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 947 C7 946 C10 945 C13 and 960 C16 turns when hydrogen bonds are formed between the backbone N 8722 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 946 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 946 turn in solution as