Project name: l111p [mutate: LA111P]

Status: done

submitted: 2017-05-19 14:22:45, status changed: 2017-05-19 17:22:43
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Chain sequence(s) A: MRSGSHHHHHHRSDITSLYKKAGSAAAPFTMENLYFQSYQGNSDCYFGNGSAYRGTHSLTESGASCLPWNSMILIGKVYTAQNPSAQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTWEYCDVPSCSTCGLRQYSQPQFRIKGGLFADIASHPWQAAIFAKHRRSPGERFLCGGILISSCWILSAAHCFQERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQLKSDSSRCAQESSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKEAHVRLYPSSRCTSQHLLNRTVTDNMLCAGDTRSGGPQANLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQKDVPGVYTKVTNYLDWIRDNMRP
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues LA111P
Energy difference between WD and mutated (by FoldX) -2.12386 kcal/mol
Show buried residues

Minimal score value
-2.6706
Maximal score value
2.1472
Average score
-0.2349
Total score value
-92.0996

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 0.6972
2 R A -1.6473
3 S A -0.5356
4 G A -0.4547
5 S A -0.1581
6 H A -0.3115
7 H A -1.0880
8 H A -0.7662
9 H A -1.2337
10 H A -1.1631
11 H A 0.0000
12 R A -1.3328
13 S A -0.5983
14 D A -1.0938
15 I A 1.6782
16 T A 0.2819
17 S A -0.1841
18 L A 0.2046
19 Y A 0.1418
20 K A -0.6943
21 K A -0.6015
22 A A -0.1169
23 G A -0.4555
24 S A 0.0000
25 A A -0.0538
26 A A 0.0440
27 A A 0.0155
28 P A 0.0000
29 F A 1.9283
30 T A 0.4654
31 M A 0.5914
32 E A -1.8952
33 N A -1.3948
34 L A 1.1811
35 Y A 1.0327
36 F A 1.9567
37 Q A 0.0391
38 S A -0.1676
39 Y A 0.0000
40 Q A -0.1888
41 G A 0.0000
42 N A -0.5677
43 S A 0.0000
44 D A -1.6506
45 C A 0.4779
46 Y A 1.7456
47 F A 2.1472
48 G A -0.1985
49 N A -0.4629
50 G A 0.0000
51 S A 0.0000
52 A A 0.0675
53 Y A 0.1929
54 R A -0.7163
55 G A -0.2318
56 T A -0.2309
57 H A -1.0062
58 S A 0.0212
59 L A 1.5359
60 T A 0.0000
61 E A 0.0000
62 S A -0.6407
63 G A -0.4984
64 A A -0.0989
65 S A -0.1953
66 C A 0.0315
67 L A 0.0000
68 P A -0.2006
69 W A 0.0000
70 N A -1.3031
71 S A -0.2078
72 M A 1.3059
73 I A 0.6034
74 L A 0.9815
75 I A 2.1403
76 G A -0.3688
77 K A -1.7428
78 V A -0.0277
79 Y A 0.3185
80 T A 0.0329
81 A A -0.1174
82 Q A -1.3065
83 N A -0.8864
84 P A 0.0000
85 S A -0.2766
86 A A -0.1292
87 Q A -0.1517
88 A A 0.0061
89 L A 0.0000
90 G A 0.1282
91 L A 0.8973
92 G A -0.4320
93 K A -1.7870
94 H A -0.5709
95 N A -0.7739
96 Y A 0.0000
97 C A 0.0724
98 R A 0.0000
99 N A 0.0000
100 P A -0.2415
101 D A -1.2896
102 G A -0.7654
103 D A -0.4588
104 A A -0.1826
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 0.1531
111 P A -0.7422 mutated: LA111P
112 K A -2.1841
113 N A -1.9294
114 R A -2.6706
115 R A -2.1164
116 L A 0.1692
117 T A 0.0928
118 W A 0.0483
119 E A -0.4326
120 Y A 0.0000
121 C A 0.0000
122 D A -1.6292
123 V A 0.0000
124 P A -0.0380
125 S A 0.0437
126 C A 0.4246
127 S A 0.0000
128 T A 0.0000
129 C A 0.0000
130 G A -0.0474
131 L A 0.0000
132 R A -0.9910
133 Q A -0.7468
134 Y A 0.2714
135 S A -0.0719
136 Q A -0.3344
137 P A -0.4959
138 Q A -0.8735
139 F A 1.5998
140 R A 0.1729
141 I A 1.7835
142 K A -0.2692
143 G A -0.3273
144 G A -0.2627
145 L A 0.5706
146 F A 1.9940
147 A A 0.0895
148 D A -1.4086
149 I A 1.6876
150 A A 0.4497
151 S A -0.0674
152 H A -0.2289
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 0.3022
160 A A 0.0000
161 K A -0.9524
162 H A -1.1599
163 R A -0.9811
164 R A -1.9795
165 S A -0.5026
166 P A -0.3545
167 G A -0.8571
168 E A -1.9766
169 R A -0.6691
170 F A 0.1942
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 -0.0724
179 S A -0.2189
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 -0.0952
187 H A -0.3305
188 C A 0.0000
189 F A 0.1261
190 Q A -1.1797
191 E A -1.7639
192 R A -2.0244
193 F A -0.0754
194 P A -0.2120
195 P A -0.3155
196 H A -1.0369
197 H A -0.3056
198 L A 0.1539
199 T A 0.0000
200 V A 0.0000
201 I A 0.0000
202 L A 0.0000
203 G A -0.2249
204 R A -0.5110
205 T A -0.0613
206 Y A -0.0812
207 R A -1.4706
208 V A 1.7715
209 V A 2.1027
210 P A 0.1943
211 G A -0.8368
212 E A -2.0297
213 E A -1.2605
214 E A -1.0553
215 Q A -0.6945
216 K A -1.7368
217 F A 0.0000
218 E A -1.7639
219 V A 0.0000
220 E A -0.8534
221 K A -1.5778
222 Y A 0.3901
223 I A 1.0494
224 V A 1.8589
225 H A 0.0380
226 K A -0.6496
227 E A 0.0000
228 F A -0.0156
229 D A -0.8266
230 D A -2.2002
231 D A -2.0733
232 T A -0.3182
233 Y A 0.1531
234 D A 0.0000
235 N A 0.0000
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 -0.1604
242 L A 0.0000
243 K A -1.7369
244 S A -0.8214
245 D A -1.8228
246 S A 0.0000
247 S A -0.4531
248 R A -1.8635
249 C A 0.0000
250 A A 0.0000
251 Q A -1.5446
252 E A -2.0584
253 S A -0.4425
254 S A -0.0489
255 V A 0.8893
256 V A 0.0000
257 R A -0.8054
258 T A 0.0000
259 V A 0.0000
260 C A 0.7055
261 L A 0.2900
262 P A -0.0409
263 P A -0.1852
264 A A -0.0529
265 D A -0.1622
266 L A 0.9931
267 Q A 0.2268
268 L A 1.4785
269 P A -0.2060
270 D A -1.7822
271 W A -0.1592
272 T A -0.0250
273 E A -0.1905
274 C A 0.0000
275 E A -0.2675
276 L A 0.0000
277 S A 0.0000
278 G A -0.0432
279 Y A 0.1827
280 G A -0.0368
281 K A 0.0000
282 H A -0.7181
283 E A -1.8885
284 A A -0.2849
285 L A 0.6995
286 S A -0.1245
287 P A -0.2052
288 F A 0.0000
289 Y A 0.5105
290 S A -0.0606
291 E A -0.3792
292 R A -0.7966
293 L A -0.0376
294 K A -0.4075
295 E A -0.3389
296 A A 0.0000
297 H A 0.0000
298 V A 0.0000
299 R A -1.6290
300 L A -0.0610
301 Y A 0.1986
302 P A -0.1280
303 S A -0.2442
304 S A -0.4594
305 R A -1.1556
306 C A 0.0000
307 T A -0.2048
308 S A -0.4589
309 Q A -1.1999
310 H A 0.0000
311 L A 1.5477
312 L A 0.0000
313 N A -1.4339
314 R A -1.0995
315 T A -0.1821
316 V A 0.2037
317 T A -0.2096
318 D A -0.9660
319 N A 0.0000
320 M A 0.0000
321 L A 0.1828
322 C A 0.0000
323 A A 0.0000
324 G A 0.0000
325 D A 0.0000
326 T A -0.1932
327 R A -1.2141
328 S A -0.4960
329 G A -0.5925
330 G A -0.6750
331 P A -0.4462
332 Q A -0.7191
333 A A -0.1936
334 N A -0.4455
335 L A 0.4656
336 H A 0.0000
337 D A -0.6611
338 A A -0.0004
339 C A 0.3048
340 Q A -0.2756
341 G A -0.1460
342 D A 0.0000
343 S A -0.0246
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 -0.5209
352 D A -1.8542
353 G A -0.6960
354 R A -0.9356
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 0.2750
362 S A 0.0000
363 W A 0.7994
364 G A 0.0346
365 L A 0.3101
366 G A -0.1849
367 C A 0.3621
368 G A -0.5552
369 Q A -1.3350
370 K A -2.1868
371 D A -2.0179
372 V A 0.0201
373 P A -0.0104
374 G A -0.2558
375 V A 0.0000
376 Y A 0.0000
377 T A 0.0000
378 K A -0.2499
379 V A 0.0000
380 T A 0.0000
381 N A 0.0000
382 Y A 0.0000
383 L A 0.1718
384 D A -0.4071
385 W A 0.0000
386 I A 0.0000
387 R A -1.8477
388 D A -1.3277
389 N A -0.3761
390 M A -0.0411
391 R A -1.7792
392 P A -0.5276

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, -0.2349 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015