Conformation dependence of the CalphaDalpha stretch mode in peptides. 1. Isolated alanine peptide structures.
Ab initio normal mode calculations have been performed on isolated alanine di- through octa-(i.e., blocked) peptides in uniform alphaR, beta, and polyproline II conformations to determine how the CalphaDalpha stretch mode, which has been proposed as a possible determinant of the varphi,psi conformation at the Calpha atom (Mirkin, N. G.; Krimm, S. J. Phys. Chem. A 2004, 108, 10923), depends on conformation and sequence length. This set of frequencies, including results on some kinked structures, demonstrates that such a discrimination is likely to be possible through experimental observations of peptides synthesized with successive deuteration at the Halpha sites, on the basis of at least three properties: the values of the frequency at the first residue, the pattern of successive frequency differences, and the frequency differences between the first and last residues.
Mirkin
Noemi G
NG
Biophysics Research Division, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109-1055, USA.
Krimm
Samuel
S
D000409:Alanine / Q000737:chemistry*; D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D011789:Quantum Theory
D004151:Dipeptides; D010455:Peptides; D000409:Alanine