The energy landscape of a peptide [Ace-Lys-Gln-Cys-Arg-Glu-Arg-Ala-Nme] in
explicit water was studied with a multicanonical molecular dynamics simulat
ion, and the AMBER parm96 force field was used for the energy calculation.
The peptide was taken from the recognition helix of the DNA-binding protein
, c-Myb. A rugged energy landscape was obtained, in which the random-coil c
onformations were dominant at room temperature. The CD spectra of the synth
esized peptide revealed that it is in the random state at room temperature.
However, the 300 K canonical ensemble, Q(300K), contained alpha -helix, 3(
10)-helix, beta -turn, and beta -hairpin structures with small but notable
probabilities of existence. The complete alpha -helix, imperfect alpha -hel
ix, and random-coil conformations were separated from one another in the co
nformational space. This means that the peptide must overcome energy barrie
rs to form the alpha -helix. The overcoming process may correspond to the h
ydrogen-bond rearrangements from peptide-water to peptide-peptide interacti
ons. The beta -turn, imperfect 3(10)-helix, and beta -hairpin structures, a
mong which there are no energy barriers at 300 K, were embedded in the ense
mble of the random-coil conformations. Two types of P-hairpin with differen
t beta -turn regions were observed in Q(300K). The two beta -hairpin struct
ures may have different mechanisms for the beta -hairpin formation. The cur
rent study proposes a scheme that the random state of this peptide consists
of both ordered and disordered conformations. In contrast, the energy land
scape obtained from the parm94 force field was funnel Like, in which the pe
ptide formed the helical conformation at room temperature and random coil a
t high temperature.