Molecular dynamics–quantum mechanical/molecular mechanical simulation of amide I infrared spectra to identify protein conformational ensembles: a case study of chignolin

Abstract To elucidate the relationship between conformational changes upon protein folding and amide I bands of infrared (IR) spectrum, we investigated amide I bands of chignolin, which not only folds to a native, β-hairpin conformation but also misfolds to another conformation. Chignolin's conformations were sampled using molecular dynamics (MD) simulations, and their spectra of amide groups were calculated using vibrational calculations with the quantum mechanical/molecular mechanical (QM/MM) method. The calculated spectrum of each microstate of chignolin reflects its conformational characteristics. Our calculations reveal how the secondary structure formation affects the contribution of each amide group to the total spectrum. We also show that the population distribution of microstates can be modified by monitoring the match between the calculated and experimental spectra, which effectively fix the bias in the initial distribution caused by the force field used. Our results suggest the existence of a misfolded state in the wild-type chignolin, although the state is not detected by nuclear magnetic resonance (NMR) experiments. The calculation method proposed here is useful for interpreting the amide I band and understanding the structure-spectrum relationship.