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This Article Full Text Full Text (PDF) Data Supplement All Versions of this Article: jimmunol.0802228v1 183/5/3249    most recent Alert me when this article is cited Alert me if a correction is posted Citation Map Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Request Permissions Google Scholar Articles by James, E. A. Articles by Kwok, W. W. PubMed PubMed Citation Articles by James, E. A. Articles by Kwok, W. W.

The Binding of Antigenic Peptides to HLA-DR Is Influenced by Interactions between Pocket 6 and Pocket 9¹

Eddie A. James^*, Antonis K. Moustakas, John Bui^*, Randi Nouv^*, George K. Papadopoulos and William W. Kwok^2,*,

^* Benaroya Research Institute at Virginia Mason, Seattle, WA 98101; Department of Immunology, University of Washington, Seattle, WA 98195; Department of Organic Farming, Technological Educational Institute of Ionian Islands, Argostoli, Cephalonia, Greece; and Laboratory of Biochemistry and Biophysics, Faculty of Agricultural Technology, Epirus Institute of Technology, Arta, Greece

Peptide binding to class II MHC protein is commonly viewed as a combination of discrete anchor residue preferences for pockets 1, 4, 6/7, and 9. However, previous studies have suggested cooperative effects during the peptide binding process. Investigation of the DRB1*0901 binding motif demonstrated a clear interaction between peptide binding pockets 6 and 9. In agreement with prior studies, pockets 1 and 4 exhibited clear binding preferences. Previously uncharacterized pockets 6 and 7 accommodated a wide variety of residues. However, although it was previously reported that pocket 9 is completely permissive, several substitutions at this position were unable to bind. Structural modeling revealed a probable interaction between pockets 6 and 9 through β9Lys. Additional binding studies with doubly substituted peptides confirmed that the amino acid bound within pocket 6 profoundly influences the binding preferences for pocket 9 of DRB1*0901, causing complete permissiveness of pocket 9 when a small polar residue is anchored in pocket 6 but accepting relatively few residues when a basic residue is anchored in pocket 6. The β9Lys residue is unique to DR9 alleles. However, similar studies with doubly substituted peptides confirmed an analogous interaction effect for DRA1/B1*0301, a β9Glu allele. Accounting for this interaction resulted in improved epitope prediction. These findings provide a structural explanation for observations that an amino acid in one pocket can influence binding elsewhere in the MHC class II peptide binding groove.

The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

¹ This work was supported in part by National Institutes of Health Contract HHSN266200400028C.

² Address correspondence and reprint requests to Dr. William W. Kwok, Benaroya Research Institute at Virginia Mason, 1201 9th Avenue, Seattle WA 98101. E-mail address: bkwok{at}benaroyaresearch.org

³ Abbreviations used in this paper: DR0901, DRA1/B1*0901; DR0301, DRA1/B1*0301; NP, influenza A/Puerto Rico/8/34 nucleoprotein; M1, influenza A/Puerto Rico/8/34 matrix protein; Flu B HA, influenza B/Hong Kong/330/2001 hemagglutinin; HA Pan, influenza A/Panama/2007/99 hemagglutinin; HA NC, influenza A/New Caledonia/20/99 hemagglutinin; RBA, relative binding affinity; RBA_adj, adjusted RBA; CRBA, corrected RBA; TT, tetanus toxin H chain; TTL, tetanus toxin L chain.

⁴ The online version of this article contains supplemental material.