Anharmonic Vibrational Analyses of Pentapeptide Conformations Explored with Enhanced Sampling Simulations.
An accurate theoretical prediction of the vibrational spectrum of polypeptides remains to be a challenge due to (1) their conformational flexibility and (2) non-negligible anharmonic effects. The former makes the search for conformers that contribute to the spectrum difficult, and the latter requires an expensive, quantum mechanical calculation for both electrons and vibrations. Here, we propose a new theoretical approach, which implements an enhanced conformational sampling by the replica-exchange molecular dynamics method, a structural clustering to identify distinct conformations, and a vibrational structure calculation by the second-order vibrational quasi-degenerate perturbation theory (VQDPT2). A systematic mode-selection scheme is developed to reduce the cost of VQDPT2 and the generation of a potential energy surface by the electronic structure calculation. The proposed method is applied to a pentapeptide, SIVSF-NH2, for which the infrared spectrum has recently been measured in the gas phase with high resolution in the OH and NH stretching region. The theoretical spectrum of the lowest energy conformer is obtained with a mean absolute deviation of 11.2 cm-1from the experimental spectrum. Furthermore, the NH stretching frequencies of the five lowest energy conformers are found to be consistent with the literature values measured for small peptides with a similar secondary structure. Therefore, the proposed method is a promising way to analyze the vibrational spectrum of polypeptides.
Hiroki
H
Otaki
Kiyoshi
K
Yagi
Laboratory for Chemistry and Life Science, Institute for Innovative Research, Tokyo Institute of Technology , 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.
Shun-Ichi
SI
Ishiuchi
Laboratory for Chemistry and Life Science, Institute for Innovative Research, Tokyo Institute of Technology , 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan.
Masaaki
M
Fujii
RIKEN Advanced Institute for Computational Science , 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.|RIKEN Quantitative Biology Center , 1-6-5 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
Yuji
Y
Sugita
D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D011789:Quantum Theory; D013055:Spectrophotometry, Infrared; D014732:Vibration
D009842:Oligopeptides