Computer simulation of the
conformations of short antigenic peptides (&lo
residues) either free or bound to their receptor,
the major histocompatibility complex (MHC)-
encoded glycoprotein H-2 Ld, was employed to
explain experimentally determined differences
in the antigenic activities within a set of related
peptides. Starting for each sequence from the
most probable conformations disclosed by a
pattern-recognition technique, several energyminimized
structures were subjected to molecular
dynamics simulations (MD) either in vacuo
or solvated by water molecules. Notably, antigenic
potencies were found to correlate to the
peptides propensity to form and maintain an
overall a-helical conformation through regular
i,i + 4 hydrogen bonds. Accordingly, less active
or inactive peptides showed a strong tendency
to form i,i+3 hydrogen bonds at their Nterminal
end. Experimental data documented
that the C-terminal residue is critical for interaction
of the peptide with H-2 Ld. This finding
could be satisfactorily explained by a 3-D
Q.S.A.R. analysis postulating interactions between
ligand and receptor by hydrophobic
forces. A 3-D model is proposed for the complex
between a high-affinity nonapeptide and the H-
2 Ld receptor. First, the H-2 Ld molecule was
built from X-ray coordinates of two homologous
proteins: HLA-A2 and HLA-Aw68, energyminimized
and studied by MD simulations. With
HLA-A2 as template, the only realistic simulation
was achieved for a solvated model with minor
deviations of the MD mean structure from
the X-ray conformation. Water simulation of the
H-2 Ld protein in complex with the antigenic
nonapeptide was then achieved with the template-
derived optimal parameters. The bound
peptide retains mainly its a-helical conformation
and binds to hydrophobic residues of H-2
Ld that correspond to highly polymorphic positions
of MHC proteins. The orientation of the
nonapeptide in the binding cleft is in accordance
with the experimentally determined distribution
of its MHC receptor-binding residues
(agretope residues). Thus, computer simulation was successfully employed to explain functional
data and predicts a-helical conformation
for the bound peptid