Effect of Charged Amino Acid Side Chain Length at Non-Hydrogen Bonded Strand Positions on β-Hairpin Stability

Abstract

β-Sheets have been implicated in various neurological disorders, and ∼20% of protein residues adopt a sheet conformation. Therefore, studies on the structural origin of sheet stability can provide fundamental knowledge with potential biomedical applications. Oppositely charged amino acids are frequently observed across one another in antiparallel β-sheets. Interestingly, the side chains of natural charged amino acids Asp, Glu, Arg, Lys have different numbers of hydrophobic methylenes linking the backbone to the hydrophilic charged functionalities. To explore the inherent effect of charged amino acid side chain length on antiparallel sheets, the stability of a designed hairpin motif containing charged amino acids with varying side chain lengths at non-hydrogen bonded positions was studied. Peptides with the guest position on the N-terminal strand and the C-terminal strand were investigated by NMR methods. The charged amino acids (Xaa) included negatively charged residues with a carboxylate group (Asp, Glu, Aad in increasing length), positively charged residues with an ammonium group (Dap, Dab, Orn, Lys in increasing length), and positively charged residues with a guanidinium group (Agp, Agb, Arg, Agh in increasing length). The fraction folded and folding free energy for each peptide were derived from the chemical shift deviation data. The stability of the peptides with the charged residues at the N-terminal guest position followed the trends: Asp > Glu > Aad, Dap < Dab < Orn ∼ Lys, and Agb < Arg < Agh < Agp. The stability of the peptides with the charged residues at the C-terminal guest position followed the trends: Asp < Glu < Aad, Dap ∼ Dab < Orn ∼ Lys, and Agb < Arg ∼ Agp < Agh. These trends were rationalized by thermodynamic sheet propensity and cross-strand interactions.

Coupling of the non-amyloid-component (NAC) domain and the KTK(E/Q)GV repeats stabilize the α-synuclein fibrils

“…We thus constructed various models hierarchically in order to investigate the effect of a salt-bridge formed by Glu and Lys on the stability of the αS fibril models (Table 1). The effect of charged residues on the stability of the β-strand has been well recognized [53, 54], thus worth examining in the context of αS fibrils.…”

Effects of Arginine Deimination and Citrulline Side‐Chain Length on Peptide Secondary Structure Formation

“…The β‐hairpin peptides were analyzed by two‐dimensional NMR spectroscopy including DQF‐COSY, TOCSY, and ROESY . The NMR spectra (chemical shifts and line widths) of analogous β‐hairpin peptides did not change with concentration (20 μ m –10 m m ), so the peptides in this study should not aggregate in solution. As such, the experimental data should have minimal interference from intermolecular interactions.…”

“…The design of the β‐hairpin peptides was based on a water‐soluble monomeric β‐hairpin system studied by Gellman and later by our group (Table ) . The Tyr residue in the parent YKL peptide—H‐Arg‐Tyr‐Val‐Glu‐Val‐ d ‐Pro‐Gly‐Orn‐Lys‐Ile‐Leu‐Gln‐NH 2 —was replaced with Thr in order to avoid the diagonal Lys9–Tyr2 cation–π interaction.…”

“…For example, HPTCitAla would have Cit at position 4 and Ala at position 9. To determine the fraction folded population and the folding free energy for these experimental HPTXaaAla peptides, fully unfolded reference peptides and fully folded reference peptides would be necessary . The Pro‐Gly turn was incorporated to give the fully unfolded reference HPTUXaaAla peptides (Table ).…”

“…The α‐helix and the β‐sheet are the two most common secondary structures, so we focused on these two structures. To understand the underlying reason for the specific number of methylene units linking the side‐chain functional group to the backbone, we have previously investigated the effect of Arg side‐chain length on α‐helix and β‐sheet formation. Along similar lines, the effect of Cit side‐chain length on secondary structure formation are also presented.…”