The Amide I Spectrum of ProteinsOptimization of Transition Dipole Coupling Parameters Using Density Functional Theory Calculations

The
amide I region of the infrared spectrum is related to the protein
backbone conformation and can provide important structural information.
However, the interpretation of the experimental results is hampered
because the theoretical description of the amide I spectrum is still
under development. Quantum mechanical calculations, for example, using
density functional theory (DFT), can be used to study the amide I
spectrum of small systems, but the high computational cost makes them
inapplicable to proteins. Other approaches that solve the eigenvalues
of the coupled amide I oscillator system are used instead. An important
interaction to be considered is transition dipole coupling (TDC).
Its calculation depends on the parameters of the transition dipole
moment. This work aims to find the optimal parameters for TDC in three
major secondary structures: α-helices, antiparallel β-sheets,
and parallel β-sheets. The parameters were suggested through
a comparison between DFT and TDC calculations. The comparison showed
a good agreement for the spectral shape and for the wavenumbers of
the normal modes for all secondary structures. The matching between
the two methods improved when hydrogen bonding to the amide oxygen
was considered. Optimal parameters for individual secondary structures
were also suggested.