Project name: l11n [mutate: LA111N]

Status: done

submitted: 2017-05-19 14:22:09, status changed: 2017-05-19 17:25:42
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Chain sequence(s) A: MRSGSHHHHHHRSDITSLYKKAGSAAAPFTMENLYFQSYQGNSDCYFGNGSAYRGTHSLTESGASCLPWNSMILIGKVYTAQNPSAQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTWEYCDVPSCSTCGLRQYSQPQFRIKGGLFADIASHPWQAAIFAKHRRSPGERFLCGGILISSCWILSAAHCFQERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQLKSDSSRCAQESSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKEAHVRLYPSSRCTSQHLLNRTVTDNMLCAGDTRSGGPQANLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQKDVPGVYTKVTNYLDWIRDNMRP
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues LA111N
Energy difference between WD and mutated (by FoldX) -1.12739 kcal/mol
Show buried residues

Minimal score value
-2.4799
Maximal score value
2.1447
Average score
-0.259
Total score value
-101.5378

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 0.6511
2 R A -1.6576
3 S A -0.6819
4 G A -0.5411
5 S A -0.3866
6 H A -0.6768
7 H A -1.2397
8 H A -1.3604
9 H A -1.3205
10 H A -0.8414
11 H A 0.0000
12 R A -1.8789
13 S A -0.6520
14 D A -0.6398
15 I A 1.3524
16 T A 0.2062
17 S A -0.1402
18 L A 0.5369
19 Y A 0.1782
20 K A -0.3126
21 K A -0.4381
22 A A -0.2139
23 G A -0.4689
24 S A -0.1224
25 A A 0.0000
26 A A 0.0124
27 A A -0.0223
28 P A 0.0145
29 F A 0.5514
30 T A -0.0246
31 M A 0.6848
32 E A -1.8537
33 N A -1.4274
34 L A 0.9298
35 Y A 1.8391
36 F A 1.9443
37 Q A -0.8566
38 S A -0.3791
39 Y A 0.2035
40 Q A 0.0000
41 G A -0.1433
42 N A 0.0000
43 S A -0.2494
44 D A -0.0370
45 C A 0.5157
46 Y A 1.7101
47 F A 2.1447
48 G A 0.1335
49 N A -0.2770
50 G A -0.2901
51 S A 0.0000
52 A A 0.0621
53 Y A -0.0025
54 R A -1.6411
55 G A -0.4569
56 T A -0.1704
57 H A -0.4998
58 S A -0.0927
59 L A 0.5843
60 T A -0.0280
61 E A -0.7626
62 S A -0.4221
63 G A -0.5699
64 A A -0.0328
65 S A -0.0109
66 C A 0.0000
67 L A 0.0000
68 P A -0.4296
69 W A 0.0000
70 N A -0.7790
71 S A -0.1529
72 M A 1.0589
73 I A 0.4935
74 L A 0.7915
75 I A 1.8520
76 G A -0.2780
77 K A -1.4870
78 V A 0.0000
79 Y A 0.2478
80 T A -0.0138
81 A A -0.2014
82 Q A -1.2233
83 N A -0.4033
84 P A -0.1332
85 S A -0.1422
86 A A 0.0109
87 Q A 0.0000
88 A A 0.0636
89 L A 0.2531
90 G A 0.0875
91 L A 0.4856
92 G A -0.3434
93 K A -1.9054
94 H A -1.2367
95 N A -0.6001
96 Y A 0.0000
97 C A 0.0000
98 R A -0.2004
99 N A 0.0000
100 P A 0.0000
101 D A -1.8635
102 G A -0.7979
103 D A -0.3355
104 A A -0.0385
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 0.4368
111 N A -1.0761 mutated: LA111N
112 K A -2.0318
113 N A -1.9965
114 R A -2.4799
115 R A -2.0393
116 L A 0.3652
117 T A 0.1197
118 W A 0.0808
119 E A -0.1496
120 Y A 0.0000
121 C A 0.0000
122 D A -1.1261
123 V A -0.0013
124 P A -0.0162
125 S A -0.0323
126 C A 0.0000
127 S A 0.0000
128 T A -0.0084
129 C A 0.0000
130 G A -0.0915
131 L A 0.0000
132 R A -1.9912
133 Q A -1.1581
134 Y A 0.0000
135 S A -0.2816
136 Q A -1.2563
137 P A -0.7021
138 Q A -1.1715
139 F A -0.1832
140 R A -1.3515
141 I A 0.4691
142 K A -1.5337
143 G A -0.4626
144 G A -0.4028
145 L A 0.7232
146 F A 2.0259
147 A A 0.0531
148 D A -1.4319
149 I A 1.6972
150 A A 0.4346
151 S A -0.2116
152 H A 0.0000
153 P A -0.0450
154 W A 0.0000
155 Q A -0.1771
156 A A 0.0000
157 A A 0.0000
158 I A 0.0000
159 F A 0.0000
160 A A -0.1559
161 K A -1.3317
162 H A -1.3064
163 R A -1.0647
164 R A -1.1420
165 S A -0.4974
166 P A -0.3936
167 G A -0.6273
168 E A -0.7125
169 R A -0.4201
170 F A 0.0000
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 -0.1204
179 S A -0.2267
180 C A 0.0000
181 W A 0.0000
182 I A 0.0000
183 L A 0.0000
184 S A 0.0000
185 A A 0.0000
186 A A -0.0605
187 H A -0.3498
188 C A 0.0000
189 F A 0.0000
190 Q A -1.3090
191 E A -2.2907
192 R A -1.9717
193 F A 0.0050
194 P A -0.3685
195 P A -0.3294
196 H A -1.0326
197 H A -0.3130
198 L A 0.0000
199 T A -0.0075
200 V A 0.0000
201 I A 0.2023
202 L A 0.0000
203 G A -0.0898
204 R A -0.2758
205 T A 0.0000
206 Y A -0.0250
207 R A -0.8149
208 V A 1.7504
209 V A 1.2382
210 P A -0.0545
211 G A -0.7841
212 E A -2.0419
213 E A -1.2228
214 E A -0.6453
215 Q A -0.8742
216 K A -0.8007
217 F A 0.0000
218 E A -0.3211
219 V A 0.0000
220 E A -0.8458
221 K A -1.2090
222 Y A 0.3973
223 I A 0.4596
224 V A 0.3275
225 H A 0.0000
226 K A -0.3527
227 E A -0.1610
228 F A 0.3307
229 D A -1.4831
230 D A -2.3349
231 D A -2.2619
232 T A -0.3147
233 Y A 0.0996
234 D A -0.1897
235 N A -0.2128
236 D A -0.2123
237 I A 0.0000
238 A A 0.0000
239 L A 0.0000
240 L A 0.0000
241 Q A -0.2686
242 L A 0.0393
243 K A -1.6338
244 S A -0.5621
245 D A -1.3876
246 S A -0.3601
247 S A -0.6027
248 R A -1.6939
249 C A 0.0000
250 A A -0.1812
251 Q A -1.6920
252 E A -2.0507
253 S A -0.4236
254 S A -0.1673
255 V A 0.2740
256 V A 0.0000
257 R A -0.4345
258 T A -0.1295
259 V A 0.0000
260 C A 0.5464
261 L A 0.0000
262 P A -0.0888
263 P A -0.0511
264 A A -0.1037
265 D A -0.7258
266 L A -0.1836
267 Q A -1.0835
268 L A 0.2210
269 P A -0.5145
270 D A -1.8112
271 W A -0.2121
272 T A -0.0193
273 E A 0.0000
274 C A 0.0000
275 E A -0.1829
276 L A 0.0000
277 S A -0.0305
278 G A 0.0000
279 Y A 0.1455
280 G A -0.1043
281 K A 0.0000
282 H A -0.4737
283 E A -1.8343
284 A A -0.2522
285 L A 0.6140
286 S A -0.0931
287 P A -0.3695
288 F A 0.0000
289 Y A 0.6064
290 S A -0.0876
291 E A 0.0000
292 R A -0.9553
293 L A 0.0000
294 K A -0.5237
295 E A 0.0000
296 A A -0.0033
297 H A 0.0000
298 V A 0.1000
299 R A -0.6750
300 L A 0.1712
301 Y A 0.0000
302 P A -0.2714
303 S A -0.2904
304 S A -0.3907
305 R A -0.6649
306 C A 0.0000
307 T A -0.1827
308 S A -0.3394
309 Q A -0.6678
310 H A -0.3160
311 L A 0.2404
312 L A 0.4725
313 N A -1.2104
314 R A -0.5886
315 T A -0.0125
316 V A 0.2030
317 T A -0.1898
318 D A -1.2665
319 N A -0.5303
320 M A 0.1754
321 L A 0.2578
322 C A 0.0000
323 A A 0.0000
324 G A 0.0000
325 D A -0.5341
326 T A -0.1703
327 R A 0.0000
328 S A -0.3218
329 G A -0.5362
330 G A -0.3145
331 P A -0.5159
332 Q A -1.2370
333 A A -0.2672
334 N A -0.2915
335 L A 1.2558
336 H A -0.8242
337 D A -0.7882
338 A A 0.0000
339 C A 0.0631
340 Q A -0.2192
341 G A -0.0918
342 D A 0.0000
343 S A -0.0270
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 0.2060
351 N A -0.6242
352 D A -2.1373
353 G A -1.0866
354 R A -2.1265
355 M A 0.0000
356 T A -0.0161
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 -0.0351
363 W A 0.0000
364 G A 0.2377
365 L A 1.4478
366 G A -0.1020
367 C A 0.0000
368 G A -0.4539
369 Q A -1.2728
370 K A -0.5207
371 D A -0.5091
372 V A 0.0000
373 P A 0.0000
374 G A 0.0000
375 V A 0.0000
376 Y A 0.0000
377 T A 0.0136
378 K A 0.0000
379 V A 0.0000
380 T A -0.0070
381 N A 0.0000
382 Y A 0.0000
383 L A 0.4910
384 D A 0.0000
385 W A 0.0000
386 I A 0.1652
387 R A -1.7937
388 D A -0.5635
389 N A 0.0216
390 M A 0.7957
391 R A -0.9987
392 P A -0.4870

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, -0.259 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015