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

Peptides containing residues with alternating D- and L-stereochemistry in t he backbone have been studied for their single-strand helix-forming capabil ity by molecular dynamics (MID) simulations. The influence of the nature of the side chain such as steric, branching and polarity on helix forming abi lity has been probed by studying t-Boc-(L-Ala-D-Ala)(4)-OMe (small hydropho bic 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), r-Boc-(D-allolle-L - Ile)(3)-OMe (gamma-branch in side chain), and t-Boc-(t-Ala-D-Ser)(4)-OMe (hydrophobic and hydrophilic side chains). Besides this, the effect of unsy mmetrical alpha,alpha-disubstitution with alternating D- and L-stereochemis try at Ca carbons on helix stability has also been investigated. The result s show that such peptides, with the exception of those with alpha,alpha-dis ubstitution, have a unique ability to form beta-helices.