Investigation of the Substrate Specificity of Lacticin 481 Synthetase by Using Nonproteinogenic Amino Acids

One enzyme, many substrates . The substrate specificity of a lantibiotic biosynthetic enzyme, lacticin 481 synthetase, was probed by using synthetic prepeptides containing a variety of nonproteinogenic amino acids, including unnatural α‐amino acids, β‐amino acids, D ‐amino acids, and peptoids.

     

Asparaginyl Ligases: New Enzymes for the Protein Engineer's Toolbox

Enzyme-catalysed site-specific protein modifications enable the precision manufacture of conjugates for the study of protein function and/or for therapeutic or diagnostic applications. Asparaginyl ligases are a class of highly efficient transpeptidases with the capacity to modify proteins bearing only a tripeptide recognition motif. Herein, we review the types of protein modification that are accessible using these enzymes, including N- and C-terminal protein labelling, head-to-tail cyclisation, and protein-protein conjugation. We describe the progress that has been made to engineer highly efficient ligases as well as efforts to chemically manipulate the enzyme reaction to favour product formation. These enzymes are powerful additions to the protein engineer‘s toolbox.     

Microbial Transglutaminase and c‐myc‐Tag: A Strong Couple for the Functionalization of Antibody‐Like Protein Scaffolds from Discovery Platforms

Antibody‐like proteins selected from discovery platforms are preferentially functionalized by site‐specific modification as this approach preserves the binding abilities and allows a side‐by‐side comparison of multiple conjugates. Here we present an enzymatic bioconjugation platform that targets the c‐myc‐tag peptide sequence (EQKLISEEDL) as a handle for the site‐specific modification of antibody‐like proteins. Microbial transglutaminase (MTGase) was exploited to form a stable isopeptide bond between the glutamine on the c‐myc‐tag and various primary‐amine‐functionalized substrates. We attached eight different functionalities to a c‐myc‐tagged antibody fragment and used these bioconjugates for downstream applications such as protein multimerization, immobilization on surfaces, fluorescence microscopy, fluorescence‐activated cell sorting, and in vivo nuclear imaging. The results demonstrate the versatility of our conjugation strategy for transforming a c‐myc‐tagged protein into any desired probe.     

Chemical biology techniques unlock the secrets of casein kinase 2 regulation by phosphorylation and glycosylation

The key to understanding: The application of expressed protein ligation and protein microarrays enabled an unparalleled insight into the complex interaction of phosphorylation and glycosylation on casein kinase 2 and its biological outcome.     

Establishing the Stability and Reversibility of Protein Pyrophosphorylation with Synthetic Peptides

Protein pyrophosphorylation is emerging as a new post‐translational modification, yet its role in cellular signaling remains poorly characterized. Important factors in determining the biological relevance of pyrophosphorylation include understanding the chemical and biochemical stability of the pyrophosphoryl group and elucidating the reversibility of modification in a cellular context. Towards this end, we prepared a series of synthetic pyrophosphopeptides, which were utilized to demonstrate that the modification is quite inert over a wide pH range but can be removed biochemically by alkaline phosphatases. Importantly, we observed enzyme‐dependent removal of the pyrophosphate in mammalian and yeast cell lysates using the synthetic pyrophosphopeptides. The findings provide evidence for the reversibility of pyrophosphorylation and thereby highlight the potential impact of this modification on cellular signal transduction pathways.     

Flexible and general synthesis of functionalized phosphoisoprenoids for the study of prenylation in vivo and in vitro

Protein modification with isoprenoid lipids affects hundreds of signaling proteins in eukaryotic cells. Modification of isoprenoids with reporter groups is the main approach for the creation of probes for the analysis of protein prenylation in vitro and in vivo. Here, we describe a new strategy for the synthesis of functionalized phosphoisoprenoids that uses an aminederivatized isoprenoid scaffold as a starting point for the synthesis of functionalized phosphoisoprenoid libraries. This overcomes a long-standing problem in the field, where multistep synthesis had to be carried out for each individual isoprenoid analogue. The described approach enabled us to synthesize a range of new compounds, including two novel fluorescent isoprenoids that previously could not be generated by conventional means. The fluorescent probes that were developed using the described approach possess significant spectroscopic advantages to all previously generated fluorescent isoprenoid analogue. Using these analogues for flow cytometry and cell imaging, we analyzed the uptake of isoprenoids by mammalian cells and zebrafish embryos. Furthermore, we demonstrate that derivatization of the scaffold can be coupled in a one-pot reaction to enzymatic incorporation of the resulting isoprenoid group into proteins. This enables rapid evaluation of functional groups for compatibility with individual prenyltransferases and identification of the prenyltransferase specific substrates.     

Exploring the Substrate Scope of the Bacterial Phosphocholine Transferase AnkX for Versatile Protein Functionalization

Site-specific protein functionalization has become an indispensable tool in modern life sciences. Here, tag-based enzymatic protein functionalization techniques are among the most versatilely applicable approaches. However, many chemo-enzymatic functionalization strategies suffer from low substrate scopes of the enzymes utilized for functional labeling probes. We report on the wide substrate scope of the bacterial enzyme AnkX towards derivatized CDP-choline analogues and demonstrate that AnkX-catalyzed phosphocholination can be used for site-specific one- and two-step protein labeling with a broad array of different functionalities, displaying fast second-order transfer rates of 5×10² to 1.8×10⁴ m ⁻¹ s⁻¹. Furthermore, we also present a strategy for the site-specific dual labeling of proteins of interest, based on the exploitation of AnkX and the delabeling function of the enzyme Lem3. Our results contribute to the wide field of protein functionalization, offering an attractive chemo-enzymatic tag-based modification strategy for in vitro labeling.     

Halogenated veneers: protein cross-linking and halogenation in the jaws of nereis, a marine polychaete worm

Mineralized tissues are produced by most living organisms for load and impact functions. In contrast, the jaws of the clam worm, Nereis, are hard without mineralization. However, they are peculiarly rich in halogens, which are associated with a variety of post-translationally modified amino acids, many of which are multiply halogenated by chlorine, bromine, and/or iodine. Several of these modified amino acids, namely dibromohistidine, bromoiodohistidine, chloroiodotyrosine, bromoiodotyrosine, chlorodityrosine, chlorotrityrosine, chlorobromotrityrosine, and bromoiodotrityrosine, have not been previously reported. We have found that the distributions of Cl, Br, and I differ: Cl is widespread whereas Br and I, although not colocalized, are concentrated in proximity to the external jaw surfaces. By using nanoindentation, we show that Br and I are unlikely to play a purely mechanical role, but that the local Zn and Cl concentrations and jaw microstructure are the prime determinants of local jaw hardness. Several of the post-translationally modified amino acids are akin to those found in various sclerotized structures of invertebrates, and we propose that they are part of a cross-linked protein casing.     

Expanding the Scope of Protein Trans‐Splicing to Fragment Ligation of an Integral Membrane Protein: Towards Modulation of Porin‐Based Ion Channels by Chemical Modification

It's raining, it's porin : Fragment ligation of OmpF ion channels was achieved by using the split Psp‐GBD Pol intein; this allowed reconstitution of active trimeric porin. In combination with cysteine modification at an internal position, the porin's conductance properties were altered.

     

A Novel Tyrosine–Heme CO Covalent Linkage in F43Y Myoglobin: A New Post‐translational Modification of Heme Proteins

Heme post‐translational modification plays a key role in tuning the structure and function of heme proteins. We herein report a novel tyrosine–heme covalent C?O bond in an artificially produced sperm whale myoglobin (Mb) mutant, F43Y Mb, which formed spontaneously in vivo between the Tyr43 hydroxy group and the heme 4‐vinyl group. This highlights the diverse chemistry of heme post‐translational modifications, and lays groundwork for further investigation of the structural and functional diversity of covalently‐bound heme proteins.     

Cover Picture: Selective Protein Degradation by Ligand‐Targeted Enzymes: Towards the Creation of Catalytic Antagonists (ChemBioChem 6/2003)

The cover picture shows a ligand‐targeted proteinase enzyme or “catalytic antagonist” acting as a molecular angler fish: By precisely positioning different binding ligands (L) around the active site “mouth” of a degradative proteinase enzyme, target proteins (TP) can be plucked from solution, locked in position adjacent to the catalytic triad “jaws”, and in this way readily and specifically degraded. The hunting strategy of the deep sea angler fish, which uses a lure above its mouth, illustrates this principle. Further details can be found in the article by B. Davis, R. R. Bott, J. B. Jones et. al. on pp. 533–537.