Project name: f415e0eba8864bf [mutate: LA36I, GA37A]

Status: done

submitted: 2017-03-10 18:21:28, status changed: 2017-03-10 20:42:09
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Chain sequence(s) A: PLFAPGEDCGPAWRAAPAAYDTSDTHLQILGKPVMERWETPYMHSLAAAAASRGGRVLEVGFGMAIAASRVQQAPIKEHWIIECNDGVFQRLQNWALKQPHKVVPLKGLWEEVAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKTHAFRLLKPGGILTYCNLTSWGELMKSKYTDITAMFEETQVPALLEAGFQRENICTEVMALVPPADCRYYAFPQMITPLVTKH
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues LA36I, GA37A
Energy difference between WD and mutated (by FoldX) 4.06692 kcal/mol
Show buried residues

Minimal score value
-2.3691
Maximal score value
2.0222
Average score
-0.2338
Total score value
-53.5417

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 P A -0.1065
8 L A 0.8407
9 F A 0.5386
10 A A 0.0649
11 P A -0.2611
12 G A -0.5656
13 E A -2.0251
14 D A -1.4104
15 C A 0.0000
16 G A 0.0000
17 P A -0.2775
18 A A 0.0003
19 W A -0.0664
20 R A -1.0051
21 A A -0.1239
22 A A 0.0051
23 P A -0.0496
24 A A 0.0000
25 A A 0.0920
26 Y A -0.0774
27 D A -1.7500
28 T A -0.3851
29 S A -0.5307
30 D A -1.5584
31 T A 0.0000
32 H A -0.2140
33 L A 0.0000
34 Q A -1.2191
35 I A 0.0000
36 I A 2.0222 mutated: LA36I
37 A A 0.2522 mutated: GA37A
38 K A -0.7319
39 P A -0.4171
40 V A 0.2060
41 M A 0.2253
42 E A 0.0000
43 R A -0.3680
44 W A 0.0000
45 E A -0.8782
46 T A -0.2397
47 P A -0.3471
48 Y A 0.0000
49 M A 0.0000
50 H A -0.8121
51 S A -0.1823
52 L A 0.0000
53 A A 0.0000
54 A A 0.0284
55 A A 0.0178
56 A A 0.0000
57 A A -0.0495
58 S A -0.5626
59 R A -1.9017
60 G A -0.4914
61 G A -0.2525
62 R A -0.7482
63 V A 0.0000
64 L A 0.0000
65 E A 0.0000
66 V A 0.0000
67 G A 0.0000
68 F A 0.0000
69 G A 0.0000
70 M A 0.1181
71 A A 0.0000
72 I A 0.0000
73 A A 0.0000
74 A A 0.0000
75 S A -0.1599
76 R A -0.5473
77 V A 0.0000
78 Q A -0.5442
79 Q A -1.3090
80 A A -0.2784
81 P A -0.4110
82 I A 0.0000
83 K A -1.8863
84 E A -1.5322
85 H A 0.0000
86 W A 0.1247
87 I A 0.0000
88 I A 0.0000
89 E A 0.0000
90 C A 0.1486
91 N A 0.0000
92 D A -1.4670
93 G A -0.4162
94 V A 0.0000
95 F A -0.0651
96 Q A -1.2913
97 R A -0.9875
98 L A 0.0000
99 Q A -0.4752
100 N A -1.2722
101 W A 0.0082
102 A A 0.0000
103 L A 1.2477
104 K A -1.4998
105 Q A -0.4583
106 P A -0.3019
107 H A 0.0000
108 K A -1.7852
109 V A 0.1914
110 V A 1.7914
111 P A 0.3794
112 L A 0.4402
113 K A -0.9279
114 G A -0.0051
115 L A 1.5276
116 W A 0.0000
117 E A -1.2240
118 E A -1.7992
119 V A 0.0000
120 A A 0.0000
121 P A -0.2581
122 T A -0.0682
123 L A 0.0000
124 P A -0.3781
125 D A -1.8114
126 G A -0.5263
127 H A -0.6127
128 F A 0.0000
129 D A -0.3240
130 G A 0.0000
131 I A 0.0000
132 L A 0.0000
133 Y A 0.0000
134 D A 0.0000
135 T A 0.0000
136 Y A 0.1964
137 P A 0.0029
138 L A 0.0000
139 S A -0.1906
140 E A -0.9216
141 E A -1.9721
142 T A -0.3607
143 W A 0.0000
144 H A -0.5889
145 T A -0.1279
146 H A -0.2235
147 Q A 0.0000
148 F A 0.7963
149 N A -0.2740
150 F A 0.0000
151 I A 0.0000
152 K A -1.1252
153 T A -0.2636
154 H A -0.1099
155 A A 0.0000
156 F A -0.0188
157 R A -1.4427
158 L A 0.0000
159 L A 0.0000
160 K A -1.1130
161 P A -0.5183
162 G A 0.0000
163 G A 0.0000
164 I A 0.2504
165 L A 0.0000
166 T A 0.0000
167 Y A 0.0000
168 C A 0.0000
169 N A 0.0000
170 L A 0.2050
171 T A 0.0000
172 S A -0.0349
173 W A 0.0000
174 G A -0.2071
175 E A -0.8703
176 L A -0.0799
177 M A -0.1150
178 K A -1.6813
179 S A -0.7851
180 K A -1.6159
181 Y A 0.2393
182 T A -0.1423
183 D A -1.0418
184 I A 0.0000
185 T A -0.0190
186 A A 0.0351
187 M A 0.7227
188 F A 0.0000
189 E A -1.1990
190 E A -1.9814
191 T A -0.3664
192 Q A 0.0000
193 V A 0.7194
194 P A 0.0998
195 A A 0.0000
196 L A 0.0000
197 L A 1.1717
198 E A -1.5178
199 A A -0.4749
200 G A -0.1212
201 F A 0.3596
202 Q A -1.4066
203 R A -2.3691
204 E A -2.2677
205 N A -1.4413
206 I A 0.6052
207 C A 0.7804
208 T A -0.0332
209 E A -0.3362
210 V A 1.6715
211 M A 0.4575
212 A A -0.0657
213 L A 0.0000
214 V A 0.2351
215 P A 0.0205
216 P A 0.0000
217 A A -0.0771
218 D A -0.7708
219 C A 0.2706
220 R A -1.5419
221 Y A 1.1983
222 Y A 1.5561
223 A A 0.6193
224 F A 1.9435
225 P A 0.0000
226 Q A -1.1911
227 M A 0.0000
228 I A 0.0000
229 T A 0.0000
230 P A 0.0000
231 L A 0.0000
232 V A 0.0000
233 T A 0.0339
234 K A 0.0000
235 H A -0.7670

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, -0.2338 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015