Aggrescan3D: claudin1 [mutate: KA65R]

Project name: claudin1 [mutate: KA65R]

Status: done

submitted: 2018-11-28 11:49:21, status changed: 2018-11-28 14:13:57

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Chain sequence(s)	A: MANAGLQLLGFILAFLGWIGAIVSTALPQWRIYSYAGDNIVTAQAMYEGLWMSCVSQSTGQIQCKVFDSLLNLSSTLQATRALMVVGILLGVIAIFVATVGMKCMKCLEDDEVQKMRMAVIGGAIFLLAGLAILVATAWYGNRIVQEFYDPMTPVNARYEFGQALFTGWAAASLCLLGGALLCCSCPRKTTSYPTPRPYPKPAPSSGKDYV
Distance of aggregation	10 Å
Dynamic mode	Yes
Mutated residues	KA65R
Energy difference between WT (input) and mutated protein (by FoldX)	0.106759 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: -3.1764
Maximal score value: 4.9359
Average score: 0.3804
Total score value: 80.2576

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	0.4089
2	A	A	0.2263
3	N	A	-0.3158
4	A	A	0.0000
5	G	A	0.3550
6	L	A	1.7887
7	Q	A	0.0000
8	L	A	1.1947
9	L	A	2.0722
10	G	A	0.0000
11	F	A	0.0000
12	I	A	2.4540
13	L	A	2.3198
14	A	A	0.0000
15	F	A	2.1070
16	L	A	2.7258
17	G	A	0.0000
18	W	A	0.0000
19	I	A	3.4460
20	G	A	2.3349
21	A	A	2.6987
22	I	A	4.0449
23	V	A	3.5023
24	S	A	0.0000
25	T	A	1.8910
26	A	A	1.8000
27	L	A	2.1375
28	P	A	1.0050
29	Q	A	0.3571
30	W	A	0.7133
31	R	A	0.0000
32	I	A	0.5528
33	Y	A	0.0000
34	S	A	-0.6195
35	Y	A	-0.6633
36	A	A	-0.5860
37	G	A	-0.3500
38	D	A	-1.0986
39	N	A	-0.7502
40	I	A	1.5852
41	V	A	1.5916
42	T	A	0.5750
43	A	A	-0.0915
44	Q	A	-0.0082
45	A	A	0.1616
46	M	A	0.8088
47	Y	A	1.2479
48	E	A	0.5338
49	G	A	0.4525
50	L	A	0.0000
51	W	A	0.3457
52	M	A	0.7737
53	S	A	0.0000
54	C	A	0.7225
55	V	A	0.0000
56	S	A	-0.0173
57	Q	A	-0.6523
58	S	A	-0.5731
59	T	A	-0.5649
60	G	A	-0.8732
61	Q	A	-0.7232
62	I	A	0.9568
63	Q	A	-0.2616
64	C	A	0.4194
65	R	A	-0.2908	mutated: KA65R
66	V	A	1.1805
67	F	A	1.7527
68	D	A	-0.0217
69	S	A	0.1910
70	L	A	1.5226
71	L	A	1.5900
72	N	A	-0.0048
73	L	A	0.5480
74	S	A	0.7536
75	S	A	0.0365
76	T	A	-0.2780
77	L	A	0.0000
78	Q	A	-0.8660
79	A	A	-0.2245
80	T	A	0.0000
81	R	A	0.0770
82	A	A	0.7985
83	L	A	1.7817
84	M	A	0.0000
85	V	A	3.6733
86	V	A	4.0896
87	G	A	0.0000
88	I	A	4.9359
89	L	A	4.9281
90	L	A	3.9239
91	G	A	0.0000
92	V	A	4.8802
93	I	A	4.6062
94	A	A	0.0000
95	I	A	3.3635
96	F	A	3.7322
97	V	A	2.8247
98	A	A	0.0000
99	T	A	1.1420
100	V	A	0.8016
101	G	A	0.0000
102	M	A	-0.7193
103	K	A	-1.5800
104	C	A	-1.2044
105	M	A	0.0000
106	K	A	-1.3506
107	C	A	-0.0597
108	L	A	-0.0947
109	E	A	-1.9351
110	D	A	-2.3663
111	D	A	-3.1764
112	E	A	-2.6383
113	V	A	-0.7173
114	Q	A	-2.1567
115	K	A	-2.1029
116	M	A	-1.2069
117	R	A	-1.3370
118	M	A	0.1088
119	A	A	0.0000
120	V	A	0.6577
121	I	A	1.8247
122	G	A	0.0000
123	G	A	0.0000
124	A	A	1.2330
125	I	A	1.9122
126	F	A	0.0000
127	L	A	1.0712
128	L	A	1.2209
129	A	A	0.0000
130	G	A	0.0000
131	L	A	0.8406
132	A	A	1.4353
133	I	A	1.3358
134	L	A	0.0000
135	V	A	0.8548
136	A	A	0.0000
137	T	A	0.0000
138	A	A	0.3200
139	W	A	0.3984
140	Y	A	0.0000
141	G	A	0.0023
142	N	A	-0.2226
143	R	A	-0.1964
144	I	A	0.0000
145	V	A	1.5413
146	Q	A	-0.2579
147	E	A	0.2410
148	F	A	1.8594
149	Y	A	1.4662
150	D	A	-0.6602
151	P	A	-0.1981
152	M	A	0.6583
153	T	A	-0.3898
154	P	A	-0.6898
155	V	A	-0.5608
156	N	A	-1.2554
157	A	A	-0.7048
158	R	A	-1.6874
159	Y	A	0.1132
160	E	A	-0.2743
161	F	A	0.8008
162	G	A	0.3098
163	Q	A	-0.3932
164	A	A	0.7272
165	L	A	0.9419
166	F	A	1.6823
167	T	A	0.8514
168	G	A	0.7185
169	W	A	0.6819
170	A	A	0.7259
171	A	A	0.0000
172	A	A	0.0000
173	S	A	0.0000
174	L	A	0.9939
175	C	A	0.0000
176	L	A	0.9953
177	L	A	0.9621
178	G	A	0.0000
179	G	A	0.0000
180	A	A	0.8130
181	L	A	1.4234
182	L	A	0.0000
183	C	A	0.4930
184	C	A	0.4937
185	S	A	0.1650
186	C	A	0.3221
187	P	A	-1.0658
188	R	A	-2.4517
189	K	A	-2.6246
190	T	A	-1.2569
191	T	A	-0.5919
192	S	A	0.1288
193	Y	A	1.0101
194	P	A	0.2242
195	T	A	-0.3410
196	P	A	-1.0586
197	R	A	-1.9793
198	P	A	-1.2453
199	Y	A	-0.5248
200	P	A	-1.1067
201	K	A	-1.8483
202	P	A	-1.1279
203	A	A	-0.7661
204	P	A	-0.5708
205	S	A	-1.2025
206	S	A	-0.5891
207	G	A	0.2738
208	K	A	0.0275
209	D	A	-0.9687
210	Y	A	1.2969
211	V	A	1.9471

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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, 0.3804 in this case) is selected and presented in A3D results.