Influence of nature of side chain on conformation of alternatingl- andd-stereo oligopeptides

Peptides containing residues with alternatingd- andl-stereochemistry in the backbone have been studied for their single-strand helix-forming capability by molecular dynamics (MD) simulations. The influence of the nature of the side chain such as steric, branching and polarity on helix forming ability has been probed by studyingt-Boc-(l-Ala-d-Ala)4-OMe (small hydrophobic side chain),t-Boc-(l-Phe-d-Phe)4-OMe (bulky hydrophobic side chain),t-Boc-(l-Val-d-Val)4-OMe (β-branch in side chain),t-Boc-(d-allolle-l-Ile)3-OMe (γ-branch in side chain), andt-Boc-(l-Ala-d-Ser)4-OMe (hydrophobic and hydrophilic side chains). Besides this, the effect of unsymmetricalα,α-disubstitution with alternatingd- andl-stereochemistry and Cα carbons on helix stability has also been investigated. The results show that such peptides, with the exception of those withα,α-disubstitution, have a unique ability to formβ-helices.