Project name: l312a [mutate: LA312A]

Status: done

submitted: 2017-05-19 14:38:11, status changed: 2017-05-19 17:18:35
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Chain sequence(s) A: MRSGSHHHHHHRSDITSLYKKAGSAAAPFTMENLYFQSYQGNSDCYFGNGSAYRGTHSLTESGASCLPWNSMILIGKVYTAQNPSAQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTWEYCDVPSCSTCGLRQYSQPQFRIKGGLFADIASHPWQAAIFAKHRRSPGERFLCGGILISSCWILSAAHCFQERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQLKSDSSRCAQESSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKEAHVRLYPSSRCTSQHLLNRTVTDNMLCAGDTRSGGPQANLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQKDVPGVYTKVTNYLDWIRDNMRP
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues LA312A
Energy difference between WD and mutated (by FoldX) -0.0731035 kcal/mol
Show buried residues

Minimal score value
-2.6287
Maximal score value
2.1822
Average score
-0.2369
Total score value
-92.8789

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 0.7309
2 R A -1.7007
3 S A -0.6540
4 G A -0.5428
5 S A -0.3550
6 H A -0.5586
7 H A -1.2474
8 H A -1.4894
9 H A -1.3600
10 H A -1.3013
11 H A 0.0000
12 R A -1.1235
13 S A -0.4551
14 D A -0.2647
15 I A 0.0000
16 T A -0.0822
17 S A 0.2125
18 L A 1.6900
19 Y A 1.4900
20 K A -0.2511
21 K A 0.0000
22 A A -0.0581
23 G A -0.4703
24 S A -0.1248
25 A A 0.0000
26 A A 0.0577
27 A A 0.0236
28 P A 0.0000
29 F A 1.0731
30 T A 0.3744
31 M A 0.6996
32 E A -1.6863
33 N A -1.5136
34 L A 0.5044
35 Y A 1.4546
36 F A 1.8897
37 Q A -0.8545
38 S A -0.3952
39 Y A 0.0202
40 Q A -0.8733
41 G A -0.3440
42 N A -0.5588
43 S A -0.3710
44 D A -1.1390
45 C A 0.1054
46 Y A 1.6841
47 F A 2.1822
48 G A 0.0000
49 N A -0.2257
50 G A 0.0000
51 S A -0.0370
52 A A -0.2585
53 Y A -0.1952
54 R A -1.8254
55 G A -0.4286
56 T A -0.2634
57 H A -1.0205
58 S A -0.0034
59 L A 1.5301
60 T A 0.0000
61 E A -1.0278
62 S A -0.4675
63 G A -0.4455
64 A A -0.0617
65 S A -0.1696
66 C A 0.1291
67 L A 0.0000
68 P A -0.0769
69 W A 0.9524
70 N A -0.8652
71 S A 0.0000
72 M A 0.0000
73 I A 0.8930
74 L A 1.5618
75 I A 0.8777
76 G A -0.0816
77 K A -1.2739
78 V A 1.2925
79 Y A 0.5096
80 T A 0.0187
81 A A -0.3844
82 Q A -1.4376
83 N A -1.5085
84 P A -0.3760
85 S A -0.1187
86 A A -0.0825
87 Q A -0.3897
88 A A -0.0744
89 L A 0.2799
90 G A 0.0728
91 L A 0.3893
92 G A -0.2265
93 K A -1.7876
94 H A -0.6712
95 N A -0.6394
96 Y A 0.0000
97 C A 0.0509
98 R A -0.2000
99 N A -0.1759
100 P A 0.0000
101 D A -0.5480
102 G A -0.5284
103 D A -0.5769
104 A A 0.0000
105 K A 0.0000
106 P A 0.0000
107 W A 0.1331
108 C A 0.0000
109 H A 0.0000
110 V A 1.5174
111 L A 1.4613
112 K A -1.8584
113 N A -1.9300
114 R A -2.6287
115 R A -2.1388
116 L A -0.0741
117 T A 0.0375
118 W A 0.0000
119 E A -0.5025
120 Y A 0.0000
121 C A 0.0000
122 D A -1.7894
123 V A 0.0000
124 P A -0.0331
125 S A 0.0000
126 C A 0.1632
127 S A 0.0000
128 T A 0.0000
129 C A 0.0000
130 G A -0.4159
131 L A -0.1878
132 R A -2.0112
133 Q A -1.4300
134 Y A 0.0000
135 S A -0.2577
136 Q A -0.3460
137 P A -0.3178
138 Q A -0.8587
139 F A 1.3848
140 R A -1.0931
141 I A 1.3445
142 K A -1.3556
143 G A -0.5387
144 G A -0.3337
145 L A 1.0846
146 F A 2.0767
147 A A 0.1459
148 D A -1.1967
149 I A 0.0000
150 A A 0.0491
151 S A -0.0453
152 H A 0.0000
153 P A -0.0318
154 W A 0.0000
155 Q A -0.1423
156 A A 0.0000
157 A A 0.0161
158 I A 0.0000
159 F A 0.2199
160 A A 0.0000
161 K A -1.7748
162 H A -0.8768
163 R A -0.9827
164 R A -0.9786
165 S A -0.4100
166 P A -0.4593
167 G A -0.6382
168 E A -0.8938
169 R A -0.5579
170 F A 0.1412
171 L A 0.1896
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 -0.0492
179 S A -0.0546
180 C A 0.1490
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 0.0000
187 H A -0.4444
188 C A 0.0000
189 F A 0.0624
190 Q A -1.0190
191 E A -2.2680
192 R A -2.1634
193 F A 0.0000
194 P A -0.3026
195 P A -0.3026
196 H A 0.0000
197 H A -1.0510
198 L A 0.0000
199 T A -0.0638
200 V A 0.0000
201 I A 0.0309
202 L A 0.0000
203 G A -0.2125
204 R A -0.3740
205 T A -0.1357
206 Y A -0.1001
207 R A -1.1943
208 V A 1.8025
209 V A 2.0134
210 P A 0.0921
211 G A -0.3525
212 E A -0.9659
213 E A -0.9694
214 E A -1.0898
215 Q A -0.8271
216 K A -1.7358
217 F A 0.0000
218 E A -0.5060
219 V A 0.0000
220 E A -0.9276
221 K A -1.7585
222 Y A -0.0924
223 I A 0.7584
224 V A 0.7074
225 H A -0.1914
226 K A -1.0181
227 E A -0.1550
228 F A 0.7274
229 D A -2.0843
230 D A -2.4867
231 D A -2.3311
232 T A -0.4689
233 Y A 0.5792
234 D A 0.0000
235 N A -0.1511
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 -0.1597
242 L A -0.1241
243 K A -1.6765
244 S A -0.7110
245 D A -1.5236
246 S A 0.0000
247 S A -0.4019
248 R A -1.7368
249 C A 0.4339
250 A A 0.0000
251 Q A -1.5175
252 E A -2.0544
253 S A -0.6696
254 S A -0.0749
255 V A 0.8953
256 V A 0.0000
257 R A -0.3587
258 T A -0.1248
259 V A 0.0000
260 C A 0.7316
261 L A 0.0000
262 P A -0.0403
263 P A -0.0598
264 A A 0.0000
265 D A -1.7894
266 L A 0.0000
267 Q A -0.8532
268 L A 1.2367
269 P A -0.3093
270 D A -1.7990
271 W A 0.0000
272 T A -0.1813
273 E A -0.5633
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 0.1894
280 G A 0.0000
281 K A 0.0000
282 H A -0.6409
283 E A -1.8724
284 A A -0.1311
285 L A 1.5198
286 S A 0.0559
287 P A 0.1210
288 F A 1.9679
289 Y A 0.6956
290 S A -0.2554
291 E A -0.5921
292 R A -0.3749
293 L A 0.0893
294 K A 0.0887
295 E A 0.0000
296 A A 0.0000
297 H A -0.0864
298 V A -0.0676
299 R A -1.1042
300 L A 0.0243
301 Y A 0.1568
302 P A -0.3575
303 S A -0.2215
304 S A -0.5788
305 R A -1.7015
306 C A 0.0000
307 T A -0.1021
308 S A -0.3347
309 Q A -1.2374
310 H A -0.3559
311 L A 0.0000
312 A A -0.2798 mutated: LA312A
313 N A -1.3610
314 R A -2.0503
315 T A -0.3357
316 V A 0.3300
317 T A -0.1235
318 D A -0.8250
319 N A 0.0000
320 M A 0.2882
321 L A 0.2596
322 C A 0.0000
323 A A 0.0000
324 G A -0.0834
325 D A -0.2167
326 T A 0.0000
327 R A -1.6259
328 S A -0.6026
329 G A -0.5183
330 G A -0.1966
331 P A -0.4848
332 Q A -1.2344
333 A A -0.3211
334 N A -0.5714
335 L A 1.3117
336 H A -0.2503
337 D A -0.4790
338 A A -0.0190
339 C A -0.0066
340 Q A -0.6843
341 G A 0.0000
342 D A 0.0000
343 S A -0.0470
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 -0.4860
352 D A -1.3779
353 G A -0.7313
354 R A -0.4770
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 0.1917
362 S A 0.0375
363 W A 0.1297
364 G A -0.0508
365 L A 0.2370
366 G A -0.1124
367 C A 0.5858
368 G A -0.3506
369 Q A -0.5914
370 K A -1.7595
371 D A -0.4939
372 V A 0.0000
373 P A -0.0337
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 0.0000
382 Y A 0.0000
383 L A 0.0000
384 D A 0.0000
385 W A 0.1456
386 I A 0.0000
387 R A -0.3005
388 D A -0.4508
389 N A -0.3146
390 M A 0.0000
391 R A -1.8910
392 P A -0.5941

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, -0.2369 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015