The establishment of microfluidic enzyme cascades is a topical field of research and development, which is currently hampered by the lack of methodologies for mild and efficient immobilization of isolated enzymes. We here describe the use of self-immobilizing fusion enzymes for the modular configuration of microfluidic packed-bed reactors. Specifically, three different enzymes, the (R)-selective alcohol dehydrogenase LbADH, the (S)-selective methylglyoxal reductase Gre2p and the NADP(H) regeneration enzyme glucose 1-dehydrogenase GDH, were genetically fused with streptavidin binding peptide, Spy and Halo-based tags, to enable their specific and directional immobilization on magnetic microbeads coated with complementary receptors. The enzyme-modified beads were loaded in four-channel microfluidic chips to create compartments that have the capability for either (R)- or (S)-selective reduction of the prochiral CS-symmetrical substrate 5-nitrononane-2,8-dione (NDK). Analysis of the isomeric hydroxyketone and diol products by chiral HPLC was used to quantitatively characterize the performance of reactors configured with different amounts of the enzymes. Long operating times of up to 14 days indicated stable enzyme immobilization and the general robustness of the reactor. Even more important, by fine-tuning of compartment size and loading, the overall product distribution could be controlled to selectively produce a single meso diol with nearly quantitative conversion (>95%) and excellent stereoselectivity (d.r. > 99:1) in a continuous flow process. We believe that our concept will be expandable to a variety of other biocatalytic or chemo-enzymatic cascade reactions.
Epigenetic modifications of histone tails play an essential role in the regulation of eukaryotic transcription. Writer and eraser enzymes establish and maintain the epigenetic code by creating or removing posttranslational marks. Specific binding proteins, called readers, recognize the modifications and mediate epigenetic signalling. Here, we present a versatile assay platform for the investigation of the interaction between methyl lysine readers and their ligands. This can be utilized for the screening of small-molecule inhibitors of such protein–protein interactions and the detailed characterization of the inhibition. Our platform is constructed in a modular way consisting of orthogonal in vitro binding assays for ligand screening and verification of initial hits and biophysical, label-free techniques for further kinetic characterization of confirmed ligands. A stability assay for the investigation of target engagement in a cellular context complements the platform. We applied the complete evaluation chain to the Tudor domain containing protein Spindlin1 and established the in vitro test systems for the double Tudor domain of the histone demethylase JMJD2C. We finally conducted an exploratory screen for inhibitors of the interaction between Spindlin1 and H3K4me3 and identified A366 as the first nanomolar small-molecule ligand of a Tudor domain containing methyl lysine reader.
The display of complex proteins on the surface of cells is of great importance for protein engineering and other fields of biotechnology. Herein, we describe a modular approach, in which the membrane anchor protein Lpp‐OmpA and a protein of interest (passenger) are expressed independently as genetically fused SpyCatcher and SpyTag units and assembled in situ by post‐translational coupling. Using fluorescent proteins, we first demonstrate that this strategy allows the construct to be installed on the surface of E. coli cells. The scope of our approach was then demonstrated by using three different functional enzymes, the stereoselective ketoreductase Gre2p, the homotetrameric glucose 1‐dehydrogenase GDH, and the bulky heme‐ and diflavin‐containing cytochrome P450 BM3 (BM3). In all cases, the SpyCatcher‐SpyTag method enabled the generation of functional whole‐cell biocatalysts, even for the bulky BM3, which could not be displayed by conventional fusion with Lpp‐OmpA. Furthermore, by using a GDH variant carrying an internal SpyTag, the system could be used to display an enzyme with unmodified N‐ and C‐termini.
We present a facile method for the combined synthesis and purification of protein‐decorated DNA origami nanostructures (DONs). DONs bearing reductively cleavable biotin groups in addition to ligands for ligation of recombinant proteins are bound to magnetic beads. Protein immobilization is conducted with a large protein excess to achieve high ligation yields. Subsequent to cleavage from the solid support, pure sample solutions are obtained which are suitable for direct AFM analysis of occupation patterns. We demonstrate the method's utility using three different orthogonal ligation methods, the “halo‐based oligonucleotide binder” (HOB), a variant of Halo‐tag, the “SpyTag/SpyCatcher” (ST/SC) system, and the enzymatic “ybbR tag” coupling. We find surprisingly low efficiency for ST/SC ligation, presumably due to electrostatic repulsion and steric hindrance, whereas the ybbR method, despite its ternary nature, shows good ligation yields. Our method is particularly useful for the development of novel ligation methods and the synthesis of mechanically fragile DONs that present protein patterns for surface‐based cell assays.
The operation of enzyme cascades in microfluidic devices is a current field of research that promises manifold applications in biocatalysis. For an optimization of flow biocatalysis systems it is desirable to model the reactor in silico in order to enable a better understanding and thus an economic optimization of the reaction systems. However, due to their high complexity, it is still difficult to simulate coupled enzyme reactions. We here describe a new model for a plug flow reactor consisting of a porous bed of compact uniform particles functionalized with an immobilized ketoreductase (Gre2) which is overflown by a mobile phase containing the enzymatic NADPH cofactor regeneration system based on glucose dehydrogenase (GDH). By studying different flow rates, lengths and layer thicknesses of the catalytic bed, we show that the synergy of experiment and mathematical modeling can optimize the space-time yields of the reaction system.
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