Conformations of heterochiral and homochiral proline‐pseudoproline segments in peptides: Context dependent cis–trans peptide bond isomerization

Abstract

The pseudoproline residue (Psi Pro, L-2,2-dimethyl-1,3-thiazolidine-4-carboxylic acid) has been introduced into heterochiral diproline segments that have been previously shown to facilitate the formation of beta-hairpins, containing central two and three residue turns. NMR studies of the octapeptide Boc-Leu-Phe-Val-(D)Pro-Psi Pro-Leu-Phe-Val-OMe (1), Boc-Leu-Val-Val-(D)Pro-Psi Pro-Leu-Val-Val-OMe (2), and the nonapeptide sequence Boc-Leu-Phe-Val-(D)Pro-Psi Pro-(D)Ala-Leu-Phe-Val-OMe (3) established well-registered beta-hairpin structures in chloroform solution, with the almost exclusive population of the trans conformation for the peptide bond preceding the Psi Pro residue. The beta-hairpin conformation of 1 is confirmed by single crystal X-ray diffraction. Truncation of the strand length in Boc-Val-(D)Pro-Psi Pro-Leu-OMe (4) results in an increase in the population of the cis conformer, with a cis/trans ratio of 3.65. Replacement of Psi Pro in 4 by (L)Pro in 5, results in almost exclusive population of the trans form, resulting in an incipient beta-hairpin conformation, stabilized by two intramolecular hydrogen bonds. Further truncation of the sequence gives an appreciable rise in the population of cis conformers in the tripeptide Piv-(D)Pro-Psi Pro-Leu-OMe (6). In the homochiral segment Piv-Pro-Psi Pro-Leu-OMe (7) only the cis form is observed with the NMR evidence strongly supporting a type VIa beta-turn conformation, stabilized by a 4-->1 hydrogen bond between the Piv (CO) and Leu (3) NH groups. The crystal structure of the analog peptide 7a (Piv-Pro-Psi(H,CH3)Pro-Leu-NHMe) confirms the cis peptide bond geometry for the Pro-Psi(H,CH3)Pro peptide bond, resulting in a type VIa beta-turn conformation.

Conformational investigation of peptides using solid‐state NMR spectroscopy—A study of polymorphism of β‐turn peptides containing diprolines

“…It is interesting to note that of the three peptides investigated, peptide 1 showed a trans configuration, peptide 2 a cis configuration, and peptide 3 a mixture of both cis and trans in nearly equal proportion. The solid‐state structures of peptides 1 and 2 match with the reported solution structures and also with X‐ray results (Chatterjee et al, ; Kantharaju et al, ). For peptide 3, both X‐ray and solution NMR results are not available.…”

“…In earlier studies carried out using DQ‐SQ correlation experiments, it has been noted that correlation peaks are obtained between protons separated typically by 3.5 Å or less (Brown, Lesage, Elena, & Emsley, ; Deschamps et al, ). In the present case, an examination of the crystallographic data of peptides 1 and 2 (Chatterjee et al, ; Kantharaju et al, ) reveals that the distances between D Pro H α and the two L Pro H δ protons in peptide 1 are 2.16 and 2.58 Å. On the other hand, the distance between the D Pro H α and L Pro H α is 4.4 Å. Conversely, for peptide 2 which adopts the cis conformation (Yarava et al, ), the distance between the H α protons of the adjacent proline residues is 1.997 Å, whereas the separation between the α and the two δ protons is in the range of 4.4–4.9 Å.…”

“…Crystalline powder samples of the three peptide samples, namely Piv‐ D Pro‐ L Pro‐ L Phe‐NHMe (peptide 1), Piv‐ L Pro‐ψ H,CH3 Pro‐Leu‐NHMe (peptide 2), and (c) Piv‐ D Pro‐ψ CH3,CH3 Pro‐Leu‐NHMe (peptide 3), used in this study were synthesized in the laboratory of Professor P. Balaram and the X‐ray structures of peptides 1 and 2 reported (Chatterjee et al, ; Kantharaju et al, ). Solid‐state NMR experiments were carried out on two different spectrometers.…”

“…Over the years, nuclear magnetic resonance spectroscopy has become one of the major tools of obtaining such structural information at the atomistic level (Judge & Watts, 2011;Knight, Felli, Pierattelli, Emsley, & Pintacuda, 2013;Patel, Pithadia, Brender, Fierke, & Ramamoorthy, 2014;Quinn & Polenova, 2017;Tang, Comellas, & Rienstra, 2013). In parallel, structural studies of small biological molecules such as peptides have also gained much importance since short stretches of amino acid sequences are known to nucleate protein folding with localized interactions (Kantharaju et al, 2009;Keller et al, 1998;Venkatraman, Shankaramma, & Balaram, 2001). In order to understand the conformational preference of the peptides, it is important to have a knowledge of the structure of the peptides in finer details.…”

“…Additionally, diproline segments have been advanced as templates for nucleation of folded structures in designed peptides (Gunasekaran et al, 1997;Sibanda & Thornton, 1985;Venkatachalam, 1968). Recent studies have shown that homochiral diproline ( L Pro-L Pro) segments at N-terminus can nucleate helical structures, whereas heterochiral ( D Pro-L Pro) segments which form type II′ turns are nucleators of β-hairpin turns and provide good registry for β-hairpin extended structures (Kantharaju et al, 2009). Further, it has been proposed that replacing prolines with pseudo-prolines leads to a higher probability for the population of the cis conformer (Guichou, Patiny, & Mutter, 2002;Keller et al, 1998;Wöhr et al, 1996).…”