Energetic asymmetry among hydrogen bonds in MHC class II⋅peptide complexes

Abstract

Comparison of crystallized MHC class II⅐peptide complexes has revealed that, in addition to pocket interactions involving the peptide side chains, peptide binding to MHC class II molecules is characterized by a series of hydrogen bonds between genetically conserved amino acid residues in the class II molecule and the main chain of the peptide. Many class II⅐peptide structures have two sets of symmetrical hydrogen bonds at the opposite ends of the class II antigen-binding groove (␤-His-81, ␤-Asn-82 vs. ␣-His-68, ␣-Asn-69). In this study, we alter these peripheral hydrogen bonds and measure the apparent contribution of each to the kinetic stability of peptide⅐class II complexes. Single conservative amino substitutions were made in the I-A d protein to eliminate participation as a hydrogen bonding residue, and the kinetic stability of a diverse set of peptides bound to the substituted I-A d proteins was measured. Although each hydrogen bond does contribute to peptide binding, our results point to the striking conclusion that those hydrogen bonds localized to the amino terminus of the peptide contribute profoundly and disproportionately to the stability of peptide interactions with I-A d . We suggest that the peripheral hydrogen bonds at the amino terminus of the bound peptide that are conserved in all class II⅐peptide crystal structures solved thus far form a cooperative network that critically regulates peptide dissociation from the class II molecule.M ajor histocompatibility complex (MHC) class II molecules are composed of two noncovalently associated, polymorphic transmembrane proteins, termed ␣ and ␤, of approximate molecular mass of 33 kDa and 28 kDa, respectively. They interact with T cell receptors to provoke an antigen-specific CD4 ϩ T cell response. Crystal structures of class II molecules have provided insight into the structural elements that control interactions with peptide. Both polymorphic and genetically conserved amino acid residues make contacts with the bound peptide (1-7). Most of the polymorphic residues face the interior of the peptide-binding groove, and thus contribute to allele-dependent peptide binding. Similar to what has been observed in class I molecules, MHC class II molecules appear to have ''pockets'' that are capable of binding to peptide side chains. In addition to these pocket interactions, MHC class II molecules bind peptide through a series of hydrogen bonds between genetically conserved amino acid residues in the class II molecule and the main chain of the peptide. These conserved residues bind at relatively regular intervals throughout the length of the peptide, and apparently stabilize the peptide in a fairly fixed polyproline type II conformation throughout the length of the peptide-binding pocket (3).One striking aspect of class II⅐peptide structures noted in murine complexes (6, 7) are two sets of symmetrical hydrogen bonds at the opposite ends of the binding pocket (Fig. 1). The hydrogen bonds contributed by ␤-His-81 and ␤-Asn-82 are localized to the bound peptide's amino...

Thermodynamic Analysis of the Increased Stability of Major Histocompatibility Complex Class II Molecule I-Ek Complexed with an Antigenic Peptide at an Acidic pH

“…In the case of a 420-residue protein, I-E k -Hb, the pI value in the denatured state is estimated to be 4.8 from the amino acid composition, and that in the native state is estimated to be 5.0 by the isoelectric focusing experiments (data not shown). Amino acid residues such as Asp and His, with charges that are affected at the pH region analyzed in this study, are thought to be involved in the structural and functional characters of MHC class II molecules (16,30,31). Therefore, the present thermodynamic results obtained in phosphate buffer, which has lower enthalpy change for the deprotonation, could be the comparable data to analyze the effects of pH on the stability difference of I-E k -Hb.…”

“…The protonation of these carboxylate groups at low pH, together with other residues such as His 81 of the ␤ subunit, facilitates the flexibility and the conformational change of the MHC class II molecule from the closed to the open form (30). In addition, the recent mutational analyses of HLA-DR, the human homologue of I-E k , have shown that His 33 of the ␣ subunit has the role of a pH-sensitive switch at low pH, which can regulate the conformational transition and the peptide exchange (31).…”

Hydrogen Bond Integrity Between MHC Class II Molecules and Bound Peptide Determines the Intracellular Fate of MHC Class II Molecules

“…Recent work has demonstrated that in I-A d class II molecules, these different sets of hydrogen bonds contribute disproportionately to peptide-MHC stability. The loss of hydrogen bonds near the amino terminus of the bound peptide, as previously demonstrated, resulted in substantial acceleration in peptide dissociation, whereas the loss of hydrogen bonds near the peptide's carboxyl terminus were shown to have significantly less effect, indicating that they contribute less to complex stability (32). We have not yet explored the relative importance of individual hydrogen bonds in human class II molecules, although the hydrogen bonding network was first noted in these crystal structures (9,33).…”

Cooperativity of Hydrophobic Anchor Interactions: Evidence for Epitope Selection by MHC Class II as a Folding Process

“…This first rearrangement would indeed trigger the involvement of the adjacent, partially disordered, ␣1/␤1 helical regions and it would facilitate the formation of the other pocket/side chain interactions. At first, the nucleus would be stabilized by the interactions in the P(Ϫ1) to P2 region, where the H-bonds between His␤ (81) and Asn␤ (82), as well as the residues from ␣ (51) to ␣ (53), and the bound peptide, have been recognized as critical for the complex stability (31)(32)(33). Then, the onrush of cooperative interactions would operate: 1) inducing the folding of the helices; 2) inducing the other hydrophobic pocket interactions; 3) stabilizing both types of binding energy; 4) inducing the folding of the peptide into a polyproline type II conformation.…”