The effect of protein backbone hydration on the amide vibrations in Raman and Raman optical activity spectra

Abstract

Raman and specifically Raman optical activity (ROA) spectroscopy are very sensitive to the solution structure and conformation of biomolecules. Because of this strong conformational sensitivity, density functional theory (DFT) calculations are often used to get a better understanding of the experimentally observed spectral patterns. While e.g. for carbohydrate structure the water molecules that surround the solute have been demonstrated to be of vital importance to get accurate modelled ROA spectra, the effect of explicit water molecules on the calculated ROA patterns of peptides and proteins is less well studied. Here, the effect of protein backbone hydration was studied using DFT calculations of HCO–(L-Ala)₅–NH₂ in specific secondary structure conformations with different treatments of the solvation. The effect of the explicit water molecules on the calculated spectra mainly arises from the formation of hydrogen bonds with the amide CO and N–H groups. Hydrogen bonding of water with the CO group determines the shape and position of the amide I band. The CO bond length increases upon formation of CO⋯H₂O hydrogen bonds. The effect of the explicit water molecules on the amide III vibrations arises from hydrogen bonding of the solvent with both the CO and N–H group, but their contributions to this spectral region differ: geometrically, the formation of a CO⋯H₂O bond decreases the C–N bond length, while upon forming a N–H⋯H₂O hydrogen bond, the N–H bond length increases.