Helix versus sheet formation in a small peptide

Document Type

Article

Publication Date

1-1-2003

Abstract

Segments with the amino acid sequence EKAYLRT (glutamine-lysine-alanine-tyrosine-leucine-arginine-threonine) appear in naturally occurring proteins both in [Formula presented]-helices and [Formula presented]-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 [Formula presented]-helix when not interacting with other molecules. However, in the vicinity of a [Formula presented]-strand, the peptide forms a [Formula presented]-strand. Because of this change in secondary structure our peptide may provide a simple model for the [Formula presented] transition that is supposedly related to the outbreak of prion diseases and similar illnesses. © 2003 The American Physical Society.

Publication Title

Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics

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