Project name: mutat4 [mutate: LA37G]

Status: done

submitted: 2017-03-16 13:40:19, status changed: 2017-03-16 16:11:29
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Chain sequence(s) A: TPIFAPGENCSPAWGAAPAAYDAADTHLRILGKPVMERWETPYMHALAAAASSKGGRVLEVGFGMAIAASKVQEAPIDEHWIIECNDGVFQRLRDWAPRQTHKVIPLKGLWEDVAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKNHAYRLLKPGGVLTYCNLTSWGELMKSKYSDITDMFEETQVPALLEAGFRRENIRTEVMANSPPADCRYYAFPQMITPLVTKS
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues LA37G
Energy difference between WD and mutated (by FoldX) 1.50428 kcal/mol
Show buried residues

Minimal score value
-2.2205
Maximal score value
1.7397
Average score
-0.3307
Total score value
-76.0602

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 -0.0515
8 P A -0.0803
9 I A 0.0000
10 F A 0.0000
11 A A -0.0185
12 P A -0.2943
13 G A -0.6535
14 E A -2.0816
15 N A -1.5557
16 C A -0.1422
17 S A -0.1022
18 P A -0.2657
19 A A 0.0113
20 W A 0.1760
21 G A -0.4109
22 A A -0.0257
23 A A -0.0056
24 P A -0.2522
25 A A -0.0357
26 A A -0.1297
27 Y A 0.0000
28 D A -0.3948
29 A A -0.0262
30 A A -0.0029
31 D A -0.3827
32 T A 0.0000
33 H A -0.1226
34 L A -0.1421
35 R A -1.4158
36 I A 0.0000
37 G A -0.5518 mutated: LA37G
38 G A -0.6577
39 K A -0.6927
40 P A -0.3088
41 V A 0.0000
42 M A 0.0000
43 E A 0.0000
44 R A -0.3983
45 W A -0.2710
46 E A -1.8062
47 T A -0.3949
48 P A -0.1806
49 Y A 0.0000
50 M A 0.0000
51 H A -0.9364
52 A A -0.1553
53 L A 0.0000
54 A A 0.0000
55 A A 0.0252
56 A A 0.0000
57 A A 0.0000
58 S A -0.1359
59 S A -0.5290
60 K A -1.7705
61 G A -0.5076
62 G A -0.2018
63 R A -0.6366
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 0.2760
70 G A -0.0294
71 M A 0.0000
72 A A 0.0594
73 I A 0.2618
74 A A 0.0000
75 A A 0.0000
76 S A -0.2360
77 K A -0.6355
78 V A 0.0000
79 Q A -0.7886
80 E A -1.8848
81 A A -0.3781
82 P A -0.3058
83 I A 0.0000
84 D A -1.8371
85 E A -0.6699
86 H A 0.0000
87 W A 0.0000
88 I A 0.0000
89 I A 0.0000
90 E A -0.3174
91 C A -0.0488
92 N A -0.5669
93 D A -1.2853
94 G A -0.3047
95 V A 0.3069
96 F A 1.1688
97 Q A -1.2294
98 R A -1.2248
99 L A -0.2007
100 R A -2.0710
101 D A -1.1112
102 W A -0.1306
103 A A 0.0541
104 P A -0.6761
105 R A -2.0806
106 Q A -1.5440
107 T A -0.3294
108 H A -0.5445
109 K A -1.6938
110 V A 0.1517
111 I A 1.0273
112 P A -0.0303
113 L A -0.1957
114 K A -1.7491
115 G A -0.4318
116 L A 1.4814
117 W A 0.0000
118 E A -0.9932
119 D A -0.6962
120 V A 0.0000
121 A A -0.1420
122 P A -0.2629
123 T A -0.0601
124 L A 0.1615
125 P A -0.5598
126 D A -1.8973
127 G A -0.7101
128 H A -0.3603
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 0.0000
137 Y A 0.0000
138 P A -0.0221
139 L A 0.1199
140 S A -0.1648
141 E A -0.7916
142 E A -1.9598
143 T A -0.3728
144 W A 0.0240
145 H A -0.6185
146 T A -0.1992
147 H A -0.2724
148 Q A 0.0000
149 F A 0.1626
150 N A -1.2023
151 F A 0.0000
152 I A 0.0000
153 K A -1.2022
154 N A -1.2676
155 H A -0.4315
156 A A 0.0000
157 Y A 0.1900
158 R A -0.5703
159 L A 0.0000
160 L A 0.0000
161 K A -1.7396
162 P A -0.6011
163 G A -0.4253
164 G A 0.0000
165 V A 0.1825
166 L A 0.0000
167 T A 0.0000
168 Y A 0.0000
169 C A 0.0000
170 N A 0.0000
171 L A 0.0000
172 T A 0.0000
173 S A 0.0000
174 W A 0.0000
175 G A 0.0000
176 E A -0.4973
177 L A 0.0600
178 M A 0.0000
179 K A -1.7130
180 S A -0.8413
181 K A -1.6090
182 Y A 0.3472
183 S A -0.1791
184 D A -1.4226
185 I A 0.0000
186 T A -0.3524
187 D A -1.8757
188 M A 0.0252
189 F A 0.0000
190 E A -2.1554
191 E A -2.1070
192 T A -0.3347
193 Q A 0.0000
194 V A 0.2397
195 P A 0.1480
196 A A 0.0000
197 L A 0.0000
198 L A 1.0382
199 E A -1.5656
200 A A -0.5418
201 G A 0.0151
202 F A 0.5474
203 R A -2.0117
204 R A -2.2205
205 E A -0.8306
206 N A -1.2103
207 I A 0.0173
208 R A -1.3923
209 T A -0.4153
210 E A -0.2410
211 V A 1.7397
212 M A 0.7790
213 A A 0.0922
214 N A -0.2720
215 S A -0.2731
216 P A 0.0000
217 P A -0.2549
218 A A 0.0000
219 D A -1.6537
220 C A 0.3590
221 R A 0.1411
222 Y A 1.2721
223 Y A 0.0000
224 A A 0.0144
225 F A 0.0000
226 P A -0.3465
227 Q A -0.9936
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 -0.0358
235 K A -0.3410
236 S A -0.2672

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, -0.3307 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015