(426a) Computational Investigation of the Effect of Backbone Chiral Inversions on Protein Folding

Zerze, G. - Presenter, Princeton University
Debenedetti, P., Princeton University
Stillinger, F. H., Princeton University
Studying a set of helix-folding polyalanine peptides and a number of β-hairpin peptides with systematically inserted chiral inversions, both in explicit water, we investigate quantitatively the effect of chiral perturbations on the structural ensembles of the peptides, thereby assessing the extent to which the backbone structure is able to fold in the presence of systematic heterochiral perturbations. For the helix-folding polyalanine peptide, we invert the backbone chiralities of Ala residues one by one along a specific perturbation pathway, starting from the homochiral L-Ala20 peptide until reaching the homochiral D-Ala20 peptide. Analysis of the helical contents of the simulated structural ensembles shows that even a single inversion in the middle of the peptide completely breaks the helical structure in its vicinity, and drastically reduces the helical content of the peptide. Further inversions in the middle of the peptide monotonically decrease the original helical content, i.e., the right handed helical content for L-Ala20, and increase the helical content of the opposite chirality. Further analysis of the polyalanine peptides using several size and shape-related order parameters also shows drastic global changes in the peptide structure due to the local effects caused by the chiral inversions, such as formation of a reverse turn. Although the degree of the structural changes introduced by opposite chirality substitutions depends on the position of the inversion, our results provide quantitative proof of that arbitrary heterochirality is not tolerated by the alpha-helical structure.

In addition to helical polyalanine peptides, we also study the hairpin peptide, GB1 hairpin, with systematic chiral inversions in explicit water. In contrast to the helical peptide, we do not find a monotonic change in the structure content, i.e. β-sheet content, along the perturbation coordinate, given by the number of L- to D-inversions. The effects of L- to D-inversions are rather position-specific for this hairpin peptide. Some inversions yield a similar or higher secondary structure content compared to the homochiral hairpin, in contrast to the helical peptide. However, similarity in secondary structure content does not imply fold similarity: we have in fact observed cases in which the peptide with inversions folds into clearly different hairpin structures with respect to the non-chirally-perturbed (native) peptide, while sharing similar secondary structure content. In other words, the chirally perturbed hairpin peptides fold into different unique structures when they are still able to fold. Therefore, our main conclusion applies to both of the structurally distinct proteins we examined, namely, that arbitrary heterochirality conspires against proper folding.