Project name: survivor [mutate: FC18E]

Status: done

submitted: 2019-10-11 03:26:33, status changed: 2019-10-11 05:55:42
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Chain sequence(s) C: LKFNQLKFRKKKLKFCKSHIHDWGLFAMEPIAADEMVIEYVGQNIRQVIADMREKRYEDEGIGSSYMFRVDHDTIIDATKCGNFARFINHSCNPNCYAKVITVESQKKIVIYSKQHINVNEEITYDYKFPIEDVKIPCLCGSENCRGTLN
Distance of aggregation 10 Å
Dynamic mode Yes
Mutated residues FC18E
Energy difference between WT (input) and mutated protein (by FoldX) 0.315445 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
-4.6487
Maximal score value
2.2483
Average score
-0.7305
Total score value
-109.5677

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 0.4380
5 K C -0.7177
6 F C 0.2214
7 N C -1.1415
8 Q C -1.1138
9 L C 0.0000
10 K C -1.0634
11 F C 0.0158
12 R C -1.3435
13 K C -1.7461
14 K C -2.3924
15 K C -2.2461
16 L C -1.2524
17 K C -1.4896
18 E C -0.9818 mutated: FC18E
19 C C -0.6869
20 K C -1.0342
21 S C -0.6600
22 H C -0.5131
23 I C 1.1702
24 H C -0.0870
25 D C -0.4973
26 W C 0.0000
27 G C -0.9271
28 L C 0.0000
29 F C -0.7143
30 A C 0.0000
31 M C -1.0775
32 E C -0.6141
33 P C 0.0000
34 I C 2.1060
35 A C 0.3771
36 A C -0.7859
37 D C -2.0220
38 E C 0.0000
39 M C -0.3438
40 V C 0.0000
41 I C 0.0000
42 E C -0.2008
43 Y C 0.0487
44 V C 0.0000
45 G C -1.0405
46 Q C -1.1271
47 N C -0.8477
48 I C 0.0000
49 R C -1.8199
50 Q C -0.5516
51 V C 1.8280
52 I C 2.2483
53 A C 0.0000
54 D C -0.3701
55 M C 0.1123
56 R C -1.4628
57 E C -2.3524
58 K C -4.3595
59 R C -4.4470
60 Y C -3.3826
61 E C -4.2842
62 D C -4.6487
63 E C -3.4761
64 G C -2.1955
65 I C -0.1136
66 G C -0.5231
67 S C 0.3002
68 S C 0.2313
69 Y C 0.7414
70 M C 0.4559
71 F C 0.0000
72 R C -1.1913
73 V C 0.0000
74 D C -1.4893
75 H C -2.1133
76 D C -2.4737
77 T C 0.0000
78 I C -1.0587
79 I C 0.0000
80 D C -0.2631
81 A C 0.0000
82 T C -0.6454
83 K C -1.7211
84 C C -1.1862
85 G C -1.1985
86 N C -1.3700
87 F C -0.5173
88 A C -0.6748
89 R C 0.0000
90 F C 0.0000
91 I C 0.0000
92 N C 0.0000
93 H C -0.6751
94 S C 0.0000
95 C C -1.6103
96 N C -2.1554
97 P C -1.8864
98 N C -2.4758
99 C C 0.0000
100 Y C -0.8363
101 A C 0.0000
102 K C -1.2239
103 V C 0.0000
104 I C 0.7193
105 T C 0.4202
106 V C 0.6476
107 E C -0.8555
108 S C -0.8378
109 Q C -0.8813
110 K C 0.0000
111 K C -0.9271
112 I C 0.0000
113 V C -0.0153
114 I C 0.0000
115 Y C -0.6914
116 S C 0.0000
117 K C -3.1676
118 Q C -2.4084
119 H C -0.7909
120 I C 1.6285
121 N C 0.4763
122 V C 0.8872
123 N C -0.7806
124 E C 0.0000
125 E C -1.7442
126 I C 0.0000
127 T C 0.0000
128 Y C 0.0000
129 D C -1.3006
130 Y C 0.0000
131 K C -0.8798
132 F C -0.2925
133 P C -0.3277
134 I C 0.2634
135 E C -1.9122
136 D C -2.1958
137 V C -0.7970
138 K C -1.6753
139 I C -0.7547
140 P C -0.3352
141 C C 0.4043
142 L C 1.1627
143 C C 0.7180
144 G C -1.1461
145 S C -1.7932
146 E C -2.8574
147 N C -2.7965
148 C C -1.9954
149 R C -2.1175
150 G C 0.0000
151 T C -0.2896
152 L C 0.0000
153 N C -1.2026

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, -0.7305 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015