Assessing high affinity binding to HLA-DQ2.5 by a novel peptide library based approach

Ulrike Jüse, Magnus Arntzen, Peter Højrup, Burkhard Fleckenstein, Ludvig M Sollid

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

Here we report on a novel peptide library based method for HLA class II binding motif identification. The approach is based on water soluble HLA class II molecules and soluble dedicated peptide libraries. A high number of different synthetic peptides are competing to interact with a limited amount of HLA molecules, giving a selective force in the binding. The peptide libraries can be designed so that the sequence length, the alignment of binding registers, the numbers and composition of random positions are controlled, and also modified amino acids can be included. Selected library peptides bound to HLA are then isolated by size exclusion chromatography and sequenced by tandem mass spectrometry online coupled to liquid chromatography. The MS/MS data are subsequently searched against a library defined database using a search engine such as Mascot, followed by manual inspection of the results. We used two dodecamer and two decamer peptide libraries and HLA-DQ2.5 to test possibilities and limits of this method. The selected sequences which we identified in the fraction eluted from HLA-DQ2.5 showed a higher average of their predicted binding affinity values compared to the original peptide library. The eluted sequences fit very well with the previously described HLA-DQ2.5 peptide binding motif. This novel method, limited by library complexity and sensitivity of mass spectrometry, allows the analysis of several thousand synthetic sequences concomitantly in a simple water soluble format.
Original languageEnglish
JournalBioorganic & Medicinal Chemistry
Volume19
Issue number7
Pages (from-to)2470-7
Number of pages8
ISSN0968-0896
DOIs
Publication statusPublished - 1. Apr 2011

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Peptide Library
Libraries
Mass spectrometry
Search Engine
Peptides
Molecules
Size exclusion chromatography
Water
Sequence Alignment
Liquid chromatography
Search engines
Tandem Mass Spectrometry
Liquid Chromatography
Gel Chromatography
Inspection
Databases
Amino Acids
Chemical analysis

Cite this

Jüse, Ulrike ; Arntzen, Magnus ; Højrup, Peter ; Fleckenstein, Burkhard ; Sollid, Ludvig M. / Assessing high affinity binding to HLA-DQ2.5 by a novel peptide library based approach. In: Bioorganic & Medicinal Chemistry. 2011 ; Vol. 19, No. 7. pp. 2470-7.
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abstract = "Here we report on a novel peptide library based method for HLA class II binding motif identification. The approach is based on water soluble HLA class II molecules and soluble dedicated peptide libraries. A high number of different synthetic peptides are competing to interact with a limited amount of HLA molecules, giving a selective force in the binding. The peptide libraries can be designed so that the sequence length, the alignment of binding registers, the numbers and composition of random positions are controlled, and also modified amino acids can be included. Selected library peptides bound to HLA are then isolated by size exclusion chromatography and sequenced by tandem mass spectrometry online coupled to liquid chromatography. The MS/MS data are subsequently searched against a library defined database using a search engine such as Mascot, followed by manual inspection of the results. We used two dodecamer and two decamer peptide libraries and HLA-DQ2.5 to test possibilities and limits of this method. The selected sequences which we identified in the fraction eluted from HLA-DQ2.5 showed a higher average of their predicted binding affinity values compared to the original peptide library. The eluted sequences fit very well with the previously described HLA-DQ2.5 peptide binding motif. This novel method, limited by library complexity and sensitivity of mass spectrometry, allows the analysis of several thousand synthetic sequences concomitantly in a simple water soluble format.",
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Assessing high affinity binding to HLA-DQ2.5 by a novel peptide library based approach. / Jüse, Ulrike; Arntzen, Magnus; Højrup, Peter; Fleckenstein, Burkhard; Sollid, Ludvig M.

In: Bioorganic & Medicinal Chemistry, Vol. 19, No. 7, 01.04.2011, p. 2470-7.

Research output: Contribution to journalJournal articleResearchpeer-review

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AU - Jüse, Ulrike

AU - Arntzen, Magnus

AU - Højrup, Peter

AU - Fleckenstein, Burkhard

AU - Sollid, Ludvig M

N1 - Copyright © 2011 Elsevier Ltd. All rights reserved.

PY - 2011/4/1

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N2 - Here we report on a novel peptide library based method for HLA class II binding motif identification. The approach is based on water soluble HLA class II molecules and soluble dedicated peptide libraries. A high number of different synthetic peptides are competing to interact with a limited amount of HLA molecules, giving a selective force in the binding. The peptide libraries can be designed so that the sequence length, the alignment of binding registers, the numbers and composition of random positions are controlled, and also modified amino acids can be included. Selected library peptides bound to HLA are then isolated by size exclusion chromatography and sequenced by tandem mass spectrometry online coupled to liquid chromatography. The MS/MS data are subsequently searched against a library defined database using a search engine such as Mascot, followed by manual inspection of the results. We used two dodecamer and two decamer peptide libraries and HLA-DQ2.5 to test possibilities and limits of this method. The selected sequences which we identified in the fraction eluted from HLA-DQ2.5 showed a higher average of their predicted binding affinity values compared to the original peptide library. The eluted sequences fit very well with the previously described HLA-DQ2.5 peptide binding motif. This novel method, limited by library complexity and sensitivity of mass spectrometry, allows the analysis of several thousand synthetic sequences concomitantly in a simple water soluble format.

AB - Here we report on a novel peptide library based method for HLA class II binding motif identification. The approach is based on water soluble HLA class II molecules and soluble dedicated peptide libraries. A high number of different synthetic peptides are competing to interact with a limited amount of HLA molecules, giving a selective force in the binding. The peptide libraries can be designed so that the sequence length, the alignment of binding registers, the numbers and composition of random positions are controlled, and also modified amino acids can be included. Selected library peptides bound to HLA are then isolated by size exclusion chromatography and sequenced by tandem mass spectrometry online coupled to liquid chromatography. The MS/MS data are subsequently searched against a library defined database using a search engine such as Mascot, followed by manual inspection of the results. We used two dodecamer and two decamer peptide libraries and HLA-DQ2.5 to test possibilities and limits of this method. The selected sequences which we identified in the fraction eluted from HLA-DQ2.5 showed a higher average of their predicted binding affinity values compared to the original peptide library. The eluted sequences fit very well with the previously described HLA-DQ2.5 peptide binding motif. This novel method, limited by library complexity and sensitivity of mass spectrometry, allows the analysis of several thousand synthetic sequences concomitantly in a simple water soluble format.

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