Effect of Side Chain Length of Charged Residues on a Diagonal Ion Pairing Interaction in a β-Hairpin and Effects of Fluorinated Amino Acids at d-Positions of Coiled Coil Structure

Ion pairing interactions play important roles in protein structure stability. Stabilizing ion pairing interactions are formed between two oppositely charged residues such as Arg/Lys and Asp/Glu. To gain insight into ion pairing interactions and their potential roles in protein structure, we have designed a β-hairpin peptide system, allowing the measurement of the stability effects of individual charged residues and ion pairing interactions. Herein, we study the effect of side chain length on cross-strand diagonal ion pairing interactions. Peptides were synthesized by solid phase methods and purified by reverse phase HPLC. The sequence specific assignments were obtained based on TOCSY, ROESY, and DQF-COSY spectra. The β-hairpin structures were confirmed by chemical shift deviation, 3JHNα coupling constants, and NOE signals. The fraction folded and ΔGfold of the peptides were derived by comparing the chemical shifts with the folded and unfolded reference peptides. The stability of the peptides followed the trend : HPDAadDab ~ HPDAadDap > HPDGluDab ~ HPDGluDap > HPDAspDab ~ HPDAspDap. The results indicate that pairing the longer side chains provides the most stable β-hairpin. Coiled coil is a common motif found in nature. These motifs are ideal models for the study of protein secondary and teriary inteactions because the relationship between sequence and stability are well-understood. Incorporation of fluorinated amino acid residues into coiled coil peptides can stabilize coiled coils. This stabilization has been referred to as the fluoro-stabilization effect. To further understand the fluoro-stabilization effect in proteins, peptides based on the leucine zipper region of the yeast transcription factor GCN4 was designed and fluorinated amino acids were incorporated at the hydrophobic positions.