Helix vs. Sheet Formation in a Small Peptide

TL;DR

This study uses simulations to explore how the peptide EKAYLRT adopts alpha-helix or beta-strand structures depending on its environment, providing insights into protein folding and disease-related structural transitions.

Contribution

It demonstrates how local environment influences secondary structure formation in a peptide, modeling the alpha to beta transition relevant to prion diseases.

Findings

Peptide forms alpha-helix in isolation

Forms beta-strand near beta-structures

Environment determines secondary structure

Abstract

Segments with the amino acid sequence EKAYLRT appear in natural occurring proteins both in $\alpha$-helices and $\beta$-sheets. For this reason, we have use 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 in gas phase and solvated EKAYLRT forms 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 $\alpha \to \beta$ transition that is supposedly related to the outbreak of Prion diseases and similar illnesses.