	C	-1.1069
79	I	C	0.0000
80	D	C	-0.7680
81	A	C	0.0000
82	T	C	-1.2041
83	K	C	-1.8638
84	C	C	-0.5673
85	G	C	-0.9125
86	N	C	-1.6273
87	F	C	0.0000
88	A	C	0.0000
89	R	C	-0.2071
90	F	C	0.0000
91	I	C	0.0000
92	N	C	0.0000
93	H	C	0.0000
94	S	C	0.0000
95	C	C	-1.1106
96	N	C	-1.6741
97	P	C	-1.2920
98	N	C	-1.2891
99	C	C	0.0000
100	Y	C	0.2975
101	A	C	0.0000
102	K	C	-0.8599
103	V	C	0.0000
104	I	C	0.5118
105	T	C	0.2731
106	V	C	0.3073
107	E	C	-1.4101
108	S	C	-0.8342
109	Q	C	-0.6028
110	K	C	0.0000
111	K	C	-0.4202
112	I	C	0.0000
113	V	C	0.0000
114	I	C	0.0000
115	Y	C	-0.2951
116	S	C	0.0000
117	K	C	-2.8176
118	Q	C	-2.8362
119	H	C	0.0000
120	N	C	-1.9136	mutated: IC120N
121	N	C	-1.2099
122	V	C	0.4265
123	N	C	-1.1659
124	E	C	0.0000
125	E	C	-1.8290
126	I	C	0.0000
127	T	C	0.0000
128	Y	C	0.0000
129	D	C	-0.8840
130	Y	C	0.0000
131	K	C	-1.3875
132	F	C	-0.5950
133	P	C	-0.2250
134	I	C	0.5586
135	E	C	-1.6549
136	D	C	-1.8034
137	V	C	-0.2896
138	K	C	-1.6558
139	I	C	-0.7986
140	P	C	-0.4822
141	C	C	0.1542
142	L	C	1.0087
143	C	C	0.0172
144	G	C	-1.3163
145	S	C	0.0000
146	E	C	-2.7073
147	N	C	-2.6554
148	C	C	-2.0667
149	R	C	-2.3700
150	G	C	0.0000
151	T	C	-0.1241
152	L	C	-0.3446
153	N	C	-1.7418

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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, -0.7799 in this case) is selected and presented in A3D results.