Project name: b72f5a622b4a7e6 [mutate: LA37S]

Status: done

submitted: 2017-03-14 08:01:11, status changed: 2017-03-14 10:26:47
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Chain sequence(s) A: TPIFAPGENCSPAWGAAPAAYDAADTHLRILGKPVMERWETPYMHALAAAASSKGGRVLEVGFGMAIAASKVQEAPIDEHWIIECNDGVFQRLRDWAPRQTHKVIPLKGLWEDVAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKNHAFRLLKPGGVLTYCNLTSWGELMKSKYSDITIMFEETQVPALLEAGFRRENIRTEVMALVPPADCRYYAFPQMITPLVTK
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues LA37S
Energy difference between WD and mutated (by FoldX) 1.26866 kcal/mol
Show buried residues

Minimal score value
-2.4352
Maximal score value
2.151
Average score
-0.3109
Total score value
-71.1962

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 -0.0998
8 P A -0.0743
9 I A 0.5487
10 F A 0.3432
11 A A 0.0470
12 P A -0.3256
13 G A -0.8668
14 E A -1.9769
15 N A -0.6826
16 C A 0.0000
17 S A -0.1398
18 P A -0.3117
19 A A 0.0085
20 W A 0.1986
21 G A -0.4324
22 A A -0.0180
23 A A -0.0054
24 P A -0.2486
25 A A 0.0000
26 A A 0.0886
27 Y A -0.1660
28 D A -1.7523
29 A A -0.3170
30 A A -0.2799
31 D A -1.7782
32 T A 0.0000
33 H A -0.2375
34 L A 0.0000
35 R A -1.8711
36 I A 0.0000
37 S A -0.3053 mutated: LA37S
38 G A -0.8120
39 K A -1.8288
40 P A -0.7083
41 V A 0.3688
42 M A 0.9836
43 E A -0.1157
44 R A -0.5735
45 W A -0.0563
46 E A -0.5437
47 T A -0.1558
48 P A -0.1431
49 Y A 0.0000
50 M A -0.0504
51 H A -0.8492
52 A A 0.0000
53 L A 0.0000
54 A A 0.0000
55 A A 0.0292
56 A A 0.0000
57 A A 0.0000
58 S A -0.3056
59 S A -0.5443
60 K A -1.7583
61 G A -0.4063
62 G A -0.4845
63 R A -0.8849
64 V A 0.0000
65 L A 0.0000
66 E A 0.0000
67 V A 0.0000
68 G A 0.0000
69 F A 0.2459
70 G A -0.1823
71 M A 0.0000
72 A A 0.1253
73 I A 0.5907
74 A A 0.0000
75 A A 0.0000
76 S A -0.2064
77 K A -0.8779
78 V A 0.0000
79 Q A -0.8098
80 E A -1.9773
81 A A -0.3401
82 P A -0.4270
83 I A -0.0622
84 D A -1.8112
85 E A -0.8450
86 H A 0.0000
87 W A 0.1199
88 I A 0.0000
89 I A 0.0000
90 E A 0.0000
91 C A 0.0000
92 N A 0.0000
93 D A -1.1414
94 G A -0.5076
95 V A 0.0000
96 F A 0.0000
97 Q A -1.5469
98 R A -1.1899
99 L A 0.0000
100 R A -2.1926
101 D A -1.5420
102 W A -0.2123
103 A A -0.1705
104 P A -0.5796
105 R A -1.9087
106 Q A -0.7015
107 T A -0.3032
108 H A -1.3374
109 K A -1.8416
110 V A -0.0816
111 I A 0.2491
112 P A -0.0479
113 L A -0.1575
114 K A -1.7017
115 G A -0.4224
116 L A 0.3572
117 W A -0.3124
118 E A -2.1372
119 D A -2.1272
120 V A 0.0000
121 A A 0.0000
122 P A -0.2671
123 T A -0.0742
124 L A 0.1740
125 P A -0.5480
126 D A -1.8460
127 G A -0.5663
128 H A -0.9986
129 F A 0.0000
130 D A -0.2327
131 G A 0.0000
132 I A 0.0000
133 L A 0.0000
134 Y A 0.0000
135 D A -0.2030
136 T A -0.0443
137 Y A 0.0000
138 P A -0.0204
139 L A 0.1220
140 S A -0.4008
141 E A -2.1718
142 E A -2.1571
143 T A -0.3989
144 W A 0.0000
145 H A -0.2611
146 T A -0.1454
147 H A -0.3438
148 Q A 0.0000
149 F A 0.5483
150 N A -0.6333
151 F A 0.0000
152 I A 0.0000
153 K A -1.0385
154 N A -0.8381
155 H A -0.4740
156 A A 0.0000
157 F A 0.1249
158 R A -1.3151
159 L A 0.0000
160 L A 0.0000
161 K A -1.1392
162 P A -0.3647
163 G A -0.2325
164 G A -0.0640
165 V A 0.2520
166 L A 0.0000
167 T A 0.0000
168 Y A 0.1336
169 C A 0.0000
170 N A 0.0000
171 L A 0.2358
172 T A 0.0302
173 S A -0.0251
174 W A 0.0000
175 G A 0.0000
176 E A -0.5993
177 L A 0.9440
178 M A 0.0000
179 K A -0.9674
180 S A -0.6206
181 K A -1.0827
182 Y A 0.9219
183 S A -0.1721
184 D A -1.0282
185 I A 0.0000
186 T A 0.3308
187 I A 2.1510
188 M A 1.4567
189 F A 0.1761
190 E A -1.4678
191 E A -1.9753
192 T A -0.3550
193 Q A 0.0000
194 V A 0.5225
195 P A -0.1080
196 A A 0.0000
197 L A 0.0000
198 L A 1.2244
199 E A -1.5437
200 A A -0.4716
201 G A -0.1028
202 F A -0.1700
203 R A -2.1729
204 R A -2.4352
205 E A -1.7462
206 N A -1.3895
207 I A 0.2531
208 R A -0.7596
209 T A -0.2440
210 E A -0.0861
211 V A 1.5894
212 M A 0.4864
213 A A 0.1373
214 L A 0.7566
215 V A 1.8430
216 P A 0.2490
217 P A -0.2553
218 A A 0.0000
219 D A -0.3592
220 C A 0.4767
221 R A -0.4510
222 Y A 1.1599
223 Y A 0.0000
224 A A 0.0127
225 F A 0.0000
226 P A -0.3127
227 Q A -0.3496
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 -0.2695
235 K A -1.7013

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, -0.3109 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015