Project name: survivor [mutate: FC87E]

Status: done

submitted: 2019-10-11 13:13:48, status changed: 2019-10-11 15:40:18
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Chain sequence(s) C: LKFNQLKFRKKKLKFCKSHIHDWGLFAMEPIAADEMVIEYVGQNIRQVIADMREKRYEDEGIGSSYMFRVDHDTIIDATKCGNFARFINHSCNPNCYAKVITVESQKKIVIYSKQHINVNEEITYDYKFPIEDVKIPCLCGSENCRGTLN
Distance of aggregation 10 Å
Dynamic mode Yes
Mutated residues FC87E
Energy difference between WT (input) and mutated protein (by FoldX) 0.148461 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
-4.4235
Maximal score value
1.8518
Average score
-0.7782
Total score value
-116.7296

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 0.4546
5 K C -1.1543
6 F C -0.0752
7 N C -1.5725
8 Q C -1.6890
9 L C 0.0000
10 K C -1.8448
11 F C -0.2174
12 R C -0.9298
13 K C 0.0000
14 K C -1.6772
15 K C -2.1920
16 L C -1.4006
17 K C -1.0935
18 F C 0.3139
19 C C 0.3635
20 K C -0.1860
21 S C 0.0539
22 H C 0.5006
23 I C 1.4342
24 H C -0.1158
25 D C -0.1465
26 W C 0.0000
27 G C -0.1966
28 L C 0.0000
29 F C -0.2457
30 A C 0.0000
31 M C -0.9240
32 E C -0.3699
33 P C 0.0000
34 I C 1.3363
35 A C 0.0000
36 A C -1.1677
37 D C -1.5329
38 E C 0.0000
39 M C 0.0000
40 V C 0.0000
41 I C 0.4607
42 E C 0.0000
43 Y C 0.6552
44 V C 0.0000
45 G C -1.4100
46 Q C -2.0762
47 N C -2.1523
48 I C 0.0000
49 R C -2.1707
50 Q C -0.9504
51 V C 1.5551
52 I C 1.5249
53 A C 0.0000
54 D C -0.6781
55 M C 0.0927
56 R C -1.8398
57 E C -3.0403
58 K C -3.8942
59 R C -4.3842
60 Y C -3.2900
61 E C -4.2332
62 D C -4.4235
63 E C -3.3897
64 G C -1.5937
65 I C 0.6050
66 G C 0.0270
67 S C -0.0030
68 S C -0.0287
69 Y C 0.0000
70 M C -0.6982
71 F C 0.0000
72 R C -2.2630
73 V C 0.0000
74 D C -1.9639
75 H C -2.5542
76 D C -3.0486
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 -1.5614
83 K C -2.7908
84 C C 0.0000
85 G C -2.0091
86 N C -2.6374
87 E C -2.8764 mutated: FC87E
88 A C -1.3010
89 R C -1.3740
90 F C 0.0000
91 I C 0.0000
92 N C 0.0000
93 H C -0.7697
94 S C 0.0000
95 C C -0.8889
96 N C -1.2116
97 P C -0.9107
98 N C -1.2026
99 C C 0.0000
100 Y C 0.0016
101 A C 0.0000
102 K C -0.4676
103 V C -0.0597
104 I C 0.0799
105 T C -0.3856
106 V C -0.3520
107 E C -1.7778
108 S C -1.2740
109 Q C -1.0268
110 K C -0.8011
111 K C 0.0220
112 I C 0.0000
113 V C 0.0000
114 I C 0.0000
115 Y C -0.5553
116 S C -1.4121
117 K C -2.6296
118 Q C -2.0661
119 H C -0.8749
120 I C 1.8518
121 N C 0.9552
122 V C 1.3931
123 N C -0.2548
124 E C 0.0000
125 E C -1.2212
126 I C 0.0000
127 T C 0.0000
128 Y C 0.0000
129 D C 0.0000
130 Y C 0.0000
131 K C -0.6952
132 F C -0.7607
133 P C -1.3402
134 I C -1.2623
135 E C -2.6008
136 D C -2.5788
137 V C -1.3825
138 K C -1.9669
139 I C 0.0000
140 P C -0.2061
141 C C 0.1464
142 L C 1.1032
143 C C 0.0413
144 G C -1.3847
145 S C -1.9002
146 E C -2.7988
147 N C -2.6481
148 C C -2.1448
149 R C -2.2451
150 G C -0.6896
151 T C -0.2851
152 L C -0.1383
153 N C -1.1640

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, -0.7782 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015