Periodic variation in side-chain polarities of T-cell antigenic peptides correlates with their structure and activity

James L. Cornette*, Hanah Margalit, Jay A. Berzofsky, Charles Delisi

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

17 Scopus citations


We present an analysis that synthesizes information on the sequence, structure, and motifs of antigenic peptides, which previously appeared to be in conflict. Fourier analysis of T-cell antigenic peptides indicates a periodic variation in amino acid polarities of 3-3.6 residues per period, suggesting an amphipathic α-helical structure. However, the diffraction patterns of major histocompatibility complex (MHC) molecules indicate that their ligands are in an extended non-α-helical conformation. We present two mutually consistent structural explanations for the source of the α-helical periodicity, based on an observation that the side chains of MHC-bound peptides generally partition with hydrophobic (hydrophilic) side chains pointing into (out of) the cleft. First, an analysis of haplotype-dependent peptide motifs indicates that the locations of their defining residues tend to force a period 3-4 variation in hydrophobicity along the peptide sequence, in a manner consistent with the spacing of pockets in the MHC. Second, recent crystallographic determination of the structure of a peptide bound to a class II MHC molecule reveals an extended but regularly twisted peptide with a rotation angle of about 130°. We show that similar structures with rotation angles of 100-130° are energetically acceptable and also span the length of the MHC cleft. These results provide a sound physical chemical and structural basis for the existence of a haplotype-independent antigenic motif which can be particularly important in limiting the search time for antigenic peptides.

Original languageAmerican English
Pages (from-to)8368-8372
Number of pages5
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number18
StatePublished - 29 Aug 1995


  • amphipathicity
  • hydrophobic moment


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