Distinct electrostatic frequency tuning rates for amide I and amide I′ vibrations

Abstract

Amide I spectroscopy probes the backbone C=O stretch vibrations of peptides and proteins. Amide I spectra are often collected in deuterated water (D2O) since this provides a cleaner background in the amide I frequency range; such data are often referred to as amide I′ spectra since deuteration induces changes in the mode structure, including a roughly ∼10 cm−1 redshift. For biological samples, however, deuteration is often not possible. As amide I frequency maps are increasingly applied to quantitative protein structural analysis, this raises the interesting challenge of drawing direct connections between amide I and amide I′ data. We here analyze amide I and amide I′ peak frequencies for a series of dipeptides and related compounds. Changes in protonation state induce large electrostatic shifts in the peak frequencies, allowing us to amass a sizable library of data points for direct amide I/amide I′ comparison. While we find an excellent linear correlation between amide I and amide I′ peak frequencies, the deuteration-induced shift is smaller for more red-shifted vibrations, indicating different electrostatic tuning rates in the two solvents. H2O/D2O shifts were negligible for proline-containing dipeptides that lack exchangeable amide hydrogens, indicating that the intrinsic properties of the solvent do not strongly influence the H/D shift. These findings indicate that the distinct tuning rates observed for the two vibrations arise from modifications to the intrinsic properties of the amide bond and provide (at least for solvated dipeptides) a simple, linear “map” for translating between amide I and amide I′ frequencies.

AIM: A Mapping Program for Infrared Spectroscopy of Proteins

“…This changes the gas-phase frequency by 10 cm –1 . It was demonstrated that this is neither well described by a simple shift nor with a simple change of reduced mass . Therefore, the spectra in D 2 O can better be modeled explicitly with mappings taking the deuteration explicitly into account as the Skinner, Jansen, and Tokmakoff ones implemented in AIM.…”

“…54 It was demonstrated that this is neither well described by a simple shift nor with a simple change of reduced mass. 15 Therefore, the spectra in D 2 O can better be modeled explicitly with mappings taking the deuteration explicitly into account as the Skinner, 41 Jansen, 42 and Tokmakoff 40 ones implemented in AIM. Isotope edited spectroscopy with 13 C and 18 O labels can easily be performed as postprocessing of the Hamiltonian trajectory generated by AIM.…”

“…This also results in (partial) exchange of the acidic hydrogen atoms in the protein with deuterium. This includes exchange of the hydrogen atoms involved in the amide-I vibrations, which shifts these vibrations by about 10 cm –1 . , To distinguish the new vibrations, they are often denoted amide-I′. Here, we will use the term amide-I to describe both, but unless otherwise stated explicitly, we will assume that the amide-I′ vibration is actually considered.…”

Using 2D-IR Spectroscopy to Measure the Structure, Dynamics, and Intermolecular Interactions of Proteins in H2O

“…A 2D-IR study compared the amide I spectrum of the bovine serum albumin protein (BSA) in H 2 O and D 2 O (Figure ), showing that the center of the amide I band shifts by around 10 cm –1 to a higher frequency in H 2 O, consistent with experiments using IR absorption and solvent subtraction methods . There is also evidence for a considerable change in 2D-band shape, with the spectrum in D 2 O appearing more elongated along the spectrum diagonal, while in H 2 O, a narrower line width and a more compact appearance were observed.…”

Asymmetry of the Electrostatic Environment as the Origin of the Symmetry Breaking Effect of the Nitrate Ion in Aqueous Solution

“…In fact, for some vibrational modes that are sensitive to intermolecular interactions (such as the OH stretching mode of water, − the amide I mode of peptide, − and the CN stretching mode of nitrile − ), such parameterization has already been accomplished and is often called a frequency map . In those cases, intermolecular electrostatic properties (electrostatic potentials and/or electric fields) on the atomic sites play a major role in inducing the frequency shifts.…”