Probing Secondary Structures of Small Peptides in Gas Phase as Well as Condensed Phase

Abstract

Secondary structures of peptides/proteins are governed by the hydrogen bonding interactions in the backbone as well as sequence of the amino acid residues present there. The most common secondary structures observed in proteins/peptides are turns, helices, and b-sheets. It has been found that turns are the most abundant secondary structures in proteins. Turns can be classified into γ (C7), β (C10), α (C13), and π (C16) turns when hydrogen bonds are formed between the backbone N−H and C=O groups amino acids residues. Although the most common turns involve the inter-residue hydrogen bond formation, there is a possibility of intra-residue hydrogen bond formation involving the same residue, specially, in the β-sheet structures. The present work deals with the study of the peptides containing Gly and Pro residues as these are quite unique among the 22 amino acid residues. Gly is the most flexible amino acid residue as it does not have any side chain while Pro is the most rigid amino acid as its side chain forms a 5-member ring with the nitrogen atom of the backbone. Combination of the Gly and Pro residues are abundant particularly in the loop region of the b-hairpin structures of proteins/peptides.First, we have explored the intra-residue hydrogen bond named as C5 hydrogen bond in a dipeptide Z-Gly-Pro-OH (Z= Benzyloxycarbonyl). Gas-phase laser spectroscopic techniques along with quantum chemical calculations reveal that the most stable conformer of Z-Gly-Pro-OH is solely stabilized by the C5 hydrogen bond. Later, we have tried to understand the sequence-dependent folding motifs of Gly-Pro and Pro-Gly containing peptides by studying model dipeptides Boc-D-Pro-Gly-NHBn-OMe and Boc-Gly-D-Pro-NHBn-OMe. We have studied the conformational preferences of these two peptides using a combination of gas phase laser spectroscopy, quantum chemistry calculations, solution phase IR and NMR spectroscopy and single crystal X-Ray diffraction (XRD). It has been found from overall study that the Pro-Gly peptide forms C10 (β-turn in solution) as well as C7-C7 (in gas phase) structures while the dominating structure for the Gly-Pro peptide is extended β-strand or PP-II having C5-C7 hydrogen bonded rings. Finally, we have extended our study on the Pro-Gly dipeptide to Pro-Gly-Ala to understand the effect of the third residue on the strength of the β-turn in the Pro-Gly peptide. The aim of the present thesis is to connect the results on the conformational studies of small peptides obtained from the spectroscopic investigation performed in the gas phase as well as condensed phases. The advantage of the gas phase study over the condensed phase is the observation of a few low energy conformations along with the global minimum conformation of the peptide.