BACKGROUND:
Endoplasmic reticulum aminopeptidase 1 (ERAP1) trims N-terminally extended
antigenic peptide precursors down to mature
antigenic peptides for presentation by
major histocompatibility complex (MHC) class I molecules. ERAP1 has unique properties for an
aminopeptidase being able to trim
peptides in vitro based on their length and the nature of their C-termini. METHODOLOGY/PRINCIPAL FINDINGS: In an effort to better understand the molecular mechanism that ERAP1 uses to trim
peptides, we systematically analyzed the enzyme's
substrate preferences using collections of
peptide substrates. We discovered strong internal sequence preferences of
peptide N-terminus trimming by ERAP1. Preferences were only found for positively charged or
hydrophobic residues resulting to trimming rate changes by up to 100 fold for single residue substitutions and more than 40,000 fold for multiple residue substitutions for
peptides with identical N-termini.
Molecular modelling of ERAP1 revealed a large internal cavity that carries a strong negative electrostatic potential and is large enough to accommodate
peptides adjacent to the enzyme's
active site. This model can readily account for the strong preference for positively charged side chains. CONCLUSIONS/SIGNIFICANCE: To our knowledge no other
aminopeptidase has been described to have such strong preferences for internal residues so
distal to the
N-terminus. Overall, our findings indicate that the internal sequence of the
peptide can affect its trimming by ERAP1 as much as the peptide's length and
C-terminus. We therefore propose that ERAP1 recognizes the full length of its peptide-substrate and not just the N- and C- termini. It is possible that ERAP1 trimming preferences influence the rate of generation and the composition of
antigenic peptides in vivo.
