Computational studies of Ca-D vibrational probes in dipeptides

PHYS 585

Elizabeth A. Ploetz, ploetz@ksu.edu1, Carrie S. Miller, ckinnama@nd.edu2, Beth A. Lindquist, blindqui@nd.edu2, and Steven A. Corcelli, scorcell@nd.edu2. (1) Department of Biochemistry, Kansas State University, Manhattan, KS 66506, (2) Department of Chemistry and Biochemistry, University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, IN 46556
Cα-D vibrational probes are useful for the study of protein structure and dynamics because they absorb within an otherwise transparent region (2000 cm-1 - 2300 cm-1) of the infrared spectra of proteins. Protein structure is generally characterized by conformation of the backbone in terms of the dihedral angles φ and ψ. To quantify the sensitivity of Cα-D bonds to local protein backbone conformation two model Cα-D labeled dipeptides were studied: alanine dipeptide (Adp-d1) and glycine dipeptide (Gdp-d2). Using density functional theory, a two-dimensional map of the Cα-D stretch frequency for Adp-d1 and the Cα-D2 symmetric and asymmetric stretch frequencies for Gdp-d2 versus local conformation were constructed. It was found that the Cα-D frequencies of Adp-d1 (Gdp-d2) exhibit as much as 160 cm-1 (180 cm-1) of sensitivity with respect to variations in the φ and ψ dihedral angles.
 

PHYS Poster Session - Computational Spectroscopy and Reaction Dynamics
7:30 PM-10:00 PM, Wednesday, April 9, 2008 Morial Convention Center -- Hall A, Poster

Division of Physical Chemistry

The 235th ACS National Meeting, New Orleans, LA, April 6-10, 2008