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The class I major histocompatibility (MHC) molecule is a heterotrimer composed of a heavy chain, the small subunit beta(2)-microglobulin (beta(2)m), and a peptide. Fluorescence anisotropy has been used to assay the interaction of a labeled peptide with a recombinant, soluble form of the class I MHC HLA-A2. Consistent with earlier work, peptide binding is shown to be a two-step process limited by a conformational rearrangement in the heavy chain/beta(2)m heterodimer. However, we identify two pathways for peptide dissociation from the heterotrimer: (1) initial peptide dissociation leaving a heavy chain/beta(2)m heterodimer and (2) initial dissociation of beta(2)m, followed by peptide dissociation from the heavy chain. Eyring analyses of rate constants measured as a function of temperature permit for the first time a complete thermodynamic characterization of peptide binding. We find that in this case peptide binding is mostly entropically driven, likely reflecting the hydrophobic character of the peptide binding groove and the peptide anchor residues. Thermodynamic and kinetic analyses of peptide-MHC interactions as performed here may be of practical use in the engineering of peptides with desired binding properties and will aid in the interpretation of the effects of MHC and peptide substitutions on peptide binding and T cell reactivity. Finally, our data suggest a role for beta(2)m in dampening conformational dynamics in the heavy chain. Remaining conformational variability in the heavy chain once beta(2)m has bound may be a mechanism to promote promiscuity in peptide binding.

Most peptides that bind to a particular MHC class I molecule share amino acid residues that are thought to physically "anchor" the peptide to polymorphic pockets within the class I binding site. Sequence analysis of endogenous peptides bound to HLA-B44 revealed two potential dominant anchor residues: Glu at P2 and Tyr, or occasionally Phe, at P9. In vitro assembly assays employing synthetic peptides and recombinant HLA-B44 produced by Escherichia coli revealed that an acidic amino acid at P2 was necessary for promoting stable peptide binding to HLA-B44. Surprisingly, although Tyr was almost exclusively found at P9 of the endogenous peptide sequences, a wide variety of amino acid residues such as Leu, Ala, Arg, Lys, His, and Phe could be tolerated at this position. Using this information, we identified antigenic peptides from the influenza virus components nonstructural protein 1 and nucleoprotein that are presented by HLA-B44 to antiinfluenza type A cytotoxic T lymphocytes. In addition, cytotoxic T lymphocytes induced by these antigenic peptides were shown to be capable of recognizing endogenously processed peptides from influenza-infected cells, indicating a potential use for these peptides in vaccine development. Finally, molecular models were created to investigate the possible ways in which the anchor residues might function to stabilize the binding of peptides to HLA-B44, and these models indicate that the acidic residue at P2 most likely interacts primarily with Lys 45 of the HLA-B44 heavy chain and makes additional contacts with Ser 67 and Tyr 9.

Major histocompatibility complex (MHC) class I molecules bind endogenously synthesized peptides for presentation to cytotoxic T-cells. The human class I molecule HLA-B27 consists of a trimolecular complex containing the HLA-B27 heavy chain, a peptide that is usually nine amino acid residues (aa) long, and beta 2-microglobulin (beta 2m). The key interactions for peptide selectivity are between Glu-45, which forms a salt bridge with the Arg at P2 of the peptide, and Asp-116 which favors the binding of peptides containing a Lys or Arg at P9. The t1/2 of dissociation of [125I]beta 2m was measured for peptide-specific HLA-B27 wild-type (wt) and mutant complexes. HLA-B27 wt and HLA-B27 D116F formed relatively stable complexes, with a t1/2 of dissociation on the scale of hours, with appropriate peptides that contained Arg at P2, whereas HLA-B27 E45T required a Gln at P2. Similarly, kinetically stable D116F complexes were formed only with peptides that contained a Leu or Val at P9 instead of Arg or Lys. The [125I]beta 2m dissociation rate data were fit to a set of equations in order to calculate relative binding coefficients for each anchor residue at P2 and P9. The P2 coefficients were sensitive to the E45T mutation but not the D116F mutation, whereas the P9 coefficients were sensitive only to the D116F mutation. Thus, drastic structural changes in one subsite do not affect the other subsite, indicating that the dominant anchor residues at P2 and P9 independently contribute to stabilizing the class I/peptide complex.

Influenza-specific cytotoxic T cells restricted by HLA-A3 recognize differences between HLA-A3 antigens that are serologically indistinguishable. To examine whether this differential recognition had a structural basis, we have compared the structures of HLA-A3 molecules from Epstein Barr virus-transformed peripheral blood lymphocytes of two individuals, E1 and M17. M17 was representative of the majority of HLA-A3-bearing individuals, whereas E1 was a variant distinguished by cytotoxic T cells. Peptide map comparisons revealed a small number of differences when particular amino acids were used to radiolabel the A3 molecules. Sequence analysis and comparison of the results with the prototypic HLA-A3 sequence localized the variability to a tryptic peptide spanning residues 147-157. To obtain the complete amino acid sequence for the E1 and M17 A3 molecules in the 147-157 region, the CNBr fragments beginning at residue 139 were isolated and sequenced. Two amino acid differences were detected between the HLA-A3 molecule of the CTL-defined variant E1 and that of M17. At position 152, Glu in donor M17 had changed to Va1 in donor E1, and at position 156, Leu in donor M17 had changed to Gln in donor E1. The finding that A3 molecules from E1 are altered in the region between residues 147 and 157 is consistent with studies on HLA-A2 variants and Kb mutants showing that this region of class I molecules is important for CTL recognition but not for recognition by serologic reagents.