Aggrescan3D: ccaeac28ee52409 [mutate: TV105V]

Project name: ccaeac28ee52409 [mutate: TV105V]

Status: done

submitted: 2019-10-06 08:57:24, status changed: 2019-10-07 19:44:28

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Chain sequence(s)	V: RPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQ
Distance of aggregation	10 Å
Dynamic mode	Yes
Mutated residues	TV105V
Energy difference between WT (input) and mutated protein (by FoldX)	0.550821 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: -3.2486
Maximal score value: 2.2644
Average score: -0.5478
Total score value: -82.1658

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
60	R	V	-1.4059
61	P	V	-0.1614
62	V	V	1.0428
63	L	V	0.0000
64	R	V	-0.0691
65	S	V	0.7568
66	V	V	1.2453
67	N	V	0.0000
68	S	V	-1.0514
69	R	V	-2.5223
70	E	V	-2.8673
71	P	V	-1.7442
72	S	V	0.0000
73	Q	V	-0.6569
74	V	V	0.0000
75	I	V	0.1341
76	F	V	0.0000
77	C	V	-0.3213
78	N	V	0.0000
79	R	V	-0.7959
80	S	V	-0.4686
81	P	V	-0.2055
82	R	V	0.3819
83	V	V	1.7814
84	V	V	0.0000
85	L	V	0.7991
86	P	V	0.0000
87	V	V	0.0000
88	W	V	0.0859
89	L	V	0.0000
90	N	V	0.0000
91	F	V	0.3653
92	D	V	-1.2642
93	G	V	-1.3778
94	E	V	-1.7761
95	P	V	-1.0815
96	Q	V	-0.5986
97	P	V	-0.2456
98	Y	V	0.5398
99	P	V	0.7675
100	T	V	0.0000
101	L	V	1.3671
102	P	V	0.2725
103	P	V	-0.3205
104	G	V	-0.8634
105	V	V	-0.5720	mutated: TV105V
106	G	V	-0.9619
107	R	V	-1.1890
108	R	V	-1.6543
109	I	V	-0.8483
110	H	V	-1.0155
111	S	V	0.0000
112	Y	V	-1.3579
113	R	V	-1.0787
114	G	V	0.1070
115	H	V	0.0000
116	L	V	0.0000
117	W	V	0.0000
118	L	V	0.0000
119	F	V	0.0000
120	R	V	0.2517
121	D	V	0.0000
122	A	V	0.1299
123	G	V	-0.6415
124	T	V	-0.7359
125	H	V	-0.7209
126	D	V	-0.2624
127	G	V	0.4765
128	L	V	1.1151
129	L	V	0.9176
130	V	V	-0.5724
131	N	V	-1.5167
132	Q	V	-1.5179
133	T	V	-1.2849
134	E	V	-2.0126
135	L	V	-0.4742
136	F	V	0.0000
137	V	V	1.7636
138	P	V	0.0000
139	S	V	0.3014
140	L	V	0.0634
141	N	V	-0.7550
142	V	V	0.3761
143	D	V	-1.4354
144	G	V	-1.4782
145	Q	V	-1.3912
146	P	V	-0.3466
147	I	V	0.0000
148	F	V	1.3381
149	A	V	0.0000
150	N	V	-0.2069
151	I	V	0.0000
152	T	V	0.1743
153	L	V	0.0000
154	P	V	0.9076
155	V	V	2.2644
156	Y	V	1.8038
157	T	V	0.5950
158	L	V	0.3532
159	K	V	-1.2444
160	E	V	-1.0359
161	R	V	-1.2802
162	C	V	-0.2683
163	L	V	0.0000
164	Q	V	-0.2997
165	V	V	0.9645
166	V	V	0.0000
167	R	V	-0.3636
168	S	V	0.4133
169	L	V	0.7966
170	V	V	-0.8713
171	K	V	-2.3540
172	P	V	-2.3436
173	E	V	-2.4381
174	N	V	-2.3468
175	Y	V	-1.5552
176	R	V	-3.2486
177	R	V	-2.7019
178	L	V	-0.5386
179	D	V	-1.3880
180	I	V	0.2620
181	V	V	0.9048
182	R	V	-1.2560
183	S	V	-0.7916
184	L	V	-0.2425
185	Y	V	-1.0386
186	E	V	-2.8126
187	D	V	-2.3340
188	L	V	0.0000
189	E	V	-3.0316
190	D	V	-2.6670
191	H	V	-2.2052
192	P	V	0.0000
193	N	V	-2.0321
194	V	V	-1.4483
195	Q	V	-2.2905
196	K	V	-2.1553
197	D	V	-1.4838
198	L	V	0.0000
199	E	V	-1.8188
200	R	V	-1.5655
201	L	V	-0.8670
202	T	V	0.0000
203	Q	V	-1.6321
204	E	V	-2.2630
205	R	V	-1.2370
206	I	V	-0.3596
207	A	V	-1.0158
208	H	V	-1.7657
209	Q	V	-1.5656

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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, -0.5478 in this case) is selected and presented in A3D results.