CONFORMATIONAL BEHAVIOR AND FLEXIBILITY OF TERMINALLY BLOCKED ALANINE DITRIPEPTIDE AND TRIPEPTIDE

Conformational and flexibility studies of the terminally blocked alanine peptides L-Ala, L-Ala-L-Ala, L-Ala-D-Ala, D-Ala-L-Ala, L-Ala-L-Ala-L-Ala, L-Ala-D-Ala-L-Ala and L-Ala-L-Ala-D-Ala are presented, The molecular mechanics program mmx based on the MM2 force field has been used, parameterized specially for peptides using published parameters. The flexibility is defined as a product of three terms: thermodynamic, kinetic and geometrical. It may be determined for single conformations, fragments (bonds) as well as for the entire molecule. It is shown that conformational behavior and flexibility are strongly influenced by substitution of an L-Ala residue in an L-chain by D-Ala. It is also revealed that the alpha-helix conformation in the pure L-chain is preferred from both an energy and flexibility point of view.