Amide Spectral Fingerprints are Hydrogen Bonding-Mediated

Abstract

The origin of the peculiar amide spectral features of proteins in aqueous solution is investigated, by exploiting a combined theoretical and experimental approach to study UV Resonance Raman (RR) spectra of peptide molecular models, namely N-acetylglycine-N-methylamide (NAGMA) and N-acetylalanine-N-methylamide (NALMA). UVRR spectra are recorded by tuning Synchrotron Radiation at several excitation wavelengths and modeled by using a recently developed multiscale protocol based on a polarizable QM/MM approach. Thanks to the unparalleled agreement between theory and experiment, we demonstrate that specific hydrogen bond interactions, which dominate hydration dynamics around these solutes, play a crucial role in the selective enhancement of amide signals. These results further argue the capability of vibrational spectroscopy methods as valuable tools for refined structural analysis of peptides and proteins in aqueous solution.

Figure 1

Top: QM/FQ representation of NAGMA (left) and NALMA (right) in aqueous solution. Virtual sites (VS) in the C=O groups are depicted in green. VS are interaction sites constructed to improve the description of the hydrogen bonding. Bottom: Radial Distribution Functions (RDFs) for the intermolecular O···H interactions in solvated dipeptides.

Figure 2

Raman (blue) and Resonance Raman (orange) spectra of NAGMA and NALMA, left and right panels, respectively. Experimental spectra were measured at room temperature in aqueous solution at a concentration which corresponds to 366 molecules of water for each molecule of peptide. QM/FQ results for spontaneous (Far From Resonance) and Resonance Raman spectra were broadened using Lorentzian functions with an fwhm of 8 and 20 cm^–1 respectively. RR intensities were calculated with a damping factor of 200 cm^–1. Sticks in the simulated spectra are also included. The dashed blue curve indicates a preresonance condition.

Figure 3

Experimental results for NAGMA and NALMA dissolved in water at a concentration corresponding to 366 molecules of water for each molecule of peptide (a) FFR and UVRR spectra collected using different excitation wavelengths ranging from visible to deep UV energies. (b) Estimated ratio of the areas of amide modes AII/AI as a function of the excitation wavelength.

Figure 4

Computational results obtained with the QM/QM_w/FQ approach applied to NAGMA and NALMA in aqueous solution. (a) Representative structure, where selected water molecules (in yellow) are part of the QM portion. (b) Comparison between UVRR spectra simulated at 173 and 190 nm. (c) Computed ratio of the areas of the amide modes AII/AI as a function of excitation wavelength.