Three-Strand β-Sheet Peptide Models. IR, VCD and ECD SPECTRA, T-Jump Dynamics and NMR Structures Support MD and DFT Simulatations

Abstract

Spectroscopic studies of peptide β-sheets is complicated by their having many forms (parallel vs. anti-parallel, twisted or flat, in and out of register) and being subject to aggregation so that the molecular state being studied experimentally becomes obscure and thus very difficult to model theoretically. We have used simple hairpin models (strand-turn-strand) to develop monomer structures that have cross-strand anti-parallel H-bonding characteristic of sheets, however these strands are also solvated on each edge. Such structures have limited stability in isolation (outside of a protein environment), but can be accessed by either promoting the turn with selected sequences, or by promoting hydrophobic cross-strand interactions. The next step in complexity and stability are three-stranded β-sheet models, composed of a double hairpin whose central strand is H-bonded to two others. We have designed and prepared a series of related three-strand hairpins based on sequence principles first proposed by Gellman and co-workers. These 23-residue peptides have two stabilized turns composed of either DPro-Gly or Aib-Gly and include cross-strand aromatic coupling of a Trp and Tyr residue to stabilize hairpin formation of two strands. CD, fluorescence, IR and VCD thermal equilibrium spectroscopic studies as well as IR-detected temperature jump dynamics measurements are supported by our determination of NMR-based structures and our theoretical modeling of both vibrational spectra and dynamics. All these designed compounds show evidence of β-sheet formation in both IR and CD, but with differing stabilities and extents depending on the aromatic residue positions. IR and VCD simulations are consistent with experimental data. ECD gives evidence of cross-strand coupling of the aromatics, and the NMR structures show them partially stacked. The structures have sharply twisted three-strand sheets with more disorder in the N-terminal strand for aromatics on strands 1-2, and less stable as well as disorder in the C-terminal strand for 2-3. MD studies show fluctuation in the turns from Type 1’ to 2’ with the 2-3 cross link having more fluctuations. Thermal variation equilibrium thermodynamic studies as well as temperature jump relaxation kinetics show that the relative stabilities favor the strand 1-2 cross strand interaction and suggest folding intermediates, at least at low temperatures.