Project name: l312r [mutate: LA312R]

Status: done

submitted: 2017-05-19 14:36:58, status changed: 2017-05-19 17:23:53
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Chain sequence(s) A: MRSGSHHHHHHRSDITSLYKKAGSAAAPFTMENLYFQSYQGNSDCYFGNGSAYRGTHSLTESGASCLPWNSMILIGKVYTAQNPSAQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTWEYCDVPSCSTCGLRQYSQPQFRIKGGLFADIASHPWQAAIFAKHRRSPGERFLCGGILISSCWILSAAHCFQERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQLKSDSSRCAQESSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKEAHVRLYPSSRCTSQHLLNRTVTDNMLCAGDTRSGGPQANLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQKDVPGVYTKVTNYLDWIRDNMRP
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues LA312R
Energy difference between WD and mutated (by FoldX) -0.499369 kcal/mol
Show buried residues

Minimal score value
-2.5093
Maximal score value
2.3028
Average score
-0.2553
Total score value
-100.0711

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 0.7226
2 R A -1.6945
3 S A -0.6384
4 G A -0.5434
5 S A -0.3883
6 H A -0.7257
7 H A -1.2424
8 H A -1.2045
9 H A -0.6161
10 H A -0.6205
11 H A -1.1414
12 R A -0.7273
13 S A -0.3707
14 D A 0.1311
15 I A 1.8322
16 T A 0.2527
17 S A -0.3002
18 L A 0.6405
19 Y A -0.0095
20 K A -1.5689
21 K A -1.2558
22 A A -0.1639
23 G A -0.2375
24 S A -0.0306
25 A A 0.0066
26 A A 0.0212
27 A A 0.0000
28 P A 0.0533
29 F A 0.5773
30 T A 0.1637
31 M A 0.3168
32 E A -1.9221
33 N A -1.3193
34 L A 1.3767
35 Y A 0.9930
36 F A 1.7795
37 Q A -0.8492
38 S A -0.1956
39 Y A 0.4372
40 Q A -0.8350
41 G A -0.5491
42 N A -1.3139
43 S A -0.5460
44 D A -1.0624
45 C A 0.0439
46 Y A 1.6844
47 F A 2.1569
48 G A 0.1280
49 N A -0.3613
50 G A 0.0000
51 S A -0.2347
52 A A 0.0038
53 Y A 0.1087
54 R A -0.3030
55 G A -0.1693
56 T A -0.1192
57 H A -0.2288
58 S A 0.0359
59 L A 1.5087
60 T A 0.0000
61 E A -0.7500
62 S A -0.4171
63 G A -0.5928
64 A A -0.1024
65 S A -0.2088
66 C A 0.0000
67 L A 0.0000
68 P A -0.1319
69 W A 0.3692
70 N A -1.1806
71 S A -0.1972
72 M A 1.4051
73 I A 2.3028
74 L A 1.1898
75 I A 0.6423
76 G A -0.0472
77 K A -1.6908
78 V A 0.1723
79 Y A 1.3138
80 T A 0.1731
81 A A 0.0434
82 Q A 0.0000
83 N A -1.2730
84 P A 0.0000
85 S A -0.1831
86 A A -0.0098
87 Q A -0.2108
88 A A 0.1257
89 L A 0.6896
90 G A 0.0716
91 L A 0.0000
92 G A -0.7943
93 K A -1.8135
94 H A -0.4660
95 N A -0.2061
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 -0.8030
102 G A -0.6757
103 D A -0.3410
104 A A 0.0000
105 K A -0.1800
106 P A 0.0000
107 W A 0.1237
108 C A 0.0000
109 H A -0.0383
110 V A 0.2521
111 L A 0.1496
112 K A -1.8442
113 N A -1.9112
114 R A -2.4055
115 R A -1.9800
116 L A 0.7781
117 T A 0.2443
118 W A 0.1320
119 E A -0.2608
120 Y A 0.0000
121 C A 0.0000
122 D A -1.7233
123 V A 0.0421
124 P A -0.0029
125 S A 0.0000
126 C A 0.1169
127 S A 0.0000
128 T A -0.0105
129 C A 0.0000
130 G A -0.2284
131 L A 0.0000
132 R A -2.1579
133 Q A -1.6610
134 Y A 0.0000
135 S A -0.3373
136 Q A 0.0000
137 P A -0.3134
138 Q A 0.0127
139 F A 1.5677
140 R A -0.8666
141 I A 1.3846
142 K A -1.3587
143 G A -0.4782
144 G A -0.1307
145 L A 0.0000
146 F A 1.8653
147 A A 0.2756
148 D A -0.4863
149 I A 0.1221
150 A A 0.0872
151 S A -0.0804
152 H A -0.1201
153 P A -0.0773
154 W A 0.0000
155 Q A -0.1612
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 -1.9684
162 H A -1.4413
163 R A -0.8888
164 R A -0.7850
165 S A -0.3866
166 P A -0.3755
167 G A -0.6984
168 E A -1.2599
169 R A -1.6213
170 F A 0.1016
171 L A 0.2478
172 C A 0.0000
173 G A -0.0479
174 G A 0.0000
175 I A 0.0000
176 L A 0.0000
177 I A 0.0000
178 S A -0.1083
179 S A -0.1726
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 0.0133
186 A A 0.0000
187 H A -0.6284
188 C A -0.0316
189 F A 0.0000
190 Q A -1.1796
191 E A -1.7567
192 R A -1.8760
193 F A 0.0000
194 P A -0.1593
195 P A -0.2754
196 H A 0.0000
197 H A -0.6629
198 L A 0.0000
199 T A -0.0205
200 V A 0.0000
201 I A 0.0000
202 L A 0.0000
203 G A -0.2443
204 R A -0.3174
205 T A -0.0873
206 Y A 0.2355
207 R A -0.2434
208 V A 1.9290
209 V A 2.0429
210 P A 0.1648
211 G A -0.8222
212 E A -2.2399
213 E A -2.5093
214 E A -2.2192
215 Q A -0.8891
216 K A -1.7446
217 F A 0.0000
218 E A -0.5665
219 V A 0.0000
220 E A -1.2965
221 K A -1.4315
222 Y A 0.1388
223 I A 0.9002
224 V A 1.0885
225 H A -0.0489
226 K A -0.5141
227 E A -0.1297
228 F A 0.8165
229 D A -0.5565
230 D A -1.8813
231 D A -1.4169
232 T A -0.1648
233 Y A 0.1739
234 D A -0.0273
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 -0.2683
242 L A -0.1353
243 K A -1.4787
244 S A -0.3775
245 D A -0.4076
246 S A 0.0000
247 S A -0.4087
248 R A -1.7926
249 C A -0.0294
250 A A -0.4241
251 Q A -1.5397
252 E A -2.0857
253 S A -0.5941
254 S A -0.2514
255 V A 0.0000
256 V A 0.0000
257 R A -0.6663
258 T A -0.1325
259 V A 0.0000
260 C A 0.7624
261 L A 0.2870
262 P A -0.0627
263 P A -0.0578
264 A A -0.1070
265 D A -0.7072
266 L A -0.1276
267 Q A -0.8587
268 L A 1.2713
269 P A -0.0119
270 D A -0.4268
271 W A 0.0100
272 T A -0.1065
273 E A -0.7154
274 C A -0.0459
275 E A -0.1947
276 L A 0.0000
277 S A -0.0353
278 G A -0.0144
279 Y A 0.1729
280 G A -0.2895
281 K A -0.5150
282 H A -0.9201
283 E A -1.9082
284 A A 0.0115
285 L A 1.7920
286 S A 0.2265
287 P A 0.0567
288 F A 2.0242
289 Y A 0.6701
290 S A -0.1734
291 E A -0.5390
292 R A -1.8441
293 L A -0.2938
294 K A -0.2998
295 E A 0.0000
296 A A 0.0000
297 H A -0.1816
298 V A 0.0000
299 R A -1.7285
300 L A 0.5857
301 Y A 0.2926
302 P A -0.1854
303 S A -0.2508
304 S A -0.5418
305 R A -1.7121
306 C A 0.0000
307 T A 0.0597
308 S A -0.4479
309 Q A -0.6751
310 H A 0.0000
311 L A 1.0570
312 R A -1.7162 mutated: LA312R
313 N A -1.0366
314 R A -1.9132
315 T A -0.1856
316 V A 0.9747
317 T A 0.0136
318 D A -0.6052
319 N A 0.0000
320 M A 0.2034
321 L A 0.2610
322 C A 0.0000
323 A A 0.0000
324 G A 0.0000
325 D A -1.7925
326 T A -0.5399
327 R A -1.0753
328 S A -0.4751
329 G A -0.5823
330 G A -0.5839
331 P A -0.5630
332 Q A -1.2339
333 A A -0.3988
334 N A -1.1645
335 L A 0.2941
336 H A -0.0539
337 D A -0.3502
338 A A 0.0000
339 C A 0.0000
340 Q A -1.1983
341 G A 0.0000
342 D A -0.1786
343 S A -0.0565
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 0.1466
351 N A -0.7194
352 D A -1.9338
353 G A -0.9427
354 R A -1.3848
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 -0.0090
363 W A 0.0266
364 G A -0.4446
365 L A 0.0000
366 G A -0.4351
367 C A -0.1611
368 G A -0.8285
369 Q A -1.5353
370 K A -1.5619
371 D A 0.0000
372 V A 0.1819
373 P A 0.0000
374 G A 0.0000
375 V A 0.2008
376 Y A 0.0000
377 T A -0.0101
378 K A 0.0000
379 V A 0.0000
380 T A 0.0000
381 N A -0.1383
382 Y A 0.0000
383 L A 0.0309
384 D A -1.0211
385 W A 0.1159
386 I A 0.0000
387 R A -2.2038
388 D A -2.1791
389 N A -0.3112
390 M A 0.2009
391 R A -1.7337
392 P A -0.5615

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, -0.2553 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015