Palladium-triggered deprotection chemistry for protein activation in living cells

Abstract

Employing small molecules or chemical reagents to modulate the function of an intracellular protein, particularly in a gain-of-function fashion, remains a challenge. In contrast to inhibitor-based loss-of-function approaches, methods based on a gain of function enable specific signalling pathways to be activated inside a cell. Here we report a chemical rescue strategy that uses a palladium-mediated deprotection reaction to activate a protein within living cells. We identify biocompatible and efficient palladium catalysts that cleave the propargyl carbamate group of a protected lysine analogue to generate a free lysine. The lysine analogue can be genetically and site-specifically incorporated into a protein, which enables control over the reaction site. This deprotection strategy is shown to work with a range of different cell lines and proteins. We further applied this biocompatible protection group/catalyst pair for caging and subsequent release of a crucial lysine residue in a bacterial Type III effector protein within host cells, which reveals details of its virulence mechanism.

Structural basis of rifampin inactivation by rifampin phosphotransferase

“…These results suggest that this conserved His residue also may function as a phosphate acceptor and donor in the phosphorylation of RIF. In addition, positively charged residues often function as catalytic bases to abstract a proton at the reaction centers of phosphatetransfer enzymes and other enzymes, including MAPK, phosphothreonine lyase, IMP dehydrogenase, pectate/pectin lyases, fumarate reductase, and L-aspartate oxidase (21)(22)(23), suggesting that Lys670 and Arg666 might be candidate residues for the catalytic bases of LmRPH.…”

Expanding the boundary of biocatalysis: design and optimization of in vitro tandem catalytic reactions for biochemical production

“…The achievements made so far have enabled several metal-catalyzed reactions in aqueous solutions, including olefin (Vougioukalakis, 2016), hydrogenation, and C-C coupling reactions (Wang et al, 2016). Importantly, a few metal catalysts such as Cu, Pd and Ru have been integrated into living cell for biorthogonal protein chemistry (Li et al, 2014; Yang et al, 2014). Although there are very few examples to integrate bio-orthogonal reactions into chemical synthetic pathways in living cells, there is an opportunity to create new cell factories for distinct chemical production by harnessing the synthetic power of transition metal catalysts.…”

Tandem Reactions Combining Biocatalysts and Chemical Catalysts for Asymmetric Synthesis

“…Recently Mascareñas and co-workers improved this scenario further by using a designed Ru complex that accumulated preferentially inside the mitochondria of mammalian cells while keeping its ability to uncage alloc-protected amines [97]. Except for the Ru catalysts, Pd complexes have also been applied in living cells for activation of intracellularly lysine-based proteins by decaging a propargyloxycarbonyl (Proc)-caged lysine analogue [98].…”