Proline Isomerization: From the Chemistry and Biology to Therapeutic Opportunities

Abstract

Proline isomerization, the process of interconversion between the cis- and trans-forms of proline, is an important and unique post-translational modification that can affect protein folding and conformations, and ultimately regulate protein functions and biological pathways. Although impactful, the importance and prevalence of proline isomerization as a regulation mechanism in biological systems have not been fully understood or recognized. Aiming to fill gaps and bring new awareness, we attempt to provide a wholistic review on proline isomerization that firstly covers what proline isomerization is and the basic chemistry behind it. In this section, we vividly show that the cause of the unique ability of proline to adopt both cis- and trans-conformations in significant abundance is rooted from the steric hindrance of these two forms being similar, which is different from that in linear residues. We then discuss how proline isomerization was discovered historically followed by an introduction to all three types of proline isomerases and how proline isomerization plays a role in various cellular responses, such as cell cycle regulation, DNA damage repair, T-cell activation, and ion channel gating. We then explore various human diseases that have been linked to the dysregulation of proline isomerization. Finally, we wrap up with the current stage of various inhibitors developed to target proline isomerases as a strategy for therapeutic development.

Proteostatic Remodeling of Small Heat Shock Chaperones─Crystallins by Ran-Binding Protein 2─and the Peptidyl-Prolyl cis–trans Isomerase and Chaperone Activities of Its Cyclophilin Domain

“…As noted earlier, crystallins are regulated developmentally, , and the CLD and the PPIase activity of CY of Ranbp2 modulate protein homeostasis in vitro and physiologically (Figure a). − ,,, The PPIase activity is used as an in vitro proxy assay to estimate varied roles of catalysis of cis–trans isomerization of a linker proline in proteostasis, protein biogenesis, and signal transduction . As shown by our prior works and other independent studies of orthologous CY of bovine and human Ranbp2 (Figure a), CY has PPIase activity with the de facto isomer-specific proteolysis-coupled assay (ISP) for measuring proline isomerase of modified substrates with the general formula, succinyl (Suc)-Ala-Xaa- cis -Pro-Phe- p -nitroanilide (pNA). ,,, In this assay, the p -nitroanilide amide bond is hydrolyzed by α-chymotrypsin only when the Xaa-Pro bond of the chromogenic tetrapeptide is in the trans conformation .…”

FASN negatively regulates p65 expression by reducing its stability via Thr254 phosphorylation and isomerization by Pin1

“…While the finding that FASN regulates p65 stability by impacting the phosphorylation status of the p65 Thr 254 residue, thereby, affecting the isomerization of p65 by Pin1 ( Fig. 8 ) is intriguing, it is not surprising since Pin1 is known to regulate stability of many proteins by binding to and isomerizing these proteins upon phosphorylation at the consensus Ser/Thr-Pro motif ( 43 ) including Thr 254 -phosphorylated p65 ( 36 ). It has been reported that activated p65 in the nucleus is not bound by the inhibitory subunit IκBα, leaving Thr 254 exposed and allowing its phosphorylation ( 36 ) followed by recruitment of and isomerization by Pin1.…”

“…Although Pin1 binding to and isomerizing phosphorylated substrate proteins, such as p65 and p53 ( 36 , 43 ) results in the stabilization of these proteins, the molecular mechanism of the protein stabilization following isomerization is unknown. However, it was thought that phosphorylation and isomerization of these proteins facilitate their translocation into nucleus where they exert their functions as transcription factors, which may prevent them from binding by E3 ubiquitin ligase and degradation by proteasomes in the cytoplasm ( 36 ).…”

SHP2–EGFR States in Dephosphorylation Can Inform Selective SHP2 Inhibitors, Dampening RasGAP Action

“…Proline’s cyclic structure facilitates cis–trans interconversion, governing protein conformation and function . In the trans configuration, proline has ω = 180°, while in cis , ω = 0°.…”

“…Proline's cyclic structure facilitates cis−trans interconversion, governing protein conformation and function. 77 In the trans configuration, proline has ω = 180°, while in cis, ω = 0°. A transition of cis to a syn (ω = 90°) state needs to overcome a ∼30 kcal mol −1 energy barrier, leading to a predominantly trans conformation.…”