Molecular Mechanics Simulation and Ftir Spectrocopy Optimization of Secondary Structure of Aβ (25-35) Peptide

Abstract In this study, we probed the secondary structure of a soluble Aβ (25-35) peptide in water solution by applying a molecular mechanics method as well as infrared spectroscopy. We have used Fourier Transformed Infrared Spectroscopy (FTIR) to examine the secondary structure of this peptide. The amide I bands of Ab (25-35) obtained from transmission-FTIR spectra consists of one main band at 1658 cm-1, at both concentrations used (200 mM and 1 mM). This band shows us that Ab (25-35) in aqueous solution was mostly organized into a a-helical structure (48 %). The contribution of the unordered structure was found to be about 12 %. The proportion of b-sheet and b-turn structures are slightly lower, 12-15 % and 13-14 %, respectively for both concentrations. FTIR spectra of the peptide in water solution (100 µM) after incubation for 12h showed Aβ peptide conformation is critically dependent on the environmental conditions used. The simulation approach reveals that the C-terminal octapeptide of this molecule preferably adopts an α-helical structure, while the N-terminal tripeptide may exist as a β-turn and unordered structures.