Project name: bf14e4ab0756b97 [mutate: LA37I, GA38A]

Status: done

submitted: 2017-03-13 21:56:58, status changed: 2017-03-14 00:39:48
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Chain sequence(s) A: TPIFAPGENCSPAWGAAPAAYDAADTHLRILGKPVMERWETPYMHALAAAASSKGGRVLEVGFGMAIAASKVQEAPIDEHWIIECNDGVFQRLRDWAPRQTHKVIPLKGLWEDVAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKNHAFRLLKPGGVLTYCNLTSWGELMKSKYSDITIMFEETQVPALLEAGFRRENIRTEVMALVPPADCRYYAFPQMITPLVTK
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues LA37I, GA38A
Energy difference between WD and mutated (by FoldX) 1.78534 kcal/mol
Show buried residues

Minimal score value
-2.5402
Maximal score value
2.3123
Average score
-0.2469
Total score value
-56.5414

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
7 T A -0.1191
8 P A 0.1155
9 I A 2.3123
10 F A 2.3054
11 A A 0.3300
12 P A -0.2666
13 G A -0.4824
14 E A -2.0640
15 N A -1.5708
16 C A -0.1156
17 S A -0.2297
18 P A -0.2902
19 A A -0.0128
20 W A 0.0000
21 G A -0.4560
22 A A -0.0196
23 A A 0.0278
24 P A -0.0263
25 A A 0.0123
26 A A -0.1314
27 Y A 0.1087
28 D A -0.8171
29 A A -0.0859
30 A A -0.1984
31 D A -1.3823
32 T A 0.0000
33 H A -0.2266
34 L A 0.0000
35 R A -1.8411
36 I A 0.0000
37 I A 2.0227 mutated: LA37I
38 A A 0.3682 mutated: GA38A
39 K A -0.2624
40 P A -0.2965
41 V A 0.0000
42 M A 1.0242
43 E A 0.0000
44 R A -1.8441
45 W A 0.0000
46 E A 0.0000
47 T A 0.0000
48 P A -0.0686
49 Y A 0.0000
50 M A 0.0000
51 H A -0.1654
52 A A -0.0192
53 L A 0.0000
54 A A 0.0000
55 A A 0.0592
56 A A 0.0000
57 A A 0.0000
58 S A -0.1164
59 S A -0.4115
60 K A -1.7980
61 G A -0.7707
62 G A 0.0000
63 R A -1.4436
64 V A 0.0000
65 L A 0.0000
66 E A -0.1967
67 V A 0.0000
68 G A 0.0000
69 F A 0.0000
70 G A 0.0000
71 M A 0.0000
72 A A 0.1398
73 I A 0.6939
74 A A 0.0000
75 A A -0.1132
76 S A -0.2762
77 K A -1.0437
78 V A 0.0000
79 Q A -0.4609
80 E A -1.8298
81 A A -0.3122
82 P A -0.2595
83 I A 0.0000
84 D A -1.9297
85 E A -1.0986
86 H A 0.0000
87 W A 0.0000
88 I A 0.0000
89 I A 0.0000
90 E A 0.0000
91 C A 0.1332
92 N A 0.0000
93 D A -1.5996
94 G A -0.4922
95 V A 0.1864
96 F A 0.0360
97 Q A -1.5841
98 R A -1.5036
99 L A 0.0000
100 R A -2.1451
101 D A -1.5462
102 W A 0.1291
103 A A 0.0000
104 P A -0.7076
105 R A -2.0768
106 Q A -1.4249
107 T A -0.3231
108 H A -0.4865
109 K A -1.6948
110 V A -0.0466
111 I A 0.3811
112 P A -0.1061
113 L A 0.0000
114 K A -1.7110
115 G A -0.3170
116 L A 0.3254
117 W A -0.1386
118 E A -1.9821
119 D A -1.3520
120 V A 0.0000
121 A A -0.0202
122 P A -0.3619
123 T A -0.1146
124 L A 0.0000
125 P A -0.5745
126 D A -1.8577
127 G A -0.4855
128 H A -0.1702
129 F A 0.0000
130 D A 0.0000
131 G A 0.0000
132 I A 0.0000
133 L A 0.0000
134 Y A 0.0000
135 D A 0.0000
136 T A -0.0069
137 Y A 0.0000
138 P A 0.0452
139 L A 0.5029
140 S A -0.0841
141 E A -0.6022
142 E A -1.8720
143 T A -0.3461
144 W A 0.0317
145 H A -0.3986
146 T A -0.1758
147 H A -0.3664
148 Q A 0.0000
149 F A 1.1791
150 N A -0.4765
151 F A 0.0000
152 I A 0.0000
153 K A -1.8839
154 N A -1.0182
155 H A 0.0000
156 A A 0.1763
157 F A 1.6187
158 R A -1.5020
159 L A 0.0000
160 L A 0.0000
161 K A -0.4638
162 P A -0.4023
163 G A -0.4549
164 G A 0.0000
165 V A 0.0000
166 L A 0.0000
167 T A 0.0000
168 Y A 0.1437
169 C A 0.0000
170 N A 0.0000
171 L A 0.0000
172 T A -0.0077
173 S A 0.0000
174 W A 0.0000
175 G A 0.0000
176 E A -1.6746
177 L A 0.1511
178 M A -0.0907
179 K A -1.7013
180 S A -0.7269
181 K A -1.4855
182 Y A 0.9659
183 S A -0.1407
184 D A -1.2368
185 I A 0.0000
186 T A 0.3334
187 I A 2.1520
188 M A 1.2576
189 F A 0.3023
190 E A -0.8514
191 E A -1.9269
192 T A -0.3817
193 Q A -0.0504
194 V A 0.3722
195 P A 0.0774
196 A A 0.0000
197 L A 0.0000
198 L A 1.3042
199 E A -0.9143
200 A A -0.2283
201 G A -0.1448
202 F A 0.0000
203 R A -2.2164
204 R A -2.5402
205 E A -2.2618
206 N A -0.7649
207 I A 0.3915
208 R A -0.6590
209 T A -0.3034
210 E A -0.2530
211 V A 1.7487
212 M A 0.7676
213 A A 0.1933
214 L A 0.6294
215 V A 1.7863
216 P A 0.1086
217 P A -0.2788
218 A A -0.3751
219 D A -1.7691
220 C A -0.2970
221 R A -0.1389
222 Y A 1.2409
223 Y A 0.0000
224 A A -0.0159
225 F A 0.0000
226 P A 0.1306
227 Q A -0.9145
228 M A 0.0000
229 I A 0.0000
230 T A 0.0000
231 P A 0.0000
232 L A 0.0000
233 V A 0.0000
234 T A 0.0000
235 K A -0.5842

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, -0.2469 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015