Question

why is proline isomerization often a rate limit step in protein folding? Explain

Answer 1

Proline is unique among the natural amino acids in having a relatively small difference in free energy between the cis configuration of its peptide bond and the more common trans form. The activation energy required to catalyse the isomerisation between cis and trans is relatively high: ~20kcal/mol (c.f. ~0kcal/mol for regular peptide bonds). Unlike regular peptide bonds, the X-prolyl peptide bond will not adopt the intended conformation spontaneously, thus, the process of cis-trans isomerization can be the rate-limiting step in the process of protein folding. Prolyl isomerases therefore function as protein folding chaperones.

Cis peptide bonds N-terminal to proline residues are often located at the first residue of certain types of tight turns in the protein backbone.

Proteins that contain structural cis-prolines in the native state include ribonuclease A, ribonuclease T1, beta lactamase, and some interleukins.

Prolyl isomerase folding can be autocatalytic and therefore the speed of folding depends on reactant concentration. Parvulin and human cytosolic FKBP are thought to catalyze their own folding processes.

Activation energies consistent with proline isomerization, which typically has an activation of about 20 kcal/mol.

Two-state folding kinetics indicative of both fast-folding and slow-folding populations in the unfolded or denatured state.

"Double-jump" assays in which proline-containing proteins are unfolded and refolded, and the population of non-native proline conformations are studied as a function of the extent of folding.

Acceleration of the in vitro folding rate by the addition of a prolyl isomerase.

Acceleration of the in vitro folding rate in mutant protein variants with one or more proline residues replaced by another amino acid