title: Infrared line shape of an alpha-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.
authors.affiliation: Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA.
authors.forename: Carrie S
authors.initials: CS
authors.lastname: Kinnaman
authors.forename: Matthew E
authors.initials: ME
authors.lastname: Cremeens
authors.forename: Floyd E
authors.initials: FE
authors.lastname: Romesberg
authors.forename: Steven A
authors.initials: SA
authors.lastname: Corcelli
mesh_terms: D000409:Alanine / Q000737:chemistry; D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D002244:Carbon / Q000737:chemistry*; D003903:Deuterium / Q000737:chemistry*; D007553:Isotope Labeling; D008958:Models, Molecular; D013055:Spectrophotometry, Infrared
chemical_list: D000596:Amino Acids; D002244:Carbon; D003903:Deuterium; D000409:Alanine