Project name: f415e0eba8864bf [mutate: GA37A]

Status: done

submitted: 2017-03-11 14:43:51, status changed: 2017-03-11 17:12:16
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Chain sequence(s) A: PLFAPGEDCGPAWRAAPAAYDTSDTHLQILGKPVMERWETPYMHSLAAAAASRGGRVLEVGFGMAIAASRVQQAPIKEHWIIECNDGVFQRLQNWALKQPHKVVPLKGLWEEVAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKTHAFRLLKPGGILTYCNLTSWGELMKSKYTDITAMFEETQVPALLEAGFQRENICTEVMALVPPADCRYYAFPQMITPLVTKH
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues GA37A
Energy difference between WD and mutated (by FoldX) 2.60787 kcal/mol
Show buried residues

Minimal score value
-2.1919
Maximal score value
2.1898
Average score
-0.2742
Total score value
-62.7917

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 0.0036
8 L A 1.3175
9 F A 0.0000
10 A A -0.0353
11 P A -0.2679
12 G A -0.3535
13 E A -1.2613
14 D A -0.7013
15 C A 0.0000
16 G A 0.0000
17 P A -0.1836
18 A A 0.0000
19 W A 0.0000
20 R A -1.8346
21 A A -0.2549
22 A A 0.0247
23 P A -0.0654
24 A A 0.0052
25 A A 0.0429
26 Y A 0.3044
27 D A -0.4381
28 T A -0.1952
29 S A -0.3430
30 D A -0.6846
31 T A -0.1742
32 H A -0.3091
33 L A 0.0000
34 Q A -0.6337
35 I A 0.0000
36 L A 1.5585
37 A A 0.1706 mutated: GA37A
38 K A -0.9656
39 P A -0.4285
40 V A 0.0000
41 M A 0.0000
42 E A -0.5024
43 R A -0.8301
44 W A 0.0000
45 E A -1.0878
46 T A -0.2547
47 P A -0.2562
48 Y A 0.0000
49 M A 0.0000
50 H A -1.0089
51 S A -0.2761
52 L A 0.0000
53 A A 0.0000
54 A A 0.0140
55 A A -0.0057
56 A A 0.0000
57 A A -0.0242
58 S A -0.5604
59 R A -1.9611
60 G A -0.7757
61 G A -0.2778
62 R A -0.5878
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 0.2371
69 G A -0.0014
70 M A 0.0000
71 A A 0.0146
72 I A 0.0000
73 A A 0.0000
74 A A 0.0022
75 S A -0.0799
76 R A -0.3570
77 V A 0.0000
78 Q A -0.3646
79 Q A -1.2478
80 A A -0.2679
81 P A -0.2531
82 I A 0.0000
83 K A -1.7440
84 E A -0.5510
85 H A 0.0000
86 W A 0.1840
87 I A 0.0000
88 I A 0.0000
89 E A 0.0000
90 C A 0.5727
91 N A 0.0000
92 D A -1.8036
93 G A -0.5307
94 V A 0.0000
95 F A 0.0614
96 Q A -1.4716
97 R A -1.9705
98 L A -0.1226
99 Q A -0.3311
100 N A -1.2312
101 W A 0.1830
102 A A 0.0000
103 L A 1.1216
104 K A -1.6696
105 Q A -1.4029
106 P A -0.3433
107 H A -0.5212
108 K A -1.6866
109 V A 0.0172
110 V A 0.4718
111 P A -0.1686
112 L A 0.0000
113 K A -1.7263
114 G A -0.4585
115 L A 0.0000
116 W A 0.0000
117 E A -2.0608
118 E A -1.6607
119 V A 0.0000
120 A A -0.0351
121 P A -0.2662
122 T A -0.0023
123 L A 0.5647
124 P A -0.4792
125 D A -1.8487
126 G A -0.5778
127 H A -1.0015
128 F A 0.0000
129 D A -0.8643
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 0.0000
137 P A 0.0000
138 L A 0.0000
139 S A -0.4814
140 E A -2.1919
141 E A -2.1659
142 T A -0.3733
143 W A 0.0000
144 H A -0.2653
145 T A -0.0713
146 H A -0.3626
147 Q A 0.0000
148 F A 0.4746
149 N A -0.6203
150 F A 0.0000
151 I A 0.0000
152 K A -1.6995
153 T A -0.3099
154 H A 0.0000
155 A A 0.0057
156 F A 0.5510
157 R A -1.7610
158 L A 0.0000
159 L A 0.0000
160 K A -1.1980
161 P A -0.4374
162 G A 0.0000
163 G A -0.1645
164 I A 0.0000
165 L A 0.1946
166 T A 0.0000
167 Y A 0.0000
168 C A 0.0000
169 N A 0.0000
170 L A 0.0000
171 T A 0.0000
172 S A 0.0000
173 W A 0.0000
174 G A 0.0000
175 E A -0.5004
176 L A 0.1290
177 M A -0.2420
178 K A -1.7151
179 S A -0.6751
180 K A -0.8777
181 Y A 0.8252
182 T A -0.1990
183 D A -1.8024
184 I A 0.0000
185 T A -0.0017
186 A A 0.1630
187 M A 1.0612
188 F A 0.0000
189 E A -1.0600
190 E A -1.9612
191 T A -0.3698
192 Q A -0.0118
193 V A 0.6481
194 P A 0.1326
195 A A 0.0000
196 L A 0.0000
197 L A 0.8925
198 E A -1.5912
199 A A -0.4238
200 G A 0.0239
201 F A 1.5732
202 Q A -0.9214
203 R A -0.8520
204 E A -2.1541
205 N A -1.4509
206 I A 0.7932
207 C A 0.7597
208 T A -0.2249
209 E A -1.3826
210 V A 0.8433
211 M A 0.4231
212 A A 0.0628
213 L A 0.0000
214 V A 2.0145
215 P A 0.1805
216 P A -0.0983
217 A A -0.2814
218 D A -1.7549
219 C A -0.5671
220 R A -1.7931
221 Y A -0.1549
222 Y A 0.0000
223 A A 0.4319
224 F A 2.1898
225 P A 0.0000
226 Q A -0.2742
227 M A 0.0000
228 I A 0.0000
229 T A -0.0070
230 P A 0.0000
231 L A 0.2061
232 V A 0.0000
233 T A -0.4493
234 K A -1.7030
235 H A 0.0000

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, -0.2742 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015