Project name: claudin1_loops

Status: done

submitted: 2017-09-13 12:50:27, status changed: 2017-09-30 22:42:20
Settings
Chain sequence(s) A: MANAGLQLLGFILAFLGWIGAIVSTALPQWRIYSYAGDNIVTAQAMYEGLWMSCVSQSTGQIQCKVFDSLLNLSSTLQATRALMVVGILLGVIAIFVATVGMKCMKCLEDDEVQKMRMAVIGGAIFLLAGLAILVATAWYGNRIVQEFYDPMTPVNARYEFGQALFTGWAAASLCLLGGALLCCSCPRKTTSYPTPRPYPKPAPSSGKDYV
Distance of aggregation 10 Å
Dynamic mode Yes
Show buried residues

Minimal score value
-2.7182
Maximal score value
3.8099
Average score
0.2651
Total score value
55.9424

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 1.2082
2 A A 0.7549
3 N A 0.7920
4 A A 1.1647
5 G A 1.2573
6 L A 2.2294
7 Q A 0.0000
8 L A 2.9894
9 L A 2.9439
10 G A 0.0000
11 F A 3.2264
12 I A 3.8099
13 L A 0.0000
14 A A 0.0000
15 F A 2.9860
16 L A 2.7753
17 G A 0.0000
18 W A 2.4358
19 I A 2.3430
20 G A 1.6320
21 A A 0.0000
22 I A 2.0343
23 V A 1.9893
24 S A 0.0000
25 T A 0.8857
26 A A 0.6986
27 L A 0.6362
28 P A -0.0502
29 Q A -0.3339
30 W A 0.0000
31 R A 0.0000
32 I A -0.2054
33 Y A 0.0000
34 S A -0.9299
35 Y A 0.0000
36 A A -0.6899
37 G A -0.5207
38 D A -1.3506
39 N A -0.8074
40 I A 1.6234
41 V A 1.8162
42 T A 0.6572
43 A A -0.0057
44 Q A -0.5189
45 A A -0.3594
46 M A 0.0000
47 Y A 0.5411
48 E A 0.0000
49 G A 0.0000
50 L A 0.0000
51 W A 0.9045
52 M A 1.9075
53 S A 0.0000
54 C A 1.2697
55 V A 0.0000
56 S A -0.1004
57 Q A -1.0082
58 S A -0.7777
59 T A -0.7631
60 G A -0.8771
61 Q A -0.8453
62 I A 0.9994
63 Q A 0.5043
64 C A 1.5062
65 K A 1.1233
66 V A 1.8656
67 F A 0.4133
68 D A -1.4743
69 S A -0.8022
70 L A -0.2030
71 L A -0.6678
72 N A -1.5445
73 L A 0.0000
74 S A -0.8303
75 S A -0.8574
76 T A -0.9396
77 L A 0.0000
78 Q A -1.6963
79 A A -0.7416
80 T A 0.0000
81 R A -1.3222
82 A A -0.2405
83 L A 1.0885
84 M A 0.0000
85 V A 1.4222
86 V A 2.0872
87 G A 0.0000
88 I A 2.4507
89 L A 3.2153
90 L A 2.9461
91 G A 0.0000
92 V A 3.6503
93 I A 3.3216
94 A A 0.0000
95 I A 2.6738
96 F A 2.8695
97 V A 0.0000
98 A A 0.0000
99 T A 1.2399
100 V A 0.7852
101 G A 0.0000
102 M A 0.2662
103 K A -0.8403
104 C A -0.1243
105 M A 0.1590
106 K A -1.0486
107 C A -0.0519
108 L A -0.0259
109 E A -2.3611
110 D A -2.7182
111 D A -2.2627
112 E A -1.4068
113 V A -1.2448
114 Q A -1.8360
115 K A 0.0000
116 M A -0.9531
117 R A -1.0388
118 M A 0.4072
119 A A 0.0000
120 V A 0.7480
121 I A 1.2552
122 G A 0.0000
123 G A 0.0000
124 A A 1.2666
125 I A 1.9776
126 F A 0.0000
127 L A 1.5248
128 L A 2.1881
129 A A 0.0000
130 G A 0.0000
131 L A 1.6688
132 A A 1.8568
133 I A 0.0000
134 L A 1.4381
135 V A 2.0983
136 A A 0.0000
137 T A 0.0000
138 A A 0.9388
139 W A 1.3519
140 Y A 0.0000
141 G A 0.0000
142 N A -0.2187
143 R A 0.0000
144 I A 0.0000
145 V A 1.5425
146 Q A -0.3181
147 E A 0.0007
148 F A 1.5293
149 Y A 1.1966
150 D A -0.7918
151 P A -0.7177
152 M A -0.3641
153 T A -0.9009
154 P A -0.8096
155 V A -0.7693
156 N A -1.8289
157 A A -1.1547
158 R A -1.6880
159 Y A 0.0000
160 E A -0.3651
161 F A 0.7485
162 G A 0.0000
163 Q A -0.8562
164 A A 0.0000
165 L A 0.0000
166 F A 0.8825
167 T A 0.3774
168 G A 0.0000
169 W A 0.0000
170 A A 0.7906
171 A A 0.0000
172 A A 0.0000
173 S A 0.0000
174 L A 1.6900
175 C A 0.0000
176 L A 1.2123
177 L A 1.3045
178 G A 0.0000
179 G A 0.0000
180 A A 0.8217
181 L A 1.5982
182 L A 0.0000
183 C A 0.5581
184 C A 0.7210
185 S A 0.0000
186 C A 0.0000
187 P A -1.2394
188 R A -2.6519
189 K A -2.6819
190 T A -1.4719
191 T A -0.6161
192 S A -0.0043
193 Y A 0.8282
194 P A -0.0929
195 T A -0.4006
196 P A -0.7915
197 R A -1.0395
198 P A -1.1047
199 Y A -0.5434
200 P A -1.1122
201 K A -1.8262
202 P A -1.1072
203 A A -0.4705
204 P A -0.6241
205 S A 0.0403
206 S A 0.2132
207 G A 0.3105
208 K A 0.0000
209 D A 0.0000
210 Y A 2.1333
211 V A 2.5607

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, 0.2651 in this case) is selected and presented in A3D results.


 

Laboratory of Theory of Biopolymers 2015