Aggrescan3D: HERGULIN [mutate: EX1D]

Project name: HERGULIN [mutate: EX1D]

Status: done

submitted: 2018-12-28 22:28:32, status changed: 2018-12-29 00:52:08

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Chain sequence(s)	X: ELLPPRLKEMKSQESAAGSKLVLRCETSSEYSSLRFKWFKNGNELNRKNKPQNIKIQKKPGKSELRINKASLADSGEYMCKVISKLGNDSASANITIVESNEIITGMPASTEGAYVSSESPIRISVSTEGANTSSSTSTSTTGTSHLVKCAEKEKTFCVNGGECFMVKDLSNPSRYLCKCQPGFTGARCTENVPMKVQNQEKAEELY
Distance of aggregation	5 Å
Dynamic mode	Yes
Mutated residues	EX1D
Energy difference between WT (input) and mutated protein (by FoldX)	0.165443 kcal/mol Changes in protein stability upon mutation are calculated using the FoldX forcefield. Computational prediction of protein stability is used with the intention of preventing the experimental characterization of proteins bearing mutations that significantly destabilize their structure. Mutations resulting in a predicted reduction in protein stability ≥ 1 kcal/mol are considered disruptive.

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Minimal score value: -2.4011
Maximal score value: 2.1258
Average score: -0.3365
Total score value: -69.6645

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	D	X	-1.5099	mutated: EX1D
2	L	X	1.5268
3	L	X	1.8452
4	P	X	0.2385
5	P	X	-0.4437
6	R	X	-1.5592
7	L	X	1.0987
8	K	X	-0.2442
9	E	X	-1.0442
10	M	X	-0.1520
11	K	X	-0.7534
12	S	X	-0.5200
13	Q	X	-0.7373
14	E	X	-1.8958
15	S	X	-0.3494
16	A	X	0.1656
17	A	X	-0.0012
18	G	X	0.0000
19	S	X	-0.7251
20	K	X	-1.7372
21	L	X	0.0000
22	V	X	0.5811
23	L	X	0.0000
24	R	X	-0.3745
25	C	X	0.0000
26	E	X	-0.0991
27	T	X	0.0000
28	S	X	-0.2327
29	S	X	-0.4756
30	E	X	-1.8133
31	Y	X	-0.2100
32	S	X	-0.1606
33	S	X	-0.2087
34	L	X	-0.1885
35	R	X	-1.7473
36	F	X	0.0000
37	K	X	-0.2538
38	W	X	0.0000
39	F	X	0.5676
40	K	X	0.0000
41	N	X	-1.3597
42	G	X	-0.8311
43	N	X	-1.1294
44	E	X	-1.9534
45	L	X	0.0000
46	N	X	-0.5599
47	R	X	-2.4011
48	K	X	-2.1411
49	N	X	-1.0989
50	K	X	-2.0426
51	P	X	-0.8081
52	Q	X	-1.4271
53	N	X	-1.1777
54	I	X	0.0000
55	K	X	-0.8138
56	I	X	0.5679
57	Q	X	-0.6056
58	K	X	-1.9049
59	K	X	-1.0649
60	P	X	-0.3979
61	G	X	-0.1810
62	K	X	-0.4648
63	S	X	0.0000
64	E	X	0.0000
65	L	X	0.0000
66	R	X	-0.2147
67	I	X	0.0000
68	N	X	-0.8712
69	K	X	-1.7929
70	A	X	0.0000
71	S	X	-0.0770
72	L	X	0.6040
73	A	X	0.2033
74	D	X	-0.5927
75	S	X	-0.3579
76	G	X	-0.4430
77	E	X	-1.8315
78	Y	X	0.0000
79	M	X	0.4930
80	C	X	0.0000
81	K	X	-0.3909
82	V	X	0.0000
83	I	X	0.2603
84	S	X	0.0000
85	K	X	-1.4073
86	L	X	1.2262
87	G	X	0.0000
88	N	X	-1.2803
89	D	X	-0.6110
90	S	X	-0.2239
91	A	X	-0.0230
92	S	X	0.0111
93	A	X	0.0000
94	N	X	-0.9096
95	I	X	0.0000
96	T	X	-0.2559
97	I	X	0.0000
98	V	X	0.9989
99	E	X	-0.1206
100	S	X	-0.3235
101	N	X	-0.5392
102	E	X	-0.8465
103	I	X	0.8758
104	I	X	2.1258
105	T	X	0.3205
106	G	X	-0.1453
107	M	X	0.0334
108	P	X	-0.2260
109	A	X	-0.0185
110	S	X	-0.1659
111	T	X	0.0000
112	E	X	-1.9008
113	G	X	-0.7580
114	A	X	0.1419
115	Y	X	1.1104
116	V	X	1.3566
117	S	X	0.0339
118	S	X	0.0000
119	E	X	-0.5845
120	S	X	0.0000
121	P	X	-0.2549
122	I	X	0.0000
123	R	X	-1.8441
124	I	X	0.0000
125	S	X	-0.0548
126	V	X	0.0000
127	S	X	-0.1483
128	T	X	-0.3757
129	E	X	-1.9042
130	G	X	-0.6322
131	A	X	0.0000
132	N	X	-1.2844
133	T	X	-0.2820
134	S	X	0.1773
135	S	X	0.1107
136	S	X	-0.2224
137	T	X	0.0000
138	S	X	-0.1640
139	T	X	-0.0430
140	S	X	-0.0225
141	T	X	0.0000
142	T	X	0.0000
143	G	X	-0.2605
144	T	X	-0.1327
145	S	X	-0.4026
146	H	X	-0.7470
147	L	X	1.4308
148	V	X	0.3449
149	K	X	-1.6251
150	C	X	0.0000
151	A	X	-0.2737
152	E	X	-2.2403
153	K	X	-2.0286
154	E	X	0.0000
155	K	X	-1.3527
156	T	X	0.0771
157	F	X	1.8235
158	C	X	1.3011
159	V	X	1.6435
160	N	X	-0.9686
161	G	X	-0.1505
162	G	X	0.0508
163	E	X	-0.3274
164	C	X	0.1642
165	F	X	0.0000
166	M	X	0.1763
167	V	X	0.0000
168	K	X	-1.8636
169	D	X	-1.1968
170	L	X	0.0000
171	S	X	-0.4213
172	N	X	-0.9089
173	P	X	-0.3016
174	S	X	0.0000
175	R	X	-0.7672
176	Y	X	0.0000
177	L	X	0.2410
178	C	X	0.1412
179	K	X	0.0000
180	C	X	0.1180
181	Q	X	-0.3116
182	P	X	-0.1831
183	G	X	-0.1077
184	F	X	1.8286
185	T	X	0.1670
186	G	X	-0.4708
187	A	X	-0.3803
188	R	X	-1.6907
189	C	X	0.3635
190	T	X	0.0046
191	E	X	-0.5701
192	N	X	-1.2940
193	V	X	0.0000
194	P	X	-0.2549
195	M	X	0.0000
196	K	X	-1.7357
197	V	X	-0.3134
198	Q	X	-1.0028
199	N	X	-1.6477
200	Q	X	-1.7457
201	E	X	-2.0087
202	K	X	-1.1839
203	A	X	-0.4657
204	E	X	-2.1418
205	E	X	-1.8468
206	L	X	1.4454
207	Y	X	1.6078

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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, -0.3365 in this case) is selected and presented in A3D results.