Project name: f415e0eba8864bf [mutate: LA36I]

Status: done

submitted: 2017-03-11 14:43:04, status changed: 2017-03-11 17:14:47
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Chain sequence(s) A: PLFAPGEDCGPAWRAAPAAYDTSDTHLQILGKPVMERWETPYMHSLAAAAASRGGRVLEVGFGMAIAASRVQQAPIKEHWIIECNDGVFQRLQNWALKQPHKVVPLKGLWEEVAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKTHAFRLLKPGGILTYCNLTSWGELMKSKYTDITAMFEETQVPALLEAGFQRENICTEVMALVPPADCRYYAFPQMITPLVTKH
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues LA36I
Energy difference between WD and mutated (by FoldX) 1.48305 kcal/mol
Show buried residues

Minimal score value
-2.1693
Maximal score value
1.9309
Average score
-0.2392
Total score value
-54.7756

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 -0.2112
8 L A 0.2903
9 F A 0.7010
10 A A 0.1329
11 P A -0.2542
12 G A -0.4388
13 E A -2.1534
14 D A -2.1034
15 C A -0.2426
16 G A 0.0000
17 P A -0.2532
18 A A -0.0329
19 W A 0.0000
20 R A -0.6878
21 A A -0.0676
22 A A -0.0662
23 P A -0.0420
24 A A 0.0079
25 A A 0.0571
26 Y A 0.0127
27 D A -1.7390
28 T A -0.4291
29 S A -0.4427
30 D A -1.2194
31 T A 0.0000
32 H A -0.1636
33 L A 0.0000
34 Q A -0.4212
35 I A 0.0000
36 I A 1.9309 mutated: LA36I
37 G A -0.3847
38 K A -1.6233
39 P A -0.3995
40 V A 0.0000
41 M A 0.2256
42 E A 0.0000
43 R A -0.5477
44 W A 0.0000
45 E A -0.6113
46 T A -0.1880
47 P A -0.2295
48 Y A 0.3074
49 M A 0.0000
50 H A -0.4144
51 S A -0.1990
52 L A 0.0000
53 A A 0.0000
54 A A 0.0393
55 A A 0.0164
56 A A 0.0000
57 A A -0.0131
58 S A -0.5337
59 R A -1.8927
60 G A -0.4183
61 G A -0.2986
62 R A -1.1845
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 -0.0476
70 M A 0.0000
71 A A 0.0473
72 I A 0.1982
73 A A 0.0432
74 A A 0.0000
75 S A -0.1118
76 R A 0.0000
77 V A 0.0000
78 Q A -0.7922
79 Q A -1.2964
80 A A -0.2416
81 P A -0.2507
82 I A 0.0000
83 K A -1.7969
84 E A -0.9729
85 H A 0.0000
86 W A 0.2323
87 I A 0.0000
88 I A 0.0000
89 E A 0.0000
90 C A 0.0720
91 N A 0.0000
92 D A -0.5661
93 G A -0.2555
94 V A 0.0000
95 F A -0.1534
96 Q A -1.5014
97 R A -2.1609
98 L A 0.0000
99 Q A -0.5555
100 N A -1.4704
101 W A -0.2770
102 A A 0.0000
103 L A 1.2485
104 K A -1.4512
105 Q A -0.5752
106 P A -0.4602
107 H A -1.1987
108 K A -1.0162
109 V A 0.2137
110 V A 0.8089
111 P A 0.0914
112 L A 0.1227
113 K A -1.6389
114 G A -0.1080
115 L A 1.5352
116 W A 0.0000
117 E A -1.3086
118 E A -1.9876
119 V A 0.0000
120 A A 0.0000
121 P A -0.2566
122 T A -0.0534
123 L A 0.0000
124 P A -0.4277
125 D A -1.8068
126 G A 0.0000
127 H A -0.9901
128 F A 0.0000
129 D A 0.0000
130 G A 0.0000
131 I A 0.0000
132 L A 0.1800
133 Y A 0.0000
134 D A -0.1808
135 T A 0.0000
136 Y A 0.0000
137 P A 0.0000
138 L A 0.1524
139 S A -0.1532
140 E A -1.0474
141 E A -0.9835
142 T A -0.1830
143 W A 0.0000
144 H A -0.1224
145 T A -0.0449
146 H A -0.1829
147 Q A 0.0000
148 F A 0.3719
149 N A -0.2408
150 F A 0.0000
151 I A 0.0000
152 K A -1.5470
153 T A -0.3822
154 H A -0.3829
155 A A 0.0000
156 F A 0.0000
157 R A -1.7543
158 L A 0.1168
159 L A 0.0000
160 K A -0.3393
161 P A -0.3235
162 G A -0.1684
163 G A 0.0000
164 I A 0.0000
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 0.0000
171 T A -0.0182
172 S A -0.0545
173 W A 0.0000
174 G A 0.0000
175 E A -1.8707
176 L A 0.4065
177 M A 0.0000
178 K A -1.9310
179 S A -0.8391
180 K A -1.4912
181 Y A 0.9853
182 T A -0.0444
183 D A -1.1277
184 I A 0.0000
185 T A -0.0073
186 A A 0.1112
187 M A 1.0618
188 F A 0.0000
189 E A -0.9153
190 E A -1.9327
191 T A -0.3719
192 Q A 0.0000
193 V A 1.2432
194 P A 0.1197
195 A A 0.0000
196 L A 0.0000
197 L A 1.4186
198 E A -0.3557
199 A A 0.0000
200 G A 0.2313
201 F A 1.3804
202 Q A -1.1924
203 R A -2.1693
204 E A -1.1910
205 N A -1.1408
206 I A 1.0895
207 C A 0.3920
208 T A -0.3347
209 E A -1.5420
210 V A 1.1889
211 M A 0.0000
212 A A 0.0344
213 L A 0.0000
214 V A 1.7248
215 P A 0.0344
216 P A -0.2878
217 A A -0.3256
218 D A -1.6397
219 C A 0.3021
220 R A -0.2007
221 Y A 0.8577
222 Y A 0.0000
223 A A 0.0867
224 F A 0.3033
225 P A -0.1171
226 Q A -0.4629
227 M A 0.0000
228 I A 0.0000
229 T A -0.0082
230 P A 0.0000
231 L A 0.2633
232 V A 0.0000
233 T A -0.1119
234 K A -0.7186
235 H A -1.0917

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, -0.2392 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015