Project name: l285n [mutate: LA285N]

Status: done

submitted: 2017-05-19 14:48:00, status changed: 2017-05-19 17:37:39
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Chain sequence(s) A: MRSGSHHHHHHRSDITSLYKKAGSAAAPFTMENLYFQSYQGNSDCYFGNGSAYRGTHSLTESGASCLPWNSMILIGKVYTAQNPSAQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTWEYCDVPSCSTCGLRQYSQPQFRIKGGLFADIASHPWQAAIFAKHRRSPGERFLCGGILISSCWILSAAHCFQERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQLKSDSSRCAQESSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKEAHVRLYPSSRCTSQHLLNRTVTDNMLCAGDTRSGGPQANLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQKDVPGVYTKVTNYLDWIRDNMRP
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues LA285N
Energy difference between WD and mutated (by FoldX) 0.974809 kcal/mol
Show buried residues

Minimal score value
-2.6391
Maximal score value
2.4143
Average score
-0.2621
Total score value
-102.7614

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 0.7007
2 R A -1.6813
3 S A -0.5576
4 G A -0.1248
5 S A -0.3209
6 H A -0.6558
7 H A -0.5361
8 H A -1.2234
9 H A -1.3605
10 H A -1.1728
11 H A 0.0000
12 R A -1.8848
13 S A -0.7582
14 D A -1.0294
15 I A 0.0000
16 T A -0.1028
17 S A -0.1136
18 L A 0.3670
19 Y A 0.0000
20 K A -1.7398
21 K A -0.5198
22 A A -0.0750
23 G A -0.4656
24 S A -0.1416
25 A A 0.0000
26 A A 0.0506
27 A A 0.0321
28 P A 0.0000
29 F A 1.9275
30 T A 0.4900
31 M A 0.7069
32 E A -1.8539
33 N A -1.5213
34 L A 0.4334
35 Y A 1.3920
36 F A 0.0000
37 Q A -0.7752
38 S A -0.3494
39 Y A 0.0000
40 Q A 0.0000
41 G A -0.2068
42 N A -0.6162
43 S A 0.0000
44 D A -1.8230
45 C A 0.2153
46 Y A 1.7085
47 F A 2.0727
48 G A 0.0000
49 N A -0.6785
50 G A 0.0000
51 S A -0.1103
52 A A -0.0281
53 Y A 0.0764
54 R A -0.5239
55 G A 0.0000
56 T A -0.3061
57 H A -1.0218
58 S A -0.0533
59 L A 1.5276
60 T A 0.0000
61 E A -1.1585
62 S A -0.4685
63 G A -0.3480
64 A A -0.0783
65 S A -0.2093
66 C A 0.0000
67 L A 0.1087
68 P A -0.2852
69 W A 0.0000
70 N A -1.2027
71 S A -0.3511
72 M A 1.1048
73 I A 2.4143
74 L A 1.9242
75 I A 0.0000
76 G A -0.4240
77 K A -1.7620
78 V A 0.0000
79 Y A 0.0705
80 T A -0.0337
81 A A -0.0550
82 Q A -0.5749
83 N A -0.3318
84 P A 0.0000
85 S A -0.1692
86 A A -0.0975
87 Q A -0.2952
88 A A 0.0000
89 L A 0.0000
90 G A 0.1589
91 L A 0.8681
92 G A -0.5826
93 K A -1.7883
94 H A 0.0000
95 N A -0.6576
96 Y A 0.0000
97 C A 0.0000
98 R A 0.0000
99 N A 0.0000
100 P A 0.0000
101 D A -1.2836
102 G A -0.3819
103 D A -0.3662
104 A A -0.0319
105 K A 0.0000
106 P A 0.0000
107 W A 0.0000
108 C A 0.0000
109 H A 0.0000
110 V A 0.0000
111 L A 0.0510
112 K A -2.2641
113 N A -1.9351
114 R A -2.6391
115 R A -2.1316
116 L A 1.1070
117 T A 0.2548
118 W A 0.2544
119 E A -0.2074
120 Y A 0.1208
121 C A 0.0000
122 D A -0.4653
123 V A 0.0918
124 P A -0.3485
125 S A -0.0419
126 C A 0.1968
127 S A 0.0000
128 T A -0.0095
129 C A 0.0000
130 G A -0.3106
131 L A 0.0000
132 R A -2.0020
133 Q A -1.1871
134 Y A 0.0000
135 S A -0.1488
136 Q A -0.3848
137 P A -0.3677
138 Q A -0.0642
139 F A 1.3693
140 R A -1.4060
141 I A 0.2084
142 K A -1.5800
143 G A -0.5624
144 G A -0.4412
145 L A 0.5211
146 F A 1.7973
147 A A 0.2777
148 D A -0.4328
149 I A 0.2571
150 A A 0.0782
151 S A -0.2218
152 H A -0.1562
153 P A -0.0519
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 -0.8349
162 H A -1.2586
163 R A -0.8083
164 R A -0.8906
165 S A -0.2663
166 P A -0.3622
167 G A -0.6219
168 E A -1.0148
169 R A -1.9223
170 F A 0.0000
171 L A 0.2688
172 C A 0.0000
173 G A 0.0000
174 G A 0.0000
175 I A 0.2427
176 L A 0.0000
177 I A 0.0000
178 S A -0.0465
179 S A -0.0488
180 C A 0.1200
181 W A 0.0000
182 I A 0.0000
183 L A 0.0000
184 S A 0.0000
185 A A 0.0061
186 A A 0.0000
187 H A -0.3247
188 C A 0.0725
189 F A -0.0962
190 Q A -1.7064
191 E A -2.3829
192 R A -2.2874
193 F A 0.0000
194 P A -0.1392
195 P A -0.4309
196 H A -1.0038
197 H A -0.5019
198 L A 0.0000
199 T A -0.0071
200 V A 0.0000
201 I A 0.0000
202 L A 0.0000
203 G A -0.0942
204 R A 0.0000
205 T A 0.0000
206 Y A 0.8877
207 R A -1.5409
208 V A 0.3823
209 V A 1.1080
210 P A -0.1686
211 G A -0.9241
212 E A -1.9834
213 E A -0.9002
214 E A -0.6890
215 Q A -0.7317
216 K A -1.6035
217 F A 0.0000
218 E A -1.7185
219 V A 0.0000
220 E A -0.5911
221 K A -1.5516
222 Y A 0.0000
223 I A 0.7055
224 V A 0.5189
225 H A 0.0000
226 K A -0.9534
227 E A 0.0000
228 F A 0.0000
229 D A -1.0049
230 D A -1.3334
231 D A -1.9412
232 T A -0.4129
233 Y A 0.1222
234 D A 0.0000
235 N A -0.1334
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 0.0000
242 L A -0.1510
243 K A -1.6802
244 S A -0.5575
245 D A -1.0948
246 S A 0.0000
247 S A -0.4471
248 R A -1.8605
249 C A 0.0000
250 A A 0.0000
251 Q A -1.5442
252 E A -2.0423
253 S A -0.6284
254 S A -0.0214
255 V A 1.9594
256 V A 1.5053
257 R A -0.1323
258 T A -0.0313
259 V A 0.3014
260 C A 0.2800
261 L A 0.0000
262 P A -0.3017
263 P A -0.3001
264 A A -0.3042
265 D A -1.1554
266 L A -0.1317
267 Q A -0.9264
268 L A 0.8878
269 P A -0.1433
270 D A -0.4721
271 W A 0.0969
272 T A -0.0814
273 E A -0.3931
274 C A 0.0000
275 E A 0.0000
276 L A 0.0000
277 S A 0.0000
278 G A 0.0000
279 Y A 0.0000
280 G A -0.1311
281 K A -0.3657
282 H A -0.5591
283 E A -1.8476
284 A A -0.5478
285 N A -1.3072 mutated: LA285N
286 S A -0.4896
287 P A 0.0656
288 F A 2.1309
289 Y A 1.6597
290 S A 0.1734
291 E A -0.3378
292 R A -0.4289
293 L A 0.0000
294 K A -1.4987
295 E A -0.5096
296 A A 0.0000
297 H A -0.0750
298 V A -0.1489
299 R A -1.8101
300 L A 0.0000
301 Y A 1.2719
302 P A -0.0095
303 S A -0.3252
304 S A -0.4551
305 R A -1.4821
306 C A 0.0000
307 T A -0.2609
308 S A -0.2914
309 Q A -0.5094
310 H A -0.5679
311 L A 0.0000
312 L A -0.1415
313 N A -1.6093
314 R A -2.0479
315 T A -0.2835
316 V A 0.1709
317 T A -0.1685
318 D A -1.0319
319 N A -0.3261
320 M A 0.0753
321 L A 0.0000
322 C A 0.0000
323 A A 0.0000
324 G A -0.4720
325 D A -1.1510
326 T A -0.3144
327 R A -0.4886
328 S A -0.3799
329 G A -0.5155
330 G A -0.1929
331 P A -0.4770
332 Q A -1.2328
333 A A -0.2638
334 N A -0.2796
335 L A 1.3705
336 H A -0.2038
337 D A -0.6700
338 A A -0.0819
339 C A -0.1427
340 Q A -1.1932
341 G A -0.2885
342 D A 0.0000
343 S A -0.0358
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 -0.4739
352 D A -1.9043
353 G A -0.9806
354 R A -0.9781
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 0.0000
363 W A 0.0000
364 G A -0.1854
365 L A 0.1886
366 G A 0.0000
367 C A 0.5386
368 G A -0.4903
369 Q A -1.1714
370 K A -1.6937
371 D A -0.5355
372 V A 0.0000
373 P A -0.0581
374 G A 0.0000
375 V A 0.0000
376 Y A 0.0000
377 T A 0.0000
378 K A -0.2348
379 V A 0.0000
380 T A -0.0074
381 N A 0.0000
382 Y A 0.0000
383 L A 0.4121
384 D A 0.0000
385 W A 0.0000
386 I A 0.0000
387 R A -0.7261
388 D A -1.3176
389 N A -0.2395
390 M A 0.8540
391 R A -0.5222
392 P A -0.3440

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, -0.2621 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015