Segments with the amino acid sequence EKAYLRT (glutamine-lysine-alanine-tyrosine-leucine-arginine-threonine) appear in naturally occurring proteins both in $\alpha$-helices and $\beta$-sheets. For this reason, we have used this peptide to study how secondary structure formation in proteins depends on the local environment. Our data rely on multicanonical Monte Carlo simulations where the interactions among all atoms are taken into account. Results in gas phase are compared with that in an implicit solvent. We find that both the solvated molecule and EKAYLRT in gas phase form an $\alpha$-helix when not interacting with other molecules. However, in the vicinity of a $\beta$-strand, the peptide forms a $\beta$-strand. Because of this change in secondary structure our peptide may provide a simple model for the $\overrightarrow{\alpha }\beta$ transition that is supposedly related to the outbreak of prion diseases and similar illnesses.

• Received 12 June 2003

DOI:https://doi.org/10.1103/PhysRevE.68.041911