Structure and orientation of the alanine dipeptide and small amides in a water-based liquid crystal

The capped alanine dipeptide (AcAlaNHMe) is a molecular benchmark employed in the development of tools for protein structure prediction. It contains flexible dihedral angles &phis; and ψ and thus represents a simple model of the peptide backbone. Previous experiments have failed to unambiguously determine the distribution of conformations {lcub}&phis;, ψ{rcub} in water. Competing force-fields make conflicting predictions regarding the relative importance of the two solution conformers lowest in energy, a polyproline turn P _II with approximate dihedrals {lcub}−90°, 130°{rcub} and a right-handed alpha-helix α_R near {lcub}−60°, −60°{rcub}. We extracted dipolar couplings of the dipeptide via LX-NMR, employing an orienting medium of magnetically aligned cesium perfluorooctanoate (CsPFO) bicelles in water. Experiments with isotopically unlabelled AcAlaNHMe and a 13C-labelled variant provided 9 and 13 couplings, respectively. Least-squares fits with one or two rigid trial geometries derived from electronic structure calculations succeed when {lcub}&phis;, ψ{rcub} adopts a P_II conformation, but fail for the α_R conformer. Incorporating corrections for hindered methyl rotations, small amplitude dihedral torsions and other internal motions within conformational wells did not alter conclusions drawn from a simple rigid model.; We examined the possibility that an α_R conformer eluded detection due to a fortuitously small orientation tensor, rather than a small relative population, by investigating the orientation of N-methylated formamides and acetamides in CsPFO/water via LX-NMR. Large orientation strengths are observed for amides that can simultaneously immerse the carbonyl group into the aqueous phase and insert N-methyl groups into the hydrophobic bicelle interior. This mechanism is consistent with the structure of the S matrices. All amides display substantial couplings irrespective of structure, offering no evidence that an α_R structure exists in a negligibly oriented state. Neither are there indications that AcAlaNHMe is driven into a particular conformation by the orienting interaction, since the dipeptide is weakly oriented in the liquid crystal.; Finally, we modified procedures for deriving high-accuracy structural and orientational parameters from dipolar couplings, focusing on vibrational corrections for formamide. Vibrations are significantly attenuated by the solvent, suggesting that simple analytical models may fail by overestimating the corrections. Improvements in vibrational models therefore promise to increase the accuracy of derived parameters.