Rotational Barriers ofcis/transIsomerization of Proline Analogues and Their Catalysis by Cyclophilin

Abstract

The rotational barriers for cis/trans isomerization of different proline analogues have been investigated by dynamic 1H NMR spectroscopy. To this end the analogues (S)-azetidine-2-carboxylic acid (Aze), (S)-piperidine-2-carboxylic acid (Pip), (R)-thiazolidine-4-carboxylic acid (4-Thz), (4R)-2-methylthiazolidine-4-carboxylic acid (2Me4-Thz), (R)-thiazolidine-2-carboxylic acid (2-Thz), (S)-oxazolidine-4-carboxylic acid (4-Oxa), (4S,5R)-5-methyloxazolidine-4-carboxylic acid (5Me4-Oxa), and (2S,4R)-4-hydroxypyrrolidine-2-carboxylic acid (Hyp) and several N-alkylated amino acids were incorporated into the sequences Ala-Yaa-(4-)nitroanilide and Ala-Gly-Yaa-Phe-(4-)nitroanilide. NMR line-shape analyses of various cis and trans proton signals of these peptides were performed at different temperatures, and the rate constants of cis/trans isomerization were fitted to the Eyring equation. The rotational barriers of all cyclic proline analogues except hydroxyproline were found to be lower than that of proline by about 10 kJ/mol, whereas all noncyclic analogues and hydroxyproline showed rotational barriers similar to that observed for proline. In addition, the ability of cytosolic porcine kidney cyclophilin (Cyp18), a member of the peptidyl prolyl cis/trans isomerase family, to catalyze cis/trans isomerization of the peptide bond preceding the proline analogues was investigated. By line-shape analyses we proved efficient catalysis by Cyp18 for the analogues Aze, 4-Thz, and 2-Thz.

Proline Residues at the C Terminus of Nascent Chains Induce SsrA Tagging during Translation Termination

“…For example, Tyr-Pro, Phe-Pro, and TrpPro peptide bonds are most likely to adopt the cis conformation in solution (39) but do not result in the highest levels of YbeL tagging. Finally, both the isomerization rate and equilibrium population of the cis isomer is higher for Xaa-Aze than Xaa-Pro peptide bonds (40), and yet Xaa-Aze dipeptides at the C terminus of the nascent chain do not cause tagging. These observations argue against isomerization being an important determinant of full-length tagging, but do not rule out this model, because cis-trans isomerization could be very different in solution than on the ribosome.…”

An Arabidopsis ATP-Dependent, DEAD-Box RNA Helicase Loses Activity upon IsoAsp Formation but Is Restored by PROTEIN ISOASPARTYL METHYLTRANSFERASE

“…PRH75 has been reported to physically interact with at least two peptidyl-prolyl cis-trans isomerases (GeneMANIA; Razick et al, 2008;WardeFarley et al, 2010) responsible for altering the relative orientation of Pro and its N-terminal neighbor in the protein backbone (Galat, 1993). Nonenzymatic Pro isomerization is known to occur slowly, overcoming a considerable energy barrier (Chen et al, 2012), although this process accelerates with increasing temperature (Kern et al, 1997), resulting in deleterious consequences for enzymatic activity, should it not be rectified (Cloos and Christgau, 2002;Wedemeyer et al, 2002). It is possible that peptidyl-prolyl cis-trans isomerase association with PRH75 underlies a propensity for the helicase to also undergo Pro isomerization and deactivation over time, a subtle protein alteration that PIMT would be incapable of reversing.…”

Using the ONIOM hybrid method to apply equation of motion CCSD to larger systems: Benchmarking and comparison with time-dependent density functional theory, configuration interaction singles, and time-dependent Hartree–Fock

“…S-azetidine-2-carboxylic acid is a non-natural amino acid that has chemical and biochemical applications [41][42][43][44][45][46] ͓see Fig. 2͑a͔͒.…”