Peptide labeling with photoactivatable trifunctional cadaverine derivative and identification of interacting partners by biotin transfer

Photoreactive Probe-Based Strategy Enables the Specific Identification of the Transient Substrates of Methyltransferase at the Proteome Scale

To decipher the biological function of protein arginine methyltransferases (PRMTs), the identification of their substrate proteins is crucial. However, this is not a trivial task as the stable and strong interacting proteins always prevail over the weak and transient substrate proteins. Herein, we report the development of a novel photoreactive probe-based strategy to identify the substrate proteins of methyltransferases. By applying it to PRMT1, we demonstrate that this strategy can effectively distinguish substrate proteins from other interacting proteins and allows the identification of highly confident substrate proteins. Noteworthily, we found for the first time that hypomethylation of proteins is a prerequisite for efficient capturing of substrate proteins. This study describes the development of a robust chemical proteomics tool for profiling the transient substrates and can be adapted for broad biomedical applications.

Identification of PDGF-BB binding to thymosin β4 by chemical cross-linking

INTRODUCTION

The purpose of our work was to identify unknown interaction partners of thymosin β4 (Tβ4). It was suggested that Tβ4 could be an antifibrotic drug for treatment of liver fibrogenesis, because Tβ4 prevents the platelet-derived growth factor-BB (PDGF-BB)-induced activation of hepatic stellate cells (HSCs). Very little information is available how Tβ4 counteracts the PDGF-BB-induced activation of HSCs. We propose the hypothesis that Tβ4 could bind directly to PDGF-BB and thereby reduce the concentration of free PDGF-BB available for binding to the PDGF-β receptor.

METHODS

To prove our suggestion of a direct interaction between Tβ4 and PDGF-BB, we carried out chemical as well as photochemical cross-linking experiments between the two pure proteins in vitro.

RESULTS

We identified an interaction between Tβ4 and PDGF-BB by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) cross-linking as well as through biotin label transfer using a bifunctional photoactivatable derivative of Tβ4. In an in vitro system, PDGF-BB was identified as the first extracellular partner interacting with Tβ4. This interaction could influence PDGF-BB binding to its receptor and abolish PDGF-BB-related effects.

CONCLUSION

Direct interaction of Tβ4 with extracellular factors should be considered as a potential mechanism to explain the pleiotropic effects of β-thymosins.