Research
Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries
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* Corresponding author: Bjoern Peters bpeters@liai.org
1 La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
2 Torrey Pines Institute for Molecular Studies, 3550 General Atomics Court, 2-129, San Diego, CA 92121, USA
Immunome Research 2008, 4:2 doi:10.1186/1745-7580-4-2
Published: 25 January 2008Additional files
Additional file 1:
Binding capacity of positional scanning combinatorial libraries for 19 HLA and H-2 class I alleles. This table lists the measured IC50 nM value of each mixture in the combinatorial library for 19 class I alleles. Binding assays were performed as described in the Methods section.
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Additional file 2:
Normalized average relative binding affinities of positional scanning combinatorial libraries for 19 HLA and H-2 class I alleles. This table lists the normalized ARB values of each mixture in the positional scanning combinatorial library for 19 class I alleles. Binding data for each mixture were normalized as described in the materials and methods, such that the optimal mixture (residue) at each position corresponds to 1.0, and residues associated with lower affinities with correspondingly lower values. The normalized values for A*0201 are also shown in matrix format in Table 2.
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Additional file 3:
Vaccinia WR-derived peptides that bind 5 common HLA alleles with high affinity. The vaccinia WR-derived peptides identified that bind A) A*3001, B) A*3201, C) B*0801, D) B*1501 or E) B*1503 with affinities of 500 nM, or better are shown. Candidate peptides were selected using the corresponding normalized combinatorial library matrix values [see Additional file 2], and tested for binding as described in the Methods. For each allele, a set of 300 candidate peptides was originally selected.
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Additional file 4:
Second generation matrices for predicting binders to HLA A*3001, A*3201 and B*1501. Second generation prediction matrices were derived combining the positional scanning combinatorial library and peptide library data, using the stabilized matrix method (SMM) approach, as previously described [56]. Scores for individual peptides represent log predicted IC50 nM values, and are calculated as the sum of the corresponding position/residue values, plus the constant. Algorithms derived by combining positional scanning and individual peptide data sets were generated.
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