Paper Citing NAMD - Abstract
Maekawa, Hiroaki; Ballano, Gema; Toniolo, Claudio; Ge, Nien-Hui
Linear and Two-Dimensional Infrared Spectroscopic Study of the Amide I and II Modes in Fully Extended Peptide Chains
JOURNAL OF PHYSICAL CHEMISTRY B, 115:5168-5182, MAY 12 2011
We have carried out structural determination of capped C(alpha,alpha)-diethylglycine (Deg) homopeptides with different chain lengths, Ac-(Deg)(n)-OtBu (n = 2-5), solvated in CDCl(3), and investigated vibrational properties of the amide I and II modes by linear and 2D IR spectroscopy, ONIOM calculations, and molecular dynamics simulations. 2D IR experiments were performed in the amide I region using the rephasing pulse sequence under the double-crossed polarization and the nonrephasing sequence under a new polarization configuration to measure cross-peak patterns in the off-diagonal regions. The 2D IR spectra measured in the amide land II regions reveal complex couplings between these modes. Model spectral calculations finely reproduced the measured spectral profiles by using vibrational parameters that were very close to the values predicted by the ONIOM method. The agreement led to a conclusion that peptide backbones are fully extended with the dihedral angles (phi,psi) approximate to (+/- 180 degrees,+/- 180 degrees) and that a sequence of intramolecular C(5) hydrogen bonds forms along the entire chain regardless of the chain length. This conclusion was endorsed by analysis of the molecular dynamics trajectories for n = 3 and 5 that showed an exclusive population of the C(5) conformation. The conformationally well-restrained Deg homopeptides serve as an ideal linear exciton chain, which is scarcely obtainable by protein amino acids. We investigated excitonic properties of the linear chain through analytic modeling and compared the measurement and calculation results of the amide I and II modes. The integrated intensity of the amide II band is larger than that of the amide I for the C(5) structure, untypical behavior in contrast with other secondary structures. This comprehensive study characterized the amide I and II spectral signatures of the fully extended conformation, which will facilitate the conformational analysis of artificial oligopeptides that contain such structural motifs.
