Energy landscape of a peptide consisting of alpha-helix, 3(10)-helix, beta-turn, beta-hairpin, and other disordered conformations.
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 simulation, 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 conformations were dominant at room temperature. The CD spectra of the synthesized 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-helix, and random-coil conformations were separated from one another in the conformational space. This means that the peptide must overcome energy barriers to form the alpha-helix. The overcoming process may correspond to the hydrogen-bond rearrangements from peptide-water to peptide-peptide interactions. The beta-turn, imperfect 3(10)-helix, and beta-hairpin structures, among which there are no energy barriers at 300 K, were embedded in the ensemble of the random-coil conformations. Two types of beta-hairpin with different beta-turn regions were observed in Q(300K). The two beta-hairpin structures may have different mechanisms for the beta-hairpin formation. The current study proposes a scheme that the random state of this peptide consists of both ordered and disordered conformations. In contrast, the energy landscape obtained from the parm94 force field was funnel like, in which the peptide formed the helical conformation at room temperature and random coil at high temperature.
Higo
J
J
Biomolecular Engineering Research Institute (BERI), Suita, Osaka 565-0874, Japan. higo@ls.toyaku.ac.jp
Ito
N
N
Kuroda
M
M
Ono
S
S
Nakajima
N
N
Nakamura
H
H
D002942:Circular Dichroism; D006358:Hot Temperature; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding; D020598:Proto-Oncogene Proteins c-myb / Q000737:chemistry; D013696:Temperature; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D010455:Peptides; D020598:Proto-Oncogene Proteins c-myb; D014867:Water