Paper Citing NAMD - Abstract
Zhao, Juan; Shi, Jipei; Wang, Jianping
Amide-I Characteristics of Helical beta-Peptides by Linear Infrared Measurement and Computations
JOURNAL OF PHYSICAL CHEMISTRY B, 118:94-106, JAN 9 2014
In this work, we have examined the amide-I characteristics of three beta-peptide oligomers in typical helical conformations (two in 14-helix and one in 12/10-helix), solvated in water, methanol, and chloroform, respectively. Local-mode frequencies and their distributions were computed using a molecular-mechanics force field based frequency map that was constructed on the basis of molecular dynamics simulations. The local-mode frequencies were found to be determined primarily by peptide backbone and side chain, rather by solvent, suggesting their local structural sensitivities. Intermode vibrational couplings computed using a transition dipole scheme were found to be very sensitive to peptide conformation, with their signs and magnitudes varying periodically along the peptide chain. Linear infrared absorption spectra of the three peptides, simulated using a frequency-frequency time-correlation function method, were found to be in fair agreement with experimental results. Normalized potential energy distribution analysis indicated that the amide-I mode can delocalize over a few amide units. However, the IR band structure appears to be more sophisticated in helical beta-peptides than in helical alpha-peptides.
