| dc.description.abstract | Insertion of amino acid residues into all polypeptide backbones leads to an expanded repertoire of secondary structures. In the present thesis an attempt has been made to explore the conformational properties of the amino acid residue gabapentin (1-aminomethylcyclohexaneacetic acid, Gpn). Gpn is a , disubstituted amino acid residue. The presence of a tetrasubstituted carbon atom in the backbone dramatically reduces the sterically allowed conformational space for gabapentin residues.
The introductory Chapter 1 briefly summarizes the work that has been reported thus far on peptides containing amino acid residues. Gpn residues can adopt C9 hydrogen bonded structures, a feature first observed in the crystal structures of Boc-(Gpn)2-NHMe and Boc-(Gpn)4-NHMe (Vasudev et. al., 2005).
Chapter 2, Section I presents a systematic study on terminally blocked oligomers of Gpn, Boc-(Gpn) n-NHMe, where n = 1-6. NMR studies establish C9 ribbon conformations in solution for the n = 2 -6 cases in CDCl3 solutions. The effect of inserting a guest Gpn residue into an all amino acid host sequence is examined in Chapter 2, Section II. Three peptides Boc-LAla-Aib-Gpn-Aib-LAla-OMe (1), Boc-Leu-Aib-Val-Gpn-Leu-Aib-Val-OMe (2) and Boc-Leu-Aib-Val-Aib-Gpn-Aib-Leu-Aib-Val-OMe (3), all of which contain a centrally positioned Gpn residue are examined. Crystals of peptide 1 were obtained, wherein it formed a C12 helix stabilized by two C12 hydrogen bonds and one C10 hydrogen bond (Vasudev et. al., 2007). . Both peptides 2 and 3, yielded clear NOE evidence in favor of helical conformations in solution. In all three peptides C12 hydrogen bonds were formed by the / segments involving the guest Gpn residue. Isolated amino acid residues inserted into host amino acid sequences, can be readily accommodated into helical folds, with an expansion of the hydrogen boded ring involving the guest amino acid residue.
Chapter 3 describes studies designated to probe the conformational preference of the alternating ()n hybrid sequences, where Gpn was used as the residue. When the residue was Aib (- aminoisobutyric acid), an ,’- disubstituted constrained amino acid residue, ()n peptides adopted C12 helical conformations. Studies described in Chapter 3, establish a considerable decrease in the population of C12 helical conformations in solution and increased conformational heterogeneity, when Aib residues are replaced by Ala.
In Chapter 4, hybrid peptides with tripeptide repeat segments ()n and ()n have been studied. A helical conformation was characterized in crystals for the peptide Boc-Leu-Gpn-Aib-Leu-Gpn-Aib-OMe (1) (Chatterjee et. al., 2008b). For the peptide 1, there was evidence of conformational exchange in solution, with the observation of medium range NOEs which were incompatible with the helical conformation characterized in crystals for 1. Observation of a single set of NH resonances in the NMR spectrum, is attributed to rapid rates of interconversion between the different conformational species. For peptides Boc-Gpn-Leu-Aib-Gpn-Leu-Aib-OMe (5) and Boc-Gpn-Val-Aib-Gpn-Val-Aib-OMe (6), with ()n tripeptide repeats, conformational studies were performed in CDCl3 solution using NMR methods. Two sets of sharp NH resonances of equal intensity were observed in the spectrum at ambient temperature. This was indicative of a slow rate of exchange between conformers which were of similar thermodynamic stability.
Chapter 5, presents a novel 12/10 helical structure established in the crystalline state for the peptide Boc-Leu-Gpn-Leu-Aib-OMe...The Leu (1)-Gpn (2) segment forms a 41 C12 hydrogen bond with the normal directionality (CO(i)…NH (i+3)). A second C10 hydrogen bonding is formed between the Gpn (2) NH and Leu (3) CO (12), in which the hydrogen bond directionality is opposite (NH(i)…CO (i+1)). Both Leu residues adopt PII conformations ( = -60 and = 120), while the Gpn residue adopts a gauche-gauche conformation with = 87, 1 = 38, 2 = 45 and = -129 (Vasudev et. al., 2008)
Chapter 6 addresses the question of the effect of inserting Gpn into sequences which have been shown to form both helices and hairpins. X-ray diffraction studies revealed a -hairpin conformation of peptide Boc-Leu-Phe-Val-Aib-Gpn-Leu-Phe-Val-OMe in crystals, nucleated by a C12 hydrogen bond across the Aib-Gpn segment. This structure provides the only example of a Gpn residue in a gauche-trans (gt) conformation with a value of 2180. In CDCl3 solutions, the peptide predominantly adopted a helical conformation, while in CD3OH, the peptide favoured a hairpin conformation as characterized in crystals. This solvent dependent conformational transition together with the presence of minor conformations in solution, indicates that the Aib-Gpn segment is not a robust -hairpin nucleating structural feature. The studies described in this thesis, establish that the Gpn residue is a versatile, stereo chemically constrained amino acid residue, which can be usefully employed in the design of hybrid peptides with well defined backbone conformations.
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