Optimization algorithms for functional deimmunization of therapeutic proteins

BMC Bioinformatics

Table 2 Full-length SakSTAR.

Variant	SakSTAR 1-136	E	B	C	ΔΔG°	S
wild type	SakSTAR	99	0	0.00	0.00	49
1 substitution
Warmerdam	R77A	95	1	0.75	0.43	47
BLOSUM	V27T	88	0	0.89	2.08	48
Conservation	M26D	79	1	1.15	1.89	41
FoldX	V112P	90	1	0.93	-0.03	47
2 substitutions
Warmerdam	R77A,E80A	98	2	2.48	1.00	51
BLOSUM	V27T,S84E	79	0	3.18	2.70	43
Conservation	M26D,V79D	68	2	1.87	3.79	35
FoldX	Y24H,V112P	82	2	1.89	0.04	43
3 substitutions
Warmerdam	R77A,E80A,D82A	105	3	4.96	0.22	55
BLOSUM	V27T,S84E,V112A	70	0	1.98	3.16	41
Conservation	M26D,I49D,V79D	58	3	1.51	7.46	31
FoldX	Y24H,V79K,V112P	75	3	2.83	0.04	39
4 substitutions
Warmerdam	K74Q,R77S,E80S,D82S	103	3	5.93	1.28	52
BLOSUM	V27T,V45A,S84E,V112A	63	0	2.36	3.98	42
Conservation	M26D,I49D,V79D,V112K	49	4	1.28	6.72	29
FoldX	Y24H,N28E,V79K,V112P	69	4	4.28	0.00	35
5 substitutions
BLOSUM	V27T,V45A,S84E,V112A,K130E	58	0	3.12	5.41	40
Conservation	M26D,I49D,V79D,V112K,F125E	41	5	1.74	12.60	25
FoldX	Y24H,N28E,Y62R,V79K,V112P	63	5	4.37	0.12	33
6 substitutions
BLOSUM	V27T,V45A,V79T,V89T,V112A,K130E	54	0	0.74	8.26	41
Conservation	M26D,I49D,Y62D,V79D,V112K,F125E	34	6	1.92	13.56	23
FoldX	Y24H,N28E,Y62K,V79K,S84T,V112P	58	5	5.32	0.01	34

Variants of the full SakSTAR protein by Warmerdam et al. [19], as well as by our dynamic programming algorithm, optimizing for ProPred and allowing mutations according to BLOSUM, conservation, or FoldX. E: number of ProPred epitopes; B, C, and ΔΔG°: total substitution penalty under BLOSUM, conservation, and FoldX, resp.; S: number of SMM-align epitopes.

ISSN: 1471-2105