Influence of nature of side chain on conformation of alternating L- and D-stereo oligopeptides

摘要

Peptides containing residues with alternating D- and L-stereo- chemistry 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 studying t-Boc-(L-Ala-D-AIa)`-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 beta-branch in side chain), t-Boc-(D-allolle-L- Ile)3-OMe (r-branch in side chain), and t-Boc-(L-Ala-D-Ser)`-OMe (hydrophobic and hydrophilic side chains). Besides this, the effect of unsymmetrical alpha,alpha- disubstitution with alternating D- and L-stereochemistry at Ca carbons on helix stability has also been investigated. The results show that such peptides, with the exception of those with alpha,alpha-disubstitution, have a unique ability to form beta-helices