Modeling the temperature-dependent peptide vibrational spectra based on implicit-solvent model and enhance sampling technique

We herein review our studies on simulating the thermal unfolding Fourier transform infrared and two-dimensional infrared spectra of peptides. The peptide-water configuration ensembles, required forspectrum modeling, aregenerated at a series of temperatures using the GB^OBC implicit solvent model and the integrated tempering sampling technique. The fluctuating vibrational Hamiltonians of the amide I vibrational band are constructed using the Frenkel exciton model. The signals are calculated using nonlinear exciton propagation. The simulated spectral features such as the intensity and ellipticity are consistent with the experimental observations. Comparing the signals for two beta-hairpin polypeptides with similar structures suggests that this technique is sensitive to peptide folding landscapes.