Project name: mutat4 [mutate: LA37S]

Status: done

submitted: 2017-03-16 17:23:38, status changed: 2017-03-16 20:02:03
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Chain sequence(s) A: TPIFAPGENCSPAWGAAPAAYDAADTHLRILGKPVMERWETPYMHALAAAASSKGGRVLEVGFGMAIAASKVQEAPIDEHWIIECNDGVFQRLRDWAPRQTHKVIPLKGLWEDVAPTLPDGHFDGILYDTYPLSEETWHTHQFNFIKNHAYRLLKPGGVLTYCNLTSWGELMKSKYSDITDMFEETQVPALLEAGFRRENIRTEVMANSPPADCRYYAFPQMITPLVTKS
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues LA37S
Energy difference between WD and mutated (by FoldX) 1.66992 kcal/mol
Show buried residues

Minimal score value
-2.1226
Maximal score value
2.0305
Average score
-0.3061
Total score value
-70.4093

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 -0.0878
8 P A 0.2718
9 I A 2.0305
10 F A 0.5734
11 A A 0.0728
12 P A -0.1486
13 G A -0.5579
14 E A -2.0905
15 N A -1.5580
16 C A -0.0127
17 S A -0.2106
18 P A -0.3346
19 A A 0.0414
20 W A 0.0341
21 G A -0.4666
22 A A -0.0422
23 A A -0.0656
24 P A -0.2172
25 A A 0.0498
26 A A -0.0365
27 Y A 0.0819
28 D A -1.0596
29 A A -0.1763
30 A A -0.2876
31 D A -1.7779
32 T A 0.0000
33 H A -0.3441
34 L A 0.0000
35 R A -0.9617
36 I A 0.3235
37 S A -0.1315 mutated: LA37S
38 G A -0.4928
39 K A -0.7235
40 P A -0.4752
41 V A 0.1824
42 M A 0.0000
43 E A -0.7600
44 R A -0.6445
45 W A 0.0000
46 E A -0.2246
47 T A -0.1190
48 P A -0.0470
49 Y A 0.0000
50 M A 0.0000
51 H A -0.9888
52 A A -0.1738
53 L A 0.0000
54 A A 0.0000
55 A A 0.0512
56 A A 0.0151
57 A A 0.0000
58 S A -0.0400
59 S A -0.3613
60 K A -1.7939
61 G A -0.8682
62 G A -0.6010
63 R A -0.3255
64 V A 0.0000
65 L A 0.0000
66 E A -0.2300
67 V A 0.0000
68 G A 0.0000
69 F A 0.0000
70 G A -0.1136
71 M A 0.0000
72 A A 0.0000
73 I A 0.4607
74 A A 0.0000
75 A A -0.0027
76 S A -0.1786
77 K A -0.8328
78 V A 0.0974
79 Q A 0.0000
80 E A -1.8882
81 A A -0.3384
82 P A -0.2461
83 I A 0.0000
84 D A -2.0503
85 E A -1.7756
86 H A 0.0000
87 W A 0.0000
88 I A 0.0000
89 I A 0.0000
90 E A -0.2020
91 C A -0.0039
92 N A -0.5113
93 D A -0.9644
94 G A -0.5667
95 V A 0.3688
96 F A 0.5115
97 Q A -0.8184
98 R A -0.9159
99 L A 0.0000
100 R A -1.7571
101 D A -2.0110
102 W A -0.3579
103 A A 0.0000
104 P A -0.5909
105 R A -1.9621
106 Q A -0.8479
107 T A -0.2184
108 H A -0.4261
109 K A -1.6511
110 V A 0.2635
111 I A 1.0646
112 P A 0.2066
113 L A 0.2205
114 K A -1.6686
115 G A -0.5796
116 L A 0.4181
117 W A 0.0000
118 E A -0.7937
119 D A -1.9012
120 V A 0.0000
121 A A 0.0008
122 P A -0.4455
123 T A -0.0255
124 L A 0.2700
125 P A -0.5266
126 D A -1.8491
127 G A -0.5770
128 H A -1.0016
129 F A 0.0000
130 D A -0.7283
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 0.2170
138 P A 0.1577
139 L A 1.5065
140 S A 0.1941
141 E A -0.5443
142 E A -1.8690
143 T A -0.4135
144 W A 0.0000
145 H A -0.2503
146 T A -0.1481
147 H A -0.1851
148 Q A 0.0000
149 F A 1.8199
150 N A -0.4120
151 F A 0.0000
152 I A 0.1029
153 K A -0.7577
154 N A -1.4650
155 H A -0.8343
156 A A 0.0000
157 Y A -0.1288
158 R A -1.6434
159 L A 0.0000
160 L A 0.0000
161 K A -1.7259
162 P A -0.4874
163 G A -0.2673
164 G A 0.0000
165 V A 0.2341
166 L A 0.0000
167 T A 0.0000
168 Y A 0.1422
169 C A 0.0000
170 N A -0.1334
171 L A 0.0000
172 T A -0.0403
173 S A -0.1265
174 W A 0.0000
175 G A -0.4164
176 E A -2.0297
177 L A -0.1450
178 M A -0.3422
179 K A -1.9752
180 S A -0.6431
181 K A -0.6541
182 Y A 0.4811
183 S A -0.2622
184 D A -1.3145
185 I A 0.0000
186 T A -0.3637
187 D A -1.7333
188 M A 0.0713
189 F A 0.0000
190 E A -1.9714
191 E A -2.1226
192 T A -0.3949
193 Q A 0.0460
194 V A 1.7211
195 P A 0.3310
196 A A -0.0480
197 L A 0.0000
198 L A 1.1764
199 E A -1.5331
200 A A -0.3687
201 G A 0.3608
202 F A 1.5667
203 R A -1.6888
204 R A -1.5900
205 E A -1.2243
206 N A -1.1921
207 I A 0.3797
208 R A -0.6395
209 T A -0.4547
210 E A -1.1000
211 V A 1.4576
212 M A 0.5057
213 A A -0.0350
214 N A -0.5529
215 S A -0.3233
216 P A -0.1068
217 P A -0.2355
218 A A 0.0000
219 D A -0.4858
220 C A 0.2813
221 R A -1.6520
222 Y A 0.0035
223 Y A 0.0000
224 A A 0.0096
225 F A 0.0000
226 P A -0.1698
227 Q A -0.2963
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 -0.0160
235 K A -0.2330
236 S A -0.2750

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, -0.3061 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015