Structural Studies of Designed Peptides by Spectroscopic Methods: PPII Helices to Extended Beta-Sheets

This thesis is focused on the structural analysis of designed peptides modeling PPII helices and beta-sheets using mainly optical spectroscopic techniques. Studies of small peptide systems provide valuable insight toward understanding PPII-helix and beta-sheet folding and aggregation. With the aid of isotopic substitution and theoretical simulation, inter-residue couplings of selected residues in designed Pron, Pro-rich and Lys-rich peptides having predominantly PPII conformations were estimated. A transition from PPII to alpha-helix structure was induced by TFE addition in Lys-rich sequences, to show the large variation in 13C=O coupling corresponding to the conformational change, which offers a new site-specific method of assigning local PPII vs. alpha-helical structure. Next, vibrational spectroscopic analyses for oligomeric glutamic acid rich peptides enhanced with 13C isotope labeling were conducted to model poly-Glu self-assembly at low pH. By comparing the isotope enhanced vibrational spectra with theoretical predications; the beta2 structure of the oligomers was deduced to have anti-parallel beta-sheets with strands out of register, sequentially stepped by one residue, in a ladder-like fashion. Finally, a set of beta-sheet conformers were synthesized with amphiphilic design. Turn segment mutation led to different stabilities as beta-sheet aggregates. For the 19 residue peptide B3pGD, conformational conversion from oligomeric beta-sheet to fibril was investigated by FRET and ThT-binding fluorescence spectroscopy. The results suggest that the peptide adopted an off-pathway oligomer first followed by oligomer disassembly and partial unfolding in order to form a heat induced fibril.