Proline, cis-trans isomerization

Hodel, A. Rice, L. M. Simonson, T. Fox, R. O. Briinger, A. T., Proline cis-trans isomerization in staphylococcal nuclease — multi-substate free-energy perturbation calculations, Prot. Sci. 1995, 4, 636-654. 

Grathwohl, C. and WUthrich, K. (1981). NMR studies of the rates of proline cis-trans isomerization in oligopeptides. Biopolymers, 20, 2623-2633. 

WW domains are signaling modules of ca. 40 amino acids that bind short proline-rich sequences such as PPLP or PPR motifs (review Macias et al., 2002). A subset of WW domains, found, e.g., in the proline cis-trans isomerase Pinl, however, specifically binds to phosphoserine-Pro and phosphothreonine-Pro motifs. The Pin 1 protein has an essential role in mitosis. It is thought that Pinl binding to phosphorylated mitotic proteins facilitates proline cis/trans isomerizations and subsequent conformational changes. For the Pinl substrate Cdc25 phosphatase it has been shown that proline isomerization facilitates the subsequent dephosphorylation of phosphorylated Cdc25 protein by the protein phosphatase PP2A. 

Figure 5 Consensus structured regions (CSRs) predicted by the analysis of families of homologous proteins (a) cytochrome c family (b) mammalian ribonuclease family. The CSRs are shown (in bold) as independent segments and are also highlighted on the ribbon drawing of the entire chain. The numbers indicate the residues delimiting the CSRs in the reference structures (cytochrome c2 and bovine ribonuclease. respectively). Proline residues are displayed in full atomic detail and highlighted in view of the effect that proline cis/trans isomerization could have on the formation of early-folding intermediates ...

Figure 6 Thermodynamic cycle for multi-substate free energy calculation. System A has n substates system B has m. The free energy difference between A and B is related to the substate free energy differences through Eq. (41). A numerical example is shown in the graph (from Ref. 39), where A and B are two isomers of a surface loop of staphylococcal nuclease, related by cis-trans isomerization of proline 117. The cis trans free energy calculation took into account 20 substates for each isomer only the six or seven most stable are included in the plot.

In the native protein these less stable ds-proline peptides are stabilized by the tertiary structure but in the unfolded state these constraints are relaxed and there is an equilibrium between ds- and trans-isomers at each peptide bond. When the protein is refolded a substantial fraction of the molecules have one or more proline-peptide bonds in the incorrect form and the greater the number of proline residues the greater the fraction of such molecules. Cis-trans isomerization of proline peptides is intrinsically a slow process and in vitro it is frequently the rate-limiting step in folding for those molecules that have been trapped in a folding intermediate with the wrong isomer. 

Immunophillins are abundant proteins that catalyze the cis-trans isomerization of proline residues within proteins, generally to aid in protein folding. Immunophillins are not essential proteins, are the intracellular binding proteins of several immunosuppressive drugs. Cyclosporin A exerts its action after binding to cyclophilin. Tacrolimus and sirolimus predominantly bind to the protein FKBP-12 (FK binding protein-12). 

In this case, we point to the fact that a fast (r < 5 s) and a slow phase have been observed in temperature-jump experiments also with the peptide Col 1-3. The slow phase - as already mentioned - has been associated with the cis-trans isomerism of peptide bonds in the direct neighborhood of the helical part. Only peptide bonds to which proline or hydroxyproline contribute their secondary nitrogen are able to assume a cry-configuration at equilibrium (cis to trans ratios of 1 40 to 1 l)l45). Therefore, the fast... 

One may conclude that the rate-determining step of the renaturation is at least partly influenced by the cis-trans isomerization of the peptide bond the secondary nitrogen atom of which arises from proline. Otherwise, only the entropy-controlled slow nuclea-tion should be observed kinetically. The covalent bridging through Lys-Lys, therefore, gives rise not only to thermodynamic stabilization of the triple helix but also to kinetic properties which have hitherto been observed in the case of type III procollagen146) and its aminoterminal fragment Col 1-3144). 

The design of this successful system started with an enzyme with a ready-made peptide binding site, with well established specificity. The cyclophilins catalyze the cis-trans isomerization of peptide bonds to proline ... 

Disulfide bond formation within the individual propeptides precedes folding and trimers are then formed by association of the C-terminal propeptides." Disulfide bonds between the chains are then formed and this formation is most likely catalyzed by PDI." As triple helix formation proceeds, the rate-limiting step in this process is the cis—trans isomerization of peptidyl-Pro bonds. This process can be catalyzed by peptidyl-prolyl cis—trans isomerases (cyclophilins and FKBPs). This activity is required to convert the proline residues to the trans form required for triple helix formation." " " ... 

Refolding is generally found to proceed by a series of exponential phases. Many of these exponentials are a consequence of cis-trans isomerization about peptidyl-prolyl bonds.14,15 The equilibrium constant for the normal peptide bond in proteins favors the trans conformation by a factor of 103-104 or so. The peptidyl-prolyl bond is an exception that has some 2-20% of cis isomer in model peptides (see Chapter 1, Figure 1.3). Further, it is often found as the cis isomer in native structures. (Replacement of ds-prolines with other amino acids by protein engineering can retain the cis stereochemistry.16) The interconversion of cis to trans in solution is quite slow, having half-lives of 10-100 s at room temperature and neutral pH. This has two important consequences. First, a protein that has several... 

The biosynthetic pathway to the ergoline nucleus proceeds through 4-dimethylallyl tryptophan (4-DMAT), chanoclavine-I, agroclavine, and lysergic acid. Two cis, trans isomerizations occur one before chanocla-vine-I and the other before agroclavine, as shown by experiments with [2- C]-mevalonic acid and [Z-CH3]-4-DMAT (Fig. 36). The peptide unit is derived from a combination of three amino acids, one of which is always proline. Several genera in the plant family Convolvulaceae Rivea, Ipomoea, etc.) also produce ergot alkaloids. 

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