Project name: l312k [mutate: LA312K]

Status: done

submitted: 2017-05-19 14:36:03, status changed: 2017-05-19 17:22:33
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Chain sequence(s) A: MRSGSHHHHHHRSDITSLYKKAGSAAAPFTMENLYFQSYQGNSDCYFGNGSAYRGTHSLTESGASCLPWNSMILIGKVYTAQNPSAQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTWEYCDVPSCSTCGLRQYSQPQFRIKGGLFADIASHPWQAAIFAKHRRSPGERFLCGGILISSCWILSAAHCFQERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQLKSDSSRCAQESSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKEAHVRLYPSSRCTSQHLLNRTVTDNMLCAGDTRSGGPQANLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQKDVPGVYTKVTNYLDWIRDNMRP
Distance of aggregation 5 Å
Dynamic mode Yes
Mutated residues LA312K
Energy difference between WD and mutated (by FoldX) -0.638917 kcal/mol
Show buried residues

Minimal score value
-2.4671
Maximal score value
2.1765
Average score
-0.2852
Total score value
-111.814

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 0.7190
2 R A -1.6907
3 S A -0.5829
4 G A -0.1824
5 S A -0.3002
6 H A -0.4711
7 H A -1.3236
8 H A -1.3504
9 H A -1.3448
10 H A -1.2716
11 H A 0.0000
12 R A -1.8819
13 S A -0.8116
14 D A -1.4849
15 I A 0.0000
16 T A -0.0937
17 S A 0.0776
18 L A 1.2188
19 Y A 0.1675
20 K A -1.7893
21 K A -1.0475
22 A A -0.1381
23 G A -0.3293
24 S A -0.2712
25 A A 0.0000
26 A A 0.0522
27 A A 0.0412
28 P A 0.1828
29 F A 0.5697
30 T A 0.2408
31 M A 0.7553
32 E A -1.7340
33 N A -1.4755
34 L A 0.3966
35 Y A 1.4960
36 F A 0.5110
37 Q A -1.1361
38 S A -0.3311
39 Y A 0.2795
40 Q A -0.8332
41 G A -0.5049
42 N A -1.2953
43 S A -0.5144
44 D A -0.8041
45 C A 0.0000
46 Y A 1.6627
47 F A 2.1765
48 G A 0.0000
49 N A -1.2927
50 G A -0.4120
51 S A -0.0588
52 A A 0.0000
53 Y A -0.0521
54 R A -1.1663
55 G A 0.0000
56 T A -0.2504
57 H A -1.0432
58 S A -0.1326
59 L A 1.5093
60 T A -0.0192
61 E A -1.3635
62 S A -0.4935
63 G A -0.4931
64 A A -0.1074
65 S A -0.2085
66 C A 0.0000
67 L A 0.0000
68 P A -0.1131
69 W A 0.0000
70 N A -0.3669
71 S A 0.0654
72 M A 1.4272
73 I A 2.1649
74 L A 0.0000
75 I A 0.2082
76 G A -0.5093
77 K A -1.7332
78 V A -0.1206
79 Y A 0.0168
80 T A 0.0258
81 A A -0.0374
82 Q A -0.4806
83 N A 0.0000
84 P A -0.0707
85 S A -0.2161
86 A A -0.3174
87 Q A 0.0000
88 A A 0.0112
89 L A 0.0000
90 G A -0.1691
91 L A 0.8070
92 G A -0.6392
93 K A -1.8716
94 H A -0.9293
95 N A -0.5296
96 Y A 0.0000
97 C A 0.0000
98 R A -0.1922
99 N A 0.0000
100 P A 0.0000
101 D A -1.8175
102 G A -0.5617
103 D A -0.2559
104 A A -0.0936
105 K A -0.2120
106 P A -0.0420
107 W A 0.1430
108 C A 0.0000
109 H A 0.0000
110 V A 0.3793
111 L A -0.0614
112 K A -2.0444
113 N A -1.8102
114 R A -1.5950
115 R A -1.9177
116 L A 0.0927
117 T A 0.1961
118 W A 0.8396
119 E A -0.3918
120 Y A 0.2411
121 C A 0.0000
122 D A -1.7307
123 V A -0.0284
124 P A 0.0043
125 S A -0.0372
126 C A 0.0890
127 S A -0.0044
128 T A 0.0000
129 C A 0.0000
130 G A -0.1619
131 L A 0.0000
132 R A -1.7863
133 Q A -1.2527
134 Y A 0.0000
135 S A -0.1928
136 Q A -0.7836
137 P A -0.4894
138 Q A -1.1579
139 F A -0.1817
140 R A -0.9791
141 I A 1.2763
142 K A -1.2023
143 G A -0.6528
144 G A -0.4012
145 L A 0.9349
146 F A 2.0687
147 A A 0.0075
148 D A -1.7494
149 I A -0.1277
150 A A 0.0200
151 S A -0.1181
152 H A 0.0000
153 P A 0.0000
154 W A 0.0000
155 Q A 0.0000
156 A A 0.0000
157 A A 0.0543
158 I A 0.0000
159 F A 0.3476
160 A A -0.2450
161 K A -1.8838
162 H A -1.6385
163 R A -2.3446
164 R A -2.2045
165 S A -0.5731
166 P A -0.3838
167 G A -0.7793
168 E A -1.6764
169 R A -0.6895
170 F A 1.3196
171 L A 0.6305
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 -0.1226
179 S A -0.0241
180 C A 0.0966
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 -0.1830
188 C A 0.0000
189 F A 0.0931
190 Q A -1.0819
191 E A -1.2056
192 R A -1.9555
193 F A 0.0071
194 P A -0.1932
195 P A -0.3058
196 H A -1.1145
197 H A -0.7673
198 L A 0.0000
199 T A -0.0106
200 V A 0.0000
201 I A 0.4161
202 L A 0.0000
203 G A -0.1914
204 R A -0.6356
205 T A -0.0325
206 Y A 0.2923
207 R A -0.4521
208 V A 1.7307
209 V A 0.9671
210 P A -0.0538
211 G A -0.8216
212 E A -1.9628
213 E A -0.8993
214 E A -1.0750
215 Q A -0.7587
216 K A -1.7515
217 F A 0.0000
218 E A -0.7584
219 V A 0.0000
220 E A -1.1123
221 K A -1.6674
222 Y A 0.7781
223 I A 1.0083
224 V A 0.5994
225 H A -0.3590
226 K A -1.7957
227 E A -0.3488
228 F A 1.5495
229 D A -1.1012
230 D A -2.4671
231 D A -2.2155
232 T A -0.3316
233 Y A 0.0091
234 D A -0.1662
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 -0.3013
242 L A 0.0000
243 K A -1.7066
244 S A -0.4314
245 D A -0.4017
246 S A 0.0000
247 S A -0.4223
248 R A -1.8044
249 C A -0.0646
250 A A 0.0000
251 Q A -1.5459
252 E A -2.0757
253 S A -0.5259
254 S A 0.0754
255 V A 1.7345
256 V A 0.0000
257 R A -0.4547
258 T A -0.1737
259 V A 0.0000
260 C A 0.7316
261 L A 0.0000
262 P A -0.1188
263 P A -0.0878
264 A A -0.0952
265 D A -0.3114
266 L A 1.2014
267 Q A -0.5990
268 L A 1.0739
269 P A -0.2894
270 D A -1.6610
271 W A 0.0000
272 T A -0.0656
273 E A -0.3763
274 C A 0.0000
275 E A 0.0000
276 L A 0.0000
277 S A 0.0000
278 G A 0.0183
279 Y A 0.4651
280 G A 0.0000
281 K A 0.0000
282 H A -0.6125
283 E A -1.8689
284 A A -0.2602
285 L A 0.2654
286 S A -0.1985
287 P A -0.1580
288 F A 0.7956
289 Y A 1.3864
290 S A -0.0246
291 E A -0.6199
292 R A -1.1878
293 L A 0.0000
294 K A -0.2520
295 E A 0.0000
296 A A 0.0000
297 H A -0.1005
298 V A 0.0000
299 R A -0.5429
300 L A 0.2013
301 Y A 0.4109
302 P A -0.2446
303 S A -0.1820
304 S A -0.4865
305 R A -1.4896
306 C A 0.0000
307 T A -0.0689
308 S A -0.4358
309 Q A -0.5010
310 H A -0.8326
311 L A 0.0000
312 K A -1.9840 mutated: LA312K
313 N A -1.8421
314 R A -1.6777
315 T A -0.3113
316 V A 0.0000
317 T A -0.2849
318 D A -1.5194
319 N A 0.0000
320 M A 0.0000
321 L A 0.2228
322 C A 0.0000
323 A A 0.0000
324 G A 0.0000
325 D A -0.3950
326 T A -0.2195
327 R A -0.5043
328 S A -0.3797
329 G A -0.5905
330 G A -0.5998
331 P A -0.5470
332 Q A -1.2319
333 A A -0.1939
334 N A -0.0761
335 L A 0.7073
336 H A -0.2425
337 D A -1.3218
338 A A 0.0000
339 C A 0.0000
340 Q A -0.3190
341 G A 0.0000
342 D A 0.0000
343 S A 0.0000
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 0.0000
352 D A -1.8005
353 G A -0.6414
354 R A -1.3751
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 -0.2720
365 L A 0.0000
366 G A -0.4183
367 C A 0.1047
368 G A -0.2534
369 Q A -1.5342
370 K A -2.1150
371 D A -1.3300
372 V A 0.0000
373 P A -0.0292
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 0.1970
380 T A 0.0000
381 N A -0.1346
382 Y A 0.2195
383 L A 0.3483
384 D A 0.0000
385 W A 0.1534
386 I A 0.0000
387 R A -0.7401
388 D A -0.4770
389 N A -0.1975
390 M A 0.7123
391 R A -1.5510
392 P A -0.5605

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, -0.2852 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015