Isomerization of proline residues

Isomerization of proline residues can he a rate-limiting step in protein folding... 

Enzymes assist formation of proper disulfide bonds during folding Isomerization of proline residues can be a rate-limiting step in protein folding Proteins can fold or unfold inside chaperonins GroEL is a cylindrical structure with a... 

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). 

Brandts, J. F., Halverson, H. R., and Brennan, M. Consideration of the possibility that the slow step in protein denaturation reactions is due to cis-trans isomerism of proline residues. Biochemistry 14, 4953-4963 (1975). 

Figure 14 The effect of cis-irans isomerism of proline residues on the direction of the main chain of the poljrpeptide, indicated by open arrows. Proline is the only amino acid that so far has shown this isomerism in protein structures...

Other exchange phenomena that manifest themselves in NMR spectra include cis-trans isomerization of proline residues, aromatic ring flipping and the rotation of primary amides of asparagine and glutamine. 

Several attempts were made to detect and identify nucleation centers, but until recently no direct evidence for their existence was obtained. The slow step observed in earlier fast reaction kinetic studies was at first attributed to a nucleation process (Tsong et ai, 1972a), and subsequently to cis-trans isomerization of proline residues. However, this last statement is still controversial. 

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. 

The fraction of Us molecules depends on the number of proline residues and on their isomeric state in the native protein. In particular, the presence of cts-prolyl peptide bonds in the folded molecules leads to a high fraction of Us, since in unfolded proteins the cis state is populated to a small extent only. Adler and Scheraga (1990) showed by NMR that in heat-unfolded RNase A the nonnative trans isomers predominate at both Pro93 and Proll4. The Up molecules dominate in the unfolded state of proteins that have only tram-prolyl peptide bonds, such as lysozyme (Kato et ai, 1981, 1982), cytochrome c (Ridge el ai, 1981 Nall,... 

Probably not all proline residues are important for protein folding. Evidence for nonessential prolines came from a comparison of several homologous pancreatic RNases (Krebs et al., 1983, 1985) and cytochromes c (Babul et ai, 1978 Nall, 1990) that differ in the number of proline residues. Such prolines could be nonessential because they do not interfere with folding, or, alternatively, because they remain nativelike as regards isomeric state, after unfolding. 

Other evidence for different classes of proline residues has come from energy calculations (Levitt, 1981 Ihara and Ooi, 1985), in which the destabilization of the native state was calculated when one proline at a time was incorporated, in its incorrect isomeric state, into the protein. Levitt (1981) classified these proline residues into three categories. Type I prolines destabilize the native state only to a small extent when in the incorrect isomeric state. Such prolines should barely affect folding. 

Figure 16.7 Fluorinated prolines in collagen, (a) The trans/cis isomerization of amide bonds and main-chain angles of proline residues. The n —> interaction, depicted by a dashed line,...

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." " " ... 

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