Project name: mutat4 [mutate: LA37G] [mutate: VA211T]

Status: done

submitted: 2017-03-16 22:13:01, status changed: 2017-03-17 00:33:12
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Chain sequence(s) A: TPIFAPGENCSPAWGAAPAAYDAADTHLRIGGKPVMERWETPYMHALAAAASSKGGRVLEVGFGMAIAASKVQEAPIDEHWIIECNDGVFQRLRDWAPRQTHKVIPLKGLWEDVAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKNHAYRLLKPGGVLTYCNLTSWGELMKSKYSDITDMFEETQVPALLEAGFRRENIRTEVMANSPPADCRYYAFPQMITPLVTKS
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues VA211T
Energy difference between WD and mutated (by FoldX) -0.042097 kcal/mol
Show buried residues

Minimal score value
-2.148
Maximal score value
1.6721
Average score
-0.3219
Total score value
-74.0433

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 -0.0769
8 P A -0.0459
9 I A 0.0000
10 F A 0.0000
11 A A 0.0000
12 P A -0.0654
13 G A 0.0000
14 E A -2.0595
15 N A -1.6155
16 C A 0.0000
17 S A 0.0000
18 P A -0.2506
19 A A -0.0188
20 W A 0.0000
21 G A -0.2544
22 A A 0.0097
23 A A 0.0110
24 P A -0.0639
25 A A 0.0000
26 A A 0.0551
27 Y A -0.1738
28 D A -1.7573
29 A A -0.3588
30 A A -0.0587
31 D A -0.6104
32 T A 0.0000
33 H A -0.3254
34 L A 0.0000
35 R A -1.8311
36 I A -0.3804
37 G A -0.5183
38 G A -0.7828
39 K A -1.3835
40 P A -0.6176
41 V A 0.5052
42 M A 1.0754
43 E A 0.0000
44 R A -0.6305
45 W A 0.0000
46 E A -1.8212
47 T A -0.3330
48 P A -0.1347
49 Y A 0.0000
50 M A 0.0000
51 H A -0.7118
52 A A 0.0000
53 L A 0.0000
54 A A 0.0175
55 A A 0.0608
56 A A 0.0165
57 A A 0.0000
58 S A -0.1994
59 S A -0.5579
60 K A -1.8291
61 G A -0.8096
62 G A -0.5472
63 R A -1.3405
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 0.0000
70 G A 0.0000
71 M A 0.0000
72 A A 0.0952
73 I A 0.5016
74 A A 0.0955
75 A A 0.0000
76 S A -0.1902
77 K A -0.6436
78 V A 0.0000
79 Q A -0.6544
80 E A -1.9176
81 A A -0.3686
82 P A -0.2856
83 I A 0.0000
84 D A -1.9777
85 E A -0.6360
86 H A 0.0000
87 W A 0.0000
88 I A 0.0000
89 I A 0.0000
90 E A 0.0000
91 C A 0.0842
92 N A 0.0000
93 D A -1.0880
94 G A 0.0000
95 V A 0.0000
96 F A 1.0054
97 Q A -0.5975
98 R A 0.0000
99 L A 0.0000
100 R A -1.7267
101 D A -1.3056
102 W A 0.0000
103 A A 0.0104
104 P A -0.5532
105 R A -2.1078
106 Q A -1.5515
107 T A -0.3257
108 H A -0.4740
109 K A -1.6252
110 V A 0.3530
111 I A 0.6134
112 P A -0.0879
113 L A -0.1228
114 K A -1.6153
115 G A -0.3241
116 L A 0.3160
117 W A 0.0000
118 E A -0.8249
119 D A -1.8804
120 V A 0.0000
121 A A -0.0990
122 P A -0.2669
123 T A -0.0409
124 L A 0.3519
125 P A -0.3955
126 D A -1.3349
127 G A -0.7200
128 H A -0.4800
129 F A 0.0000
130 D A -0.2842
131 G A -0.0983
132 I A 0.0000
133 L A 0.1735
134 Y A 0.0000
135 D A 0.0000
136 T A 0.0000
137 Y A 0.0000
138 P A 0.0000
139 L A 0.1602
140 S A -0.1715
141 E A -0.9348
142 E A -1.9358
143 T A -0.3332
144 W A 0.0632
145 H A -0.4833
146 T A -0.1867
147 H A -0.1840
148 Q A 0.0000
149 F A 0.8600
150 N A -0.2712
151 F A 0.0000
152 I A 0.0000
153 K A -0.7330
154 N A 0.0000
155 H A -0.9901
156 A A 0.0000
157 Y A 0.0000
158 R A -1.8089
159 L A -0.1165
160 L A 0.0000
161 K A -0.8243
162 P A -0.4791
163 G A -0.5119
164 G A 0.0000
165 V A 0.3363
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 -0.0325
174 W A 0.0000
175 G A 0.0000
176 E A -0.9245
177 L A 0.0000
178 M A -0.1091
179 K A -1.2441
180 S A -0.6433
181 K A -1.6724
182 Y A -0.0834
183 S A -0.4411
184 D A -1.7150
185 I A 0.3243
186 T A 0.0000
187 D A -1.5896
188 M A 0.7759
189 F A 0.0000
190 E A -1.5237
191 E A -2.0410
192 T A -0.3248
193 Q A 0.0000
194 V A 1.2637
195 P A 0.2436
196 A A 0.0000
197 L A 0.0000
198 L A 1.1728
199 E A -1.5078
200 A A -0.4170
201 G A 0.3926
202 F A 1.6721
203 R A -1.4132
204 R A -2.1480
205 E A -0.8026
206 N A -1.1881
207 I A 0.1154
208 R A -1.7202
209 T A -0.4217
210 E A -0.3278
211 T A -0.0754 mutated: VA211T
212 M A 0.3096
213 A A 0.0040
214 N A -0.4329
215 S A -0.2872
216 P A 0.0000
217 P A -0.2461
218 A A -0.3661
219 D A -1.7621
220 C A -0.4682
221 R A -1.7008
222 Y A 0.2641
223 Y A 0.0000
224 A A 0.0257
225 F A 0.0000
226 P A -0.2091
227 Q A -0.4047
228 M A 0.0000
229 I A 0.0000
230 T A 0.0000
231 P A 0.0000
232 L A 0.1673
233 V A 0.0000
234 T A -0.0208
235 K A -0.2939
236 S A -0.2550

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, -0.3219 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015