MHC I Stabilizing Potential
of Computer-Designed
Octapeptides
Table 1
Experimentally tested octapeptides. Sequences are given in single-letter code; motif anchor positions fulfilling the SYFPEITHI motif are underlined. S-score: SYFPEITHI score [6]. IEDB-ANN score: predicted IC50 values by IEDB-ANN method [25]. 500 nM: recommended cutoff for IEDB-ANN score [25] for binders predicted with intermediate affinity; active: IEDB-ANN score 500 nM; 0: IEDB-ANN score 500 nM. EC50 values correspond to the peptide concentration required for 50% of maximal MHC I protein stabilization; values in brackets are standard deviations (). n.d.: not detectable.
Peptide number
Sequence
S-score
IEDB-ANN score [M]
500 nM
Experimental [M]
Stabilizing peptides
1
FRYPYKTL
27
0.5
active
24.0 (11)
2
FRYIYHTL
27
0.2
active
20.0 (4.0)
3
FHWDYRGL
22
0.4
active
25.0 (11)
4
WRFKYDNL
22
2.3
0
7.0 (4.0)
5
WRFVYWRL
20
1.2
0
8.0 (4.0)
6
WRFIYFNL
21
0.4
active
3.6 (1.2)
7
WDFKFDSV
17
4.7
0
9.0 (4.0)
8
WKFIFDPV
16
3.0
0
0.4 (0.1)
9
FHHAHRTV
8
10.5
0
9.0 (4.0)
Nonstabilizing peptides of category (i)
10
FRYEYRSL
28
0.1
active
n.d.
11
WRYIYHSI
22
2.5
0
n.d.
12
HRYVYRNI
24
0.4
active
n.d.
13
FHYAYRSV
23
0.1
active
n.d.
14
YRYKYDRL
27
0.5
0
n.d.
15
WRYQYDNL
27
0.7
0
n.d.
16
WRYRYWSL
27
0.6
0
n.d.
17
WRYNYDPL
26
1.7
0
n.d.
18
WRYHYDPL
26
2.4
0
n.d.
19
WKYQYDNL
27
0.3
active
n.d.
20
WKYIFDPV
22
1.2
0
n.d.
21
WKYPFDPV
22
2.0
0
n.d.
Nonstabilizing peptides of category (ii)
22
FRYLYKNA
17
1.2
0
n.d.
23
FRYVWRTL
18
1.7
0
n.d.
24
FHYLYHTA
17
0.9
0
n.d.
25
FRYPYHTP
17
17.8
0
n.d.
26
FRWEYRGL
22
0.7
0
n.d.
27
FRHIYRTI
18
9.3
0
n.d.
28
FRHGYRQI
18
12.6
0
n.d.
29
FHWAYHTV
17
1.2
0
n.d.
30
WRWLYKGV
16
4.3
0
n.d.
31
WRFPYDQL
21
6.6
0
n.d.
32
WRFKYDPL
21
3.3
0
n.d.
33
WRFPYDKL
21
6.8
0
n.d.
34
WRFVYDNL
21
1.9
0
n.d.
35
WKFKFDPV
17
2.8
0
n.d.
36
WKINFDPV
17
8.2
0
n.d.
37
TTEWYTKI
18
3.4
0
n.d.
5 of 23 nonstabilizing peptides of category (iii)
38
RGEVFTAT
13
24.0
0
n.d.
39
FHYDHRNA
9
6.5
0
n.d.
40
HRWVFWQP
11
26.0
0
n.d.
41
SIKNFHYY
12
13.6
0
n.d.
42
FRHDYHSP
11
29.2
0
n.d.
7 of 120 nonstabilizing peptides of category (iv)
43
TVEQGVTQ
1
37.5
0
n.d.
44
FHHGHNVP
0
36.8
0
n.d.
45
QDGHEIHR
1
38.4
0
n.d.
46
TVEQGVTQ
1
37.5
0
n.d.
47
GVDQSYLK
0
38.1
0
n.d.
48
SVENPILR
2
33.7
0
n.d.
49
NEGWTIHR
1
38.8
0
n.d.
50
SVDHSIFK
2
36.1
0
n.d.
For category (iii) 5 of 23 octapeptides are given as examples. The remaining 18 octapeptides of category (iii) are listed in Suppl. 2 (Seq. No. 51–68). For category (iv) 7 of 120 ostapeptides are given as examples. The remaining 113 octapeptides of category (iv) are listed in Suppl. 2 (Seq. No. 69–180).
