Influence of backbone fluorine substitution upon the folding equilibrium of a beta-heptapeptide.

Explicit solvent molecular dynamics (MD) simulations of three beta-heptapeptides with a central beta- HAla(alpha-F) amino acid (Figure 1) in methanol are reported. They aim at an analysis of the conformational consequences of C(alpha) carbon atom bound fluoro atoms, and the particular configuration of the central fluoro-beta-amino acid: peptide 3 with an S configuration of the C(alpha) bound fluor atom, peptide 4 with an R configuration of the C(alpha) bound fluor atom, and peptide 5 with a difluoro substitution at the C(alpha) atom of residue 4. The NMR and CD spectra of these three beta-peptides were earlier (Mathad et al. Helv. Chim. Acta 2005, 88, 266-280) interpreted to indicate a decrease in propensity of 3(14)-helical structure from peptide 4 to peptide 5 to peptide 3. This result was at odds with previous experimental data for beta-heptapeptides with a central beta-HAla(alpha-Me) amino acid which showed that the beta-heptapeptide with the S,S configuration of the central beta-HAla(alpha-Me) was the most 3(14)-helical, whereas the S,R configuration did not lead to any detected helicity. The reported MD simulations resolve this paradox. The MD trajectories of all three peptides do agree with the primary, measured data: NMR nuclear Overhauser effect (NOE) atom-atom distance bounds and (3)J-coupling constants. A conformational analysis of the MD trajectory conformations shows, however, a decrease in 3(14)-helical character from peptide 3 to peptide 5 to peptide 4, which is in line with the results for the nonfluorinated peptides. It is shown that interpretation of NMR NOE data using single-structure refinement in vacuo based on local (along the sequence) and limited atom-atom distance data as in ref 1 (Mathad et al. Helv. Chim. Acta 2005, 88, 266-280) may lead to molecular structures that are not representative for the ensemble of molecular conformations.