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Proc Natl Acad Sci U S A. 2011 Feb 1;108(5):1794-8. doi: 10.1073/pnas.1017317108. Epub 2011 Jan 4.

Populations of the three major backbone conformations in 19 amino acid dipeptides.

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  • 1National Institute of Chemistry, Hajdrihova 19, SI 1000 Ljubljana, Slovenia.

Abstract

The amide III region of the peptide infrared and Raman spectra has been used to determine the relative populations of the three major backbone conformations (P(II), β, and α(R)) in 19 amino acid dipeptides. The results provide a benchmark for force field or other methods of predicting backbone conformations in flexible peptides. There are three resolvable backbone bands in the amide III region. The major population is either P(II) or β for all dipeptides except Gly, whereas the α(R) population is measurable but always minor (≤ 10%) for 18 dipeptides. (The Gly ϕ,ψ map is complex and so is the interpretation of the amide III bands of Gly.) There are substantial differences in the relative β and P(II) populations among the 19 dipeptides. The band frequencies have been assigned as P(II), 1,317-1,306 cm(-1); α(R), 1,304-1,294 cm(-1); and β, 1,294-1,270 cm(-1). The three bands were measured by both attenuated total reflection spectroscopy and by Raman spectroscopy. Consistent results, both for band frequency and relative population, were obtained by both spectroscopic methods. The β and P(II) bands were assigned from the dependence of the (3)J(H(N),H(α)) coupling constant (known for all 19 dipeptides) on the relative β population. The P(II) band assignment agrees with one made earlier from Raman optical activity data. The temperature dependences of the relative β and P(II) populations fit the standard model with Boltzmann-weighted energies for alanine and leucine between 30 and 60 °C.

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