Towards Determining Amyloid Fibril Structures Using Experimental Constraints from Raman Spectroscopy

Using amylin(20-29) as a model system, we demonstrate that experimental constraints measured by Raman spectroscopy can be used to determine the molecular structure of amyloid fibrils. We employ polarized Raman spectroscopy measurements and the conformationally-sensitive Amide III3 mode to determine the distributions of peptide backbone amide C=O and CN bond orientations, as well as Ramachandran Psi dihedral angles, adopted by amylin(20-29) fibrils. We then use these experimentally measured distributions as structural constraints to guide molecular dynamics (MD) simulations of an amylin20-29 fibril structure. The resulting model indicates that amylin(20-29) fibrils adopt an antiparallel beta-sheet structure in excellent agreement with previous studies. Overall, our results show that Raman spectroscopy provides the ability to visualize the molecular structure of amyloid fibrils that complements gold standard techniques such as solid-state NMR and cryogenic electron microscopy. We anticipate that the Raman methods developed here will aide in determining detailed structural models of amyloid fibrils directly in physiologically relevant systems such as biological tissue and cell cultures.