Functional structures and folding dynamics of two peptides

The folding dynamics and structural characteristics of peptides RTKAWNRQLYPEW (P1) and RTKQLYPEW (P2) are investigated by using all-atomic simulation procedure CHARMM in this work. The results show that P1, a segment of an antigen, has a folding motif of \alpha-helix, whereas P2, which is derived by deleting four residues AWNR from peptide P1, prevents the formation of helix and presents a \beta-strand. And peptide P1 experiences a more rugged energy landscape than peptide P2. From our results, it is inferred that the antibody CD8 cytolytic T lymphocyte prefers an antigen with a \beta-folding structure to that with an α-helical one.