Precise and Controlled Modification of Proteins using Multifunctional Chemical Constructs

Abstract

Bioconjugation of chemical entities to biologically active proteins has increased our insight in the inner workings of a cell and resulted in novel therapeutic agents. A current challenge is the efficient generation of homogeneous conjugates of native proteins, not only when isolated, but also when still present in their native environment. To do this, various features of protein-modifying enzymes have been combined in artificial constructs. In this concept, the current status of this approach is evaluated, and the interplay between designs and protein modification will be discussed. Particular focus is directed on the protein-binding anchor, the chemistry that is used for the modification, and the linker that connects these two units. Suggestions how to include additional elements such as a trigger-responsive switch that regulated protein modification are also presented.

DNA nanocrane-based catalysts for region-specific protein modification

“…Due to the density of functional groups on the surface of proteins, controlling post-biosynthesis modification of wild-type or native proteins has only been achieved for a limited set of proteins. 1–5 Although finely-tuned chemical agents and precisely tailored catalytic constructs have yielded approaches that enable the modification of a selective subset of identical functional groups, 2,3,6–9 precise control over modification of native proteins remains challenging, especially within a complex biological setting such as a cell. Our past studies were directed at the development of DNAzymes as enzyme mimics for protein modification, 10–12 the enrichment of thrombin-binding aptamer with catalytic moieties that lead to trigger-responsive site-selective and protein-selective modification, 12 and calibration of the modification efficiency and range with respect to the distance between catalyst and protein.…”

“…In this study, we integrated various elements into novel catalytic structures that (i) reversibly interact with the target protein, (ii) enable control over the protein region that is subjected to modification, and (iii) allow this modification to be performed in the complex mixture of a cell lysate. 8,13–15 To achieve this we use the programmable nature of synthetic DNA to construct various DNA-based nanometer-sized cranes to control modification of native proteins, ideally including external control over the site of the protein that is modified (Fig. 1).…”