title: Computational and experimental determination of the alpha-helix unfolding reaction coordinate.
abstract: We demonstrate a calculated alpha-helix peptide folding energy landscape which accurately simulates the first experimentally measured alpha-helix melting energy landscape. We examine a 21-amino acid, mainly polyalanine peptide and calculate the free energy along the Psi Ramachandran angle secondary folding coordinate. The experimental free energy landscape was determined using UV resonance Raman spectroscopy. The relative free energy values are very close as are the equilibrium peptide conformations. We find 2.3 kcal/mol activation barriers between the alpha-helix-like and PPII-like basins. We also find that the alpha-helix-like conformations are quite defective and the alpha-helix-like structure dynamically samples 310-helix and pi-bulges.
authors.affiliation: Department of Chemistry and Biochemistry, Center for Computational, Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, USA. ekasciut@gmail.com
authors.forename: Eliana K
authors.initials: EK
authors.lastname: Asciutto
authors.forename: Aleksandr V
authors.initials: AV
authors.lastname: Mikhonin
authors.forename: Sanford A
authors.initials: SA
authors.lastname: Asher
authors.forename: Jeffry D
authors.initials: JD
authors.lastname: Madura
mesh_terms: D011489:Protein Denaturation; D013059:Spectrum Analysis, Raman