Project name: V208S [mutate: VA208S, VA208S]

Status: done

submitted: 2017-05-19 15:02:44, status changed: 2017-05-19 17:50:06
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Chain sequence(s) A: MRSGSHHHHHHRSDITSLYKKAGSAAAPFTMENLYFQSYQGNSDCYFGNGSAYRGTHSLTESGASCLPWNSMILIGKVYTAQNPSAQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTWEYCDVPSCSTCGLRQYSQPQFRIKGGLFADIASHPWQAAIFAKHRRSPGERFLCGGILISSCWILSAAHCFQERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQLKSDSSRCAQESSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKEAHVRLYPSSRCTSQHLLNRTVTDNMLCAGDTRSGGPQANLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQKDVPGVYTKVTNYLDWIRDNMRP
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues VA208S, VA208S
Energy difference between WD and mutated (by FoldX) -0.0937005 kcal/mol
Show buried residues

Minimal score value
-2.4419
Maximal score value
2.2733
Average score
-0.2676
Total score value
-104.8851

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
1 M A 0.7210
2 R A -1.6597
3 S A -0.4589
4 G A -0.4918
5 S A -0.3765
6 H A -1.1771
7 H A -1.2962
8 H A -1.3491
9 H A -1.1916
10 H A -0.7599
11 H A -1.3745
12 R A -2.0692
13 S A -0.7202
14 D A -1.8026
15 I A 0.0000
16 T A -0.0986
17 S A -0.1191
18 L A 0.2004
19 Y A 0.1404
20 K A -0.3338
21 K A -0.3787
22 A A -0.0499
23 G A -0.2457
24 S A -0.0700
25 A A 0.0000
26 A A 0.2842
27 A A 0.0154
28 P A 0.0000
29 F A 1.8341
30 T A 0.4758
31 M A 0.8384
32 E A -1.5486
33 N A -0.7039
34 L A 1.4877
35 Y A 1.6491
36 F A 0.4066
37 Q A -1.1640
38 S A -0.1995
39 Y A 1.1129
40 Q A -0.1744
41 G A -0.4183
42 N A -0.5850
43 S A -0.4615
44 D A -1.8122
45 C A -0.0233
46 Y A 1.6910
47 F A 2.1800
48 G A 0.4209
49 N A -0.5636
50 G A -0.1621
51 S A -0.1177
52 A A 0.0517
53 Y A -0.0340
54 R A -1.8798
55 G A -0.8177
56 T A -0.2933
57 H A -1.0153
58 S A 0.0916
59 L A 1.5399
60 T A 0.0000
61 E A -0.3374
62 S A -0.3502
63 G A -0.4948
64 A A -0.0646
65 S A -0.1082
66 C A 0.0000
67 L A 0.0000
68 P A -0.4252
69 W A 0.0000
70 N A -1.3144
71 S A -0.2674
72 M A 1.3897
73 I A 2.2733
74 L A 0.7645
75 I A 0.2410
76 G A -0.5505
77 K A -1.7513
78 V A 0.0000
79 Y A 0.0000
80 T A -0.0613
81 A A -0.0379
82 Q A -0.6103
83 N A -0.9564
84 P A 0.0000
85 S A 0.0000
86 A A -0.0694
87 Q A 0.0000
88 A A 0.0441
89 L A 0.1364
90 G A 0.1330
91 L A 1.4538
92 G A -0.4668
93 K A -1.9573
94 H A -1.1557
95 N A -0.3926
96 Y A 0.0000
97 C A 0.0000
98 R A 0.0000
99 N A 0.0000
100 P A -0.3794
101 D A -1.8773
102 G A -0.8659
103 D A -0.5640
104 A A 0.0000
105 K A 0.0000
106 P A -0.0054
107 W A 0.1215
108 C A 0.0000
109 H A 0.0000
110 V A 0.0000
111 L A 0.1283
112 K A -2.0718
113 N A -1.9466
114 R A -2.4419
115 R A -2.3126
116 L A 0.0673
117 T A 0.2040
118 W A 0.5696
119 E A -0.3536
120 Y A 0.0348
121 C A 0.0000
122 D A -1.7341
123 V A -0.0602
124 P A -0.0529
125 S A -0.0611
126 C A 0.0000
127 S A 0.0000
128 T A 0.0000
129 C A 0.0000
130 G A -0.1781
131 L A -0.1810
132 R A -1.7539
133 Q A -1.4822
134 Y A 0.0000
135 S A -0.2626
136 Q A -1.2051
137 P A 0.0000
138 Q A -0.8256
139 F A 1.3619
140 R A -1.0895
141 I A 1.4371
142 K A -0.9815
143 G A -0.6547
144 G A -0.2984
145 L A 0.6512
146 F A 1.9548
147 A A 0.0229
148 D A -1.6337
149 I A 0.0000
150 A A -0.1341
151 S A -0.2171
152 H A 0.0000
153 P A 0.0000
154 W A 0.0000
155 Q A 0.0000
156 A A 0.0000
157 A A 0.0000
158 I A 0.0000
159 F A 0.0000
160 A A 0.0000
161 K A -0.8496
162 H A -1.4557
163 R A -2.2753
164 R A -1.8177
165 S A -0.4237
166 P A -0.3616
167 G A -0.6854
168 E A -1.1728
169 R A -0.8184
170 F A 0.1518
171 L A 0.0000
172 C A 0.0000
173 G A 0.0000
174 G A 0.0000
175 I A 0.0000
176 L A 0.0000
177 I A 0.0000
178 S A -0.1525
179 S A -0.0638
180 C A 0.1431
181 W A 0.1504
182 I A 0.0000
183 L A 0.0000
184 S A 0.0000
185 A A 0.0000
186 A A 0.1700
187 H A 0.0000
188 C A 0.3833
189 F A 1.0476
190 Q A -1.1141
191 E A -1.3483
192 R A -1.8116
193 F A -0.0841
194 P A -0.1954
195 P A 0.0000
196 H A -1.3416
197 H A -0.6842
198 L A 0.0000
199 T A -0.0103
200 V A 0.0000
201 I A 0.0083
202 L A 0.0000
203 G A 0.0000
204 R A 0.0000
205 T A 0.0000
206 Y A 0.0162
207 R A -0.2392
208 S A -0.0621 mutated: VA208S
209 V A 1.1632
210 P A 0.0000
211 G A -0.8054
212 E A -1.9578
213 E A -0.7290
214 E A -0.7466
215 Q A -0.7707
216 K A -1.7435
217 F A 0.0000
218 E A -1.8199
219 V A 0.0000
220 E A -1.4153
221 K A -1.5653
222 Y A 0.0054
223 I A 0.6000
224 V A 1.1376
225 H A -0.0446
226 K A -0.6200
227 E A 0.0000
228 F A 1.6496
229 D A -0.5267
230 D A -2.2067
231 D A -2.1090
232 T A 0.0000
233 Y A 0.5198
234 D A -0.2347
235 N A -0.2594
236 D A 0.0000
237 I A 0.0000
238 A A 0.0000
239 L A 0.0000
240 L A 0.0000
241 Q A -0.2355
242 L A -0.1191
243 K A -1.6775
244 S A -0.5356
245 D A -0.6292
246 S A 0.0000
247 S A -0.3248
248 R A -1.0438
249 C A 0.0000
250 A A -0.2392
251 Q A -1.6391
252 E A -2.0850
253 S A -0.5744
254 S A -0.0380
255 V A 0.7420
256 V A 0.3165
257 R A 0.0000
258 T A -0.0632
259 V A 0.0000
260 C A 0.5609
261 L A 0.0000
262 P A -0.0626
263 P A -0.0425
264 A A -0.3014
265 D A -1.6254
266 L A 0.5062
267 Q A 0.1226
268 L A 0.7118
269 P A -0.4309
270 D A -1.8093
271 W A -0.2300
272 T A -0.0995
273 E A -0.4686
274 C A 0.0000
275 E A 0.0000
276 L A 0.1501
277 S A 0.0054
278 G A 0.0000
279 Y A 0.0000
280 G A 0.0000
281 K A 0.0000
282 H A -0.3478
283 E A -0.7940
284 A A 0.1594
285 L A 1.4290
286 S A -0.0602
287 P A -0.0798
288 F A 1.3174
289 Y A 0.5428
290 S A -0.0616
291 E A -0.5423
292 R A -1.5127
293 L A 0.0000
294 K A -0.2794
295 E A 0.0000
296 A A -0.0594
297 H A -0.1561
298 V A 0.0000
299 R A -1.6928
300 L A 0.2309
301 Y A 0.2367
302 P A -0.2250
303 S A -0.2947
304 S A -0.4294
305 R A -1.0004
306 C A 0.0000
307 T A -0.0587
308 S A -0.4445
309 Q A -1.2388
310 H A 0.0000
311 L A 0.3650
312 L A 1.3905
313 N A -0.7431
314 R A 0.0000
315 T A -0.0055
316 V A 0.3341
317 T A -0.0670
318 D A -0.3899
319 N A -0.2908
320 M A 0.0000
321 L A 0.3771
322 C A 0.0000
323 A A 0.0000
324 G A -0.2239
325 D A -0.9000
326 T A 0.0000
327 R A -1.8830
328 S A -0.6393
329 G A -0.5354
330 G A -0.2826
331 P A -0.5113
332 Q A -1.2366
333 A A -0.2828
334 N A -0.3790
335 L A 1.3800
336 H A -0.0502
337 D A -0.4796
338 A A -0.0650
339 C A -0.0827
340 Q A -0.6323
341 G A -0.1963
342 D A 0.0000
343 S A -0.0691
344 G A 0.0000
345 G A 0.0000
346 P A 0.0000
347 L A 0.0000
348 V A 0.0000
349 C A 0.0000
350 L A 0.0000
351 N A -0.4261
352 D A -1.8698
353 G A -0.7667
354 R A -0.7435
355 M A 0.0000
356 T A 0.0000
357 L A 0.0000
358 V A 0.0000
359 G A 0.0000
360 I A 0.0000
361 I A 0.0000
362 S A 0.0556
363 W A 0.3511
364 G A -0.2567
365 L A 0.0000
366 G A 0.0000
367 C A 0.0841
368 G A -0.6540
369 Q A -1.6083
370 K A -2.0690
371 D A -1.0350
372 V A 0.0808
373 P A -0.0043
374 G A 0.0000
375 V A 0.0000
376 Y A 0.0000
377 T A 0.0000
378 K A 0.0000
379 V A 0.0000
380 T A 0.0000
381 N A -0.1669
382 Y A 0.0000
383 L A 0.0000
384 D A -0.6118
385 W A 0.0000
386 I A -0.1218
387 R A -2.1429
388 D A -2.3317
389 N A -1.2539
390 M A -0.1464
391 R A -1.8121
392 P A -0.5779

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, -0.2676 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015