Project name: l59t [mutate: LA59T]

Status: done

submitted: 2017-05-19 14:44:48, status changed: 2017-05-19 17:27:08
Settings
Chain sequence(s) A: MRSGSHHHHHHRSDITSLYKKAGSAAAPFTMENLYFQSYQGNSDCYFGNGSAYRGTHSLTESGASCLPWNSMILIGKVYTAQNPSAQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTWEYCDVPSCSTCGLRQYSQPQFRIKGGLFADIASHPWQAAIFAKHRRSPGERFLCGGILISSCWILSAAHCFQERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQLKSDSSRCAQESSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKEAHVRLYPSSRCTSQHLLNRTVTDNMLCAGDTRSGGPQANLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQKDVPGVYTKVTNYLDWIRDNMRP
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues LA59T
Energy difference between WD and mutated (by FoldX) -0.205576 kcal/mol
Show buried residues

Minimal score value
-2.4711
Maximal score value
2.2427
Average score
-0.2526
Total score value
-99.0053

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 0.7236
2 R A -1.6949
3 S A -0.6686
4 G A -0.5470
5 S A -0.5125
6 H A -1.2160
7 H A -1.2538
8 H A -0.7758
9 H A -1.2481
10 H A -1.3433
11 H A -1.5082
12 R A -2.0709
13 S A -0.6077
14 D A -0.2570
15 I A 0.2179
16 T A -0.0324
17 S A -0.0963
18 L A 0.5584
19 Y A 0.0000
20 K A -1.7654
21 K A -0.6977
22 A A -0.0604
23 G A -0.2927
24 S A 0.0000
25 A A 0.0000
26 A A 0.3535
27 A A 0.2490
28 P A 0.0000
29 F A 1.9361
30 T A 0.4791
31 M A 0.6454
32 E A -1.8484
33 N A -1.4530
34 L A 0.8627
35 Y A 1.8435
36 F A 1.9672
37 Q A -0.8678
38 S A -0.2311
39 Y A 0.8439
40 Q A -0.5095
41 G A -0.8542
42 N A -1.3780
43 S A -0.5387
44 D A -1.2457
45 C A 0.1412
46 Y A 1.6857
47 F A 2.1352
48 G A -0.0344
49 N A -0.9137
50 G A 0.0000
51 S A -0.1979
52 A A 0.0000
53 Y A 0.0000
54 R A -1.1879
55 G A -0.6482
56 T A -0.3178
57 H A -1.0177
58 S A -0.2451
59 T A -0.0288 mutated: LA59T
60 T A -0.1525
61 E A -0.8186
62 S A -0.3428
63 G A -0.4738
64 A A -0.0649
65 S A -0.1814
66 C A 0.1452
67 L A 0.3240
68 P A -0.1462
69 W A -0.1631
70 N A -1.2578
71 S A -0.1316
72 M A 0.0000
73 I A 1.8679
74 L A 1.6527
75 I A 0.0000
76 G A -0.1736
77 K A -1.4808
78 V A 0.0694
79 Y A 0.0000
80 T A -0.0609
81 A A 0.0464
82 Q A 0.0000
83 N A -0.2488
84 P A -0.1855
85 S A -0.2220
86 A A 0.0159
87 Q A 0.0000
88 A A 0.0620
89 L A 0.1584
90 G A 0.2200
91 L A 0.5487
92 G A -0.6517
93 K A -1.8654
94 H A -0.8683
95 N A -0.6734
96 Y A 0.0085
97 C A 0.0000
98 R A -0.3186
99 N A 0.0000
100 P A 0.0000
101 D A 0.0000
102 G A -0.4663
103 D A 0.0000
104 A A 0.0000
105 K A 0.0000
106 P A -0.0543
107 W A 0.0000
108 C A 0.0000
109 H A 0.0000
110 V A 0.6552
111 L A 0.1846
112 K A -1.8434
113 N A -1.8362
114 R A -2.4030
115 R A -2.1493
116 L A -0.0058
117 T A 0.0796
118 W A 0.3878
119 E A 0.0000
120 Y A 0.0000
121 C A -0.0573
122 D A -0.5599
123 V A 0.9633
124 P A -0.0343
125 S A -0.1025
126 C A 0.0000
127 S A -0.0222
128 T A 0.0000
129 C A 0.0000
130 G A 0.0047
131 L A 0.0000
132 R A -2.0639
133 Q A -1.5067
134 Y A -0.1072
135 S A -0.2614
136 Q A -0.5339
137 P A -0.5674
138 Q A -1.1816
139 F A -0.2086
140 R A -1.3260
141 I A 1.6374
142 K A 0.1329
143 G A -0.5545
144 G A -0.3064
145 L A 0.7143
146 F A 2.0192
147 A A 0.3891
148 D A -0.5364
149 I A 1.8425
150 A A 0.3452
151 S A -0.2323
152 H A -0.1587
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 0.2480
160 A A 0.0000
161 K A -0.8069
162 H A -1.4655
163 R A -2.4011
164 R A -2.2160
165 S A -0.3804
166 P A -0.3433
167 G A -0.5962
168 E A -0.5444
169 R A 0.0000
170 F A 0.3507
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 -0.2255
179 S A -0.0848
180 C A 0.1160
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 -0.2731
188 C A 0.0794
189 F A 0.0603
190 Q A -1.1495
191 E A -2.2131
192 R A -1.4938
193 F A 0.0000
194 P A -0.2690
195 P A -0.3276
196 H A -1.0523
197 H A -0.4383
198 L A 0.0000
199 T A 0.0000
200 V A 0.0000
201 I A 0.2338
202 L A 0.0000
203 G A 0.0000
204 R A 0.0000
205 T A 0.2149
206 Y A 0.9793
207 R A -1.3687
208 V A 1.5594
209 V A 2.0354
210 P A 0.2431
211 G A -0.6716
212 E A -2.2002
213 E A -2.2426
214 E A -1.0827
215 Q A -1.2571
216 K A -1.8280
217 F A 0.0000
218 E A -0.8914
219 V A 0.0000
220 E A -0.8215
221 K A -1.6871
222 Y A 0.6231
223 I A 2.2427
224 V A 1.0630
225 H A 0.0000
226 K A -1.7364
227 E A -0.3886
228 F A 0.3800
229 D A -1.9638
230 D A -2.4711
231 D A -2.1483
232 T A -0.5192
233 Y A 0.2095
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 -0.3889
242 L A 0.0000
243 K A -0.9039
244 S A -0.5734
245 D A -1.0899
246 S A 0.0000
247 S A -0.4650
248 R A -1.8697
249 C A 0.0000
250 A A -0.4310
251 Q A -1.5066
252 E A -1.9642
253 S A -0.5193
254 S A 0.0446
255 V A 0.6613
256 V A 0.0000
257 R A -1.1478
258 T A 0.0000
259 V A 0.0000
260 C A 0.7464
261 L A 0.2818
262 P A -0.0459
263 P A -0.0468
264 A A -0.0544
265 D A -0.5402
266 L A 0.0000
267 Q A -0.3692
268 L A 0.6417
269 P A -0.4349
270 D A -1.7948
271 W A -0.0976
272 T A -0.1797
273 E A -0.9073
274 C A 0.0000
275 E A -0.2042
276 L A 0.0000
277 S A -0.0261
278 G A 0.0000
279 Y A 0.0000
280 G A -0.1165
281 K A 0.0000
282 H A -0.6213
283 E A -1.8662
284 A A -0.0467
285 L A 1.5428
286 S A 0.2489
287 P A 0.1493
288 F A 0.0000
289 Y A 1.2982
290 S A 0.1464
291 E A -0.5576
292 R A -0.3022
293 L A 0.0000
294 K A -0.5189
295 E A -0.3774
296 A A -0.0970
297 H A -0.1493
298 V A 0.0000
299 R A -1.2240
300 L A 0.0503
301 Y A 0.3403
302 P A -0.1300
303 S A -0.2799
304 S A -0.5162
305 R A -1.5347
306 C A 0.0000
307 T A -0.1672
308 S A -0.3744
309 Q A -1.0418
310 H A -0.8768
311 L A 0.0000
312 L A 1.3101
313 N A -1.3366
314 R A -2.0924
315 T A -0.3917
316 V A 0.0000
317 T A -0.0887
318 D A -0.3644
319 N A -0.1562
320 M A 0.1360
321 L A 0.2119
322 C A 0.0000
323 A A 0.0000
324 G A 0.0000
325 D A -0.1888
326 T A -0.1266
327 R A -0.5352
328 S A -0.3749
329 G A -0.5375
330 G A -0.3765
331 P A -0.3803
332 Q A -0.5921
333 A A -0.0934
334 N A -0.0106
335 L A 1.4652
336 H A -0.1692
337 D A -1.8110
338 A A -0.2899
339 C A 0.0000
340 Q A -0.1712
341 G A -0.0802
342 D A 0.0000
343 S A -0.0225
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 0.0037
351 N A -1.4009
352 D A -2.1689
353 G A -0.9087
354 R A -1.0725
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 -0.1663
365 L A 0.2620
366 G A 0.1019
367 C A 0.6119
368 G A -0.5568
369 Q A -1.6823
370 K A -2.0614
371 D A -1.1004
372 V A 0.0864
373 P A -0.0377
374 G A 0.0000
375 V A 0.0000
376 Y A 0.0000
377 T A 0.0000
378 K A -0.1847
379 V A 0.0000
380 T A 0.0000
381 N A 0.0000
382 Y A 0.2953
383 L A 0.7503
384 D A 0.0000
385 W A 0.1215
386 I A 0.0000
387 R A -0.7956
388 D A -0.3834
389 N A -0.1833
390 M A 0.5628
391 R A -1.7270
392 P A -0.5666

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, -0.2526 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015