Project name: survivor [mutate: IC120S]

Status: done

submitted: 2019-10-12 13:19:24, status changed: 2019-10-12 15:44:47
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Chain sequence(s) C: LKFNQLKFRKKKLKFCKSHIHDWGLFAMEPIAADEMVIEYVGQNIRQVIADMREKRYEDEGIGSSYMFRVDHDTIIDATKCGNFARFINHSCNPNCYAKVITVESQKKIVIYSKQHINVNEEITYDYKFPIEDVKIPCLCGSENCRGTLN
Distance of aggregation 10 Å
Dynamic mode Yes
Mutated residues IC120S
Energy difference between WT (input) and mutated protein (by FoldX) 0.58794 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.

Show buried residues

Minimal score value
-4.3433
Maximal score value
1.9887
Average score
-0.7918
Total score value
-118.7694

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 0.8452
5 K C -0.2092
6 F C 0.2863
7 N C -1.1054
8 Q C -1.2976
9 L C 0.0000
10 K C -0.8374
11 F C 0.3404
12 R C -1.2622
13 K C -1.9724
14 K C 0.0000
15 K C -1.9370
16 L C -0.7507
17 K C -1.1299
18 F C -0.2205
19 C C -0.1638
20 K C -1.4536
21 S C -0.8480
22 H C -0.7200
23 I C 1.0090
24 H C -0.5437
25 D C -0.7699
26 W C -0.3142
27 G C -0.3054
28 L C 0.0000
29 F C 0.4698
30 A C 0.0000
31 M C 0.0517
32 E C -0.2456
33 P C 0.1649
34 I C -0.0093
35 A C -0.2151
36 A C -1.4292
37 D C -2.3815
38 E C 0.0000
39 M C -0.2323
40 V C 0.0000
41 I C 0.0000
42 E C 0.0000
43 Y C 0.0003
44 V C 0.0000
45 G C -1.3257
46 Q C -1.6373
47 N C -1.6520
48 I C 0.0000
49 R C -1.6812
50 Q C -0.4167
51 V C 1.8567
52 I C 1.9887
53 A C 0.0000
54 D C -0.6318
55 M C 0.5210
56 R C -1.2968
57 E C -2.3372
58 K C -4.0173
59 R C -3.9232
60 Y C -2.9094
61 E C -4.1829
62 D C -4.3433
63 E C -3.6151
64 G C -1.8644
65 I C 0.6817
66 G C 0.1549
67 S C 0.6456
68 S C -0.1114
69 Y C 0.0144
70 M C -0.1703
71 F C 0.0000
72 R C -1.3981
73 V C 0.0000
74 D C -1.9430
75 H C -2.2337
76 D C -1.9417
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 -1.1071
83 K C -2.0290
84 C C -1.2648
85 G C -1.0314
86 N C -1.0882
87 F C 0.0000
88 A C -0.8803
89 R C -0.9509
90 F C 0.0000
91 I C 0.0000
92 N C 0.0000
93 H C -0.3778
94 S C -0.8141
95 C C -1.0130
96 N C -1.6261
97 P C -1.4236
98 N C -2.2084
99 C C 0.0000
100 Y C -0.8681
101 A C 0.0000
102 K C -0.9824
103 V C 0.0000
104 I C 0.4605
105 T C -0.2449
106 V C -0.2592
107 E C -1.7423
108 S C -1.5478
109 Q C -1.1542
110 K C 0.0000
111 K C -0.0922
112 I C 0.0000
113 V C 0.0000
114 I C 0.0000
115 Y C -0.6946
116 S C 0.0000
117 K C -3.1581
118 Q C -2.8508
119 H C -1.9735
120 S C -0.8205 mutated: IC120S
121 N C 0.0000
122 V C 1.4218
123 N C 0.2135
124 E C 0.0000
125 E C -0.6175
126 I C 0.0000
127 T C 0.0000
128 Y C 0.0000
129 D C -1.2904
130 Y C 0.0000
131 K C -1.5248
132 F C 0.0000
133 P C -1.1188
134 I C -1.3897
135 E C -2.8541
136 D C -2.8347
137 V C -2.2242
138 K C -2.7927
139 I C -1.6133
140 P C -0.8444
141 C C -0.1964
142 L C 0.6106
143 C C 0.0000
144 G C -1.1417
145 S C -1.7970
146 E C -2.7416
147 N C -2.4645
148 C C -1.5944
149 R C -2.0144
150 G C -1.1208
151 T C -0.5094
152 L C 0.0000
153 N C -1.6319

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, -0.7918 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015