1. Observation of a weak intra-residue C5 hydrogen-bond in a dipeptide containing Gly-Pro sequence
Satish Kumar, Kamal K Mishra, Santosh K Singh, Kshetrimayum Borish, Sanjit Dey, Biplab Sarkar, Aloke Das J Chem Phys. 2019 Sep 14;151(10):104309. doi: 10.1063/1.5115040.
Specific folded structures of peptides and proteins depend on the sequence of various amino acid residues as well as different types of noncovalent interactions induced by the backbone as well as side-chains of those residues. In general, secondary structures of peptides and proteins are stabilized by C6 (δ-turn), C7 (γ-turn), C10 (β-turn), C13 (α-turn), and C15 (π-turn) hydrogen-bonded rings formed through inter-residue interactions. However, it has been reported recently that an intraresidue C5 hydrogen-bond, which is relatively weak in strength, can contribute significantly to the stability of peptides and proteins. The C5 hydrogen-bond is mostly present in the β-sheet structures of peptides and proteins along with other inter-residue noncovalent interactions. In this work, we have studied structures and conformational preferences of a dipeptide Z-Gly-Pro-OH (Z = benzyloxycarbonyl) using mass-selected vibrationally resolved electronic spectroscopy and IR-UV double resonance spectroscopy coupled with quantum chemistry calculations. Two conformers of the peptide are observed in the experiment. One of the conformers has an extended β-strand type structure stabilized by C5 hydrogen-bonding, while the other one is folded through O-H ⋯ π interaction. The noncovalent interactions present in the two observed structures of the peptide are validated by natural bond orbital and noncovalent interaction calculations.
2. Substrate-dependent competency of the catalytic triad of prolyl oligopeptidase
Zoltán Szeltner, Dean Rea, Tünde Juhász, Veronika Renner, Zoltán Mucsi, György Orosz, Vilmos Fülöp, László Polgár J Biol Chem. 2002 Nov 22;277(47):44597-605. doi: 10.1074/jbc.M207386200. Epub 2002 Sep 11.
Prolyl oligopeptidase, a serine peptidase unrelated to trypsin and subtilisin, is implicated in memory disorders and is an important target of drug design. The catalytic competence of the Asp(641) residue of the catalytic triad (Ser(554), Asp(641), His(680)) was studied using the D641N and D641A variants of the enzyme. Both variants displayed 3 orders of magnitude reduction in k(cat)/K(m) for benzyloxycarbonyl-Gly-Pro-2-naphthylamide. Using an octapeptide substrate, the decrease was 6 orders of magnitude, whereas with Z-Gly-Pro-4-nitrophenyl ester there was virtually no change in k(cat)/K(m). This indicates that the contribution of Asp(641) is very much dependent on the substrate-leaving group, which was not the case for the classic serine peptidase, trypsin. The rate constant for benzyloxycarbonyl-Gly-Pro-thiobenzylester conformed to this series as demonstrated by a method designed for monitoring the hydrolysis of thiolesters in the presence of thiol groups. Alkylation of His(680) with Z-Gly-Pro-CH(2)Cl was concluded with similar rate constants for wild-type and D641A variant. However, kinetic measurements with Z-Gly-Pro-OH, a product-like inhibitor, indicated that the His(680) is not accessible in the enzyme variants. Crystal structure determination of these mutants revealed subtle perturbations related to the catalytic activity. Many of these observations show differences in the catalysis between trypsin and prolyl oligopeptidase.
3. Effect of copper(II) chloride on suppression of racemization in peptide synthesis by the carbodiimide method
T Miyazawa, T Otomatsu, Y Fukui, T Yamada, S Kuwata Int J Pept Protein Res. 1992 Mar;39(3):237-44. doi: 10.1111/j.1399-3011.1992.tb00795.x.
Copper(II) chloride was found to be an extremely efficient racemization-suppressing additive in the DCC method as compared with the hitherto known ones, by employing the model coupling Z-Gly-L-Val-OH + H-L-Val-OMe in DMF. Although some other copper salts also had a profound effect, copper(II) chloride was the best from the viewpoint of both racemization suppression and coupling efficiency. The effectiveness of copper(II) chloride was further confirmed by employing the EDC-mediated couplings of Z-Gly-containing dipeptides with amino acid esters or dipeptide esters, and those of Z-L-Ala (or L-Val)-L-Val-OH with amino acid esters or dipeptide esters. In almost all the cases studied, no detectable amount (less than 0.1%) of epimer was observed by the HPLC analysis in the presence of copper(II) chloride. This was also the case even with an extremely stringent coupling system Z-L-Pro-L-Val-OH + H-L-Pro-OMe. With reference to the mechanism of racemization suppression, it was found that copper(II) chloride has a strong ability to suppress the racemization of the 5(4H)-oxazolone, which may be formed from an activated carboxyl component during the coupling.