Computational and experimental determination of the alpha-helix unfolding reaction coordinate.
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.
Asciutto
Eliana K
EK
Department of Chemistry and Biochemistry, Center for Computational, Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, USA. ekasciut@gmail.com
Mikhonin
Aleksandr V
AV
Asher
Sanford A
SA
Madura
Jeffry D
JD
D011489:Protein Denaturation; D013059:Spectrum Analysis, Raman