Randomizing Intrinsic Conformational Biases by Nearest Neighbor Interactions between Unlike Residues

Abstract

To explore the influence of nearest neighbors on conformational biases in unfolded model peptides, we combined vibrational (IR, Vibrational Circular Dichroism, Raman), and 2D-NMR spectroscopy to study selected “GxyG” host-guest peptides in aqueous solution: GDyG, GSyG, GxLG, GxVG, where x/y={A,K,LV}. To obtain the conformational ensemble of each x/y residue, we utilized an excitonic coupling theory based formalism to simulate experimental amide I’ profiles with conformational distributions composed of 2D-Gaussian distribution in Ramachandran space representing pPII-, β-strand-, helical-, and turn-like conformations. Experimental J coupling constants were similarly reproduced using these conformational distributions along with appropriate Karplus equations. Our data reveal large changes in conformational distributions due to neighbor interactions, contrary to the isolated pair hypothesis. Interestingly, residues that have large intrinsic biases towards specific sub-populations tend to loose these preferences upon interaction with a dissimilar neighbors, indicating a degree of conformational randomization. For instance, residues that prefer turn-like conformations (namely aspartic acid and serine) lose this turn preference in favor of increased pPII populations, which ultimately increases the total extended state sampling. In addition, we observe a decreased pPII content for alanine upon insertion of non-alanine neighbors, which generally increases with the bulkiness of the neighbors’ side chain. Strong effects induced by residues with bulky aliphatic side chains suggests that the underlying mechanism occurs through disruption of the hydration shell. Thermodynamic analysis of 3J(HNHα) (T) data for each x,y residue reveals that modest changes in the conformational ensemble masks larger changes of enthalpy and entropy governing the pPII/β equilibrium suggesting a significant residue dependent temperature dependence of the peptides’ conformational ensembles.