Infrared Line Shape of an α-Carbon Deuterium-Labeled Amino Acid

Abstract

The viability of alpha-carbon deuterated bonds (Calpha-D) as infrared (IR) probes of protein backbone dynamics was explored through a combination of experiment and theory. alpha-Carbon deuterated alanine (Ala-d1) served as a convenient model system for a comparison of experiment, density functional theory (DFT), and combined quantum mechanical/molecular mechanical (QM/MM) simulations of the Calpha-D IR line shape. In addition to the primary Calpha-D absorption, the experimental spectrum contains three features that likely result from Fermi resonances. DFT calculations supported the assignments and identified the lower frequency modes participating in the Fermi resonances. A QM/MM simulation of the Ala-d1 line shape was in qualitative agreement with the experiment, including the presence of classical analogues of Fermi resonances. These studies demonstrated that the Calpha-D line shape is sensitive, via Fermi resonances, to lower frequency collective vibrations that are expected to play a role in protein dynamics and function, and that the QM/MM approach, which is applicable to proteins, is capable of aiding in their interpretation.

Sum frequency generation and solid-state NMR study of the structure, orientation, and dynamics of polystyrene-adsorbed peptides

“…Features near 2;130 cm −1 and 2;080 cm −1 are related to the CD 3 Fermi resonance (r þ FR ) and the CD stretching mode of the γ-carbon in the isopropyl group, respectively (51,52). A weak additional peak observed in the ppp spectra near 2;150 cm −1 is most likely explained by a Fermi resonance of the CD moiety (53,54). The peak intensities vary significantly for the three polarization combinations.…”

A direct comparison of azide and nitrile vibrational probes

“…As noted previously for 3-azidopyridine, 28 the potential complex absorption profiles for the azide and nitrile probes must be considered when using them to study biomolecular structure and dynamics. These complexities 28, 57, 58 could result in significant difficulties in the interpretation of the infrared signature of azide and nitrile groups in biological systems. A general experimental method to address this issue is currently under investigation.…”

Efforts Toward the Direct Experimental Characterization of Enzyme Microenvironments: Tyrosine100 in Dihydrofolate Reductase

“…As part of a program to develop general probes of protein microenvironments and dynamics we have developed the use of carbon-deuterium (C À D) bonds as FTIR probes. [16][17][18][19][20][21][22][23][24] C À D bonds are sensitive to their environment and may be incorporated anywhere throughout a protein. While they are weaker than the other endogenous chromophores, their detection and analysis are facilitated by their unique absorption in an otherwise transparent region (ca.…”