Aggrescan3D: Arg848 [mutate: AX848R]

Project name: Arg848 [mutate: AX848R]

Status: done

submitted: 2019-01-30 09:13:40, status changed: 2019-01-30 11:32:53

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Chain sequence(s)	X: EVTIKVNLIFADGKIQTAEFKGTFEEATAEAYRYADLLAKVNGEYTADLEDGGNHMNIKFA
Distance of aggregation	10 Å
Dynamic mode	Yes
Mutated residues	AX848R
Energy difference between WT (input) and mutated protein (by FoldX)	0.0337047 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: -2.9353
Maximal score value: 1.4901
Average score: -0.8789
Total score value: -52.7317

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
820	E	X	-1.4021
821	V	X	0.0889
822	T	X	-0.7824
823	I	X	0.0000
824	K	X	-1.9557
825	V	X	0.0000
826	N	X	-0.8786
827	L	X	0.0000
828	I	X	1.1778
829	F	X	0.7630
830	A	X	-0.3583
831	D	X	-1.7164
832	G	X	-1.5545
833	K	X	-1.1749
834	I	X	0.8661
835	Q	X	-0.0550
836	T	X	-0.6956
837	A	X	-1.4221
838	E	X	-2.6740
839	F	X	0.0000
840	K	X	-2.3008
841	G	X	-1.6214
842	T	X	-0.9728
843	F	X	-0.5316
844	E	X	-1.9472
845	E	X	-2.0167
846	A	X	0.0000
847	T	X	-1.3442
848	R	X	-1.9488	mutated: AX848R
849	E	X	-1.7053
850	A	X	0.0000
851	Y	X	-0.3667
852	R	X	-1.5819
853	Y	X	-0.7470
854	A	X	-0.4958
855	D	X	-1.7586
856	L	X	-0.3595
857	L	X	0.0000
858	A	X	-1.3732
859	K	X	-1.3990
860	V	X	-0.1023
861	N	X	-1.5316
862	G	X	-1.2009
863	E	X	-1.2752
864	Y	X	-0.0512
865	T	X	-0.1557
866	A	X	0.1056
867	D	X	-1.0151
868	L	X	-0.5878
869	E	X	-2.6291
870	D	X	-2.9353
871	G	X	-1.9063
872	G	X	-1.5634
873	N	X	-1.6660
874	H	X	-2.0234
875	M	X	-1.0102
876	N	X	-0.6050
877	I	X	0.0000
878	K	X	0.1754
879	F	X	1.4901

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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, -0.8789 in this case) is selected and presented in A3D results.