Nearest Neighbor Interactions Attenuate Intrinsic Amino Acid Conformational Preferences: A Combined Vibrational and NMR Study

Contrary to the isolated pair hypothesis, a pivotal ingredient of the random coil model, conformational distributions of amino acid residues in unfolded proteins cannot be considered as isolated from their nearest neighbors. To enable structural predictions of unfolded proteins or peptides (IDPs) knowledge about intrinsic propensities of amino acid residues must be complemented by information on nearest-neighbor interactions. To explore this influence, we preformed a joint vibrational and 2D-NMR spectroscopy study of selected “GxyG” host-guest peptides in aqueous solution: GDyG, GSyG, GxLG, GxVG, where x/y={A,K,LV}. The choice of D and S (L and V) for the x (y) position was motivated by their documented ability to drastically change the distribution of alanine in xAy tripeptides of truncated coil libraries. The observed spectral information were analyzed in terms of superpositions of 2D-Gaussian functions in the Ramachandran space, representing sub-ensembles of pPII-, β-strand-, helical-, and turn-like conformations. Results reveal that “turn forming residues” and hydrophobic residues have very strong effects on the conformation of their nearest neighbors. A direct comparison of the conformational distribution for S and D in GSAG ,GSLG, and GDAG with corresponding distributions in GxG peptiess reveals that hydrophobic neighbors cause drastic reductions of turn propensities. As a neighbor, K eliminates the asx turn propensity of D. In addition, insertion of these 'turn forming' residues (S, and D) causes conformational redistributions of L, A, and K from pPII to more extended β strand-like conformations while at the same time increasing the overall turn content. Concomitantly, the positions of pPII and particularly of β distributions are shifted to lower ψ values. Taken together, our results indicate that Dx and Sx motifs might act as conformational randomizers in proteins, attenuating intrinsic propensities of neighboring residues.