Frank Bordusa

Rhodamine 110 (R110) peptide conjugates are widely used fluorogenic substrates in proteolytic assays; however, their inherent symmetry results in two identical hydrolysis sites, complicating their application as well-defined substrates. Here, we report a preparative enzymatic strategy for the desymmetrization of the symmetric derivative (Acetyl-Leu-Pro-Lys)₂-R110 using the bovine trypsin variant D189S. Due to pronounced differences in the rates of the two sequential hydrolysis steps, a mono-substituted intermediate accumulates under controlled reaction conditions. On a preparative scale, Acetyl-Leu-Pro-Lys-R110 was generated by partial hydrolysis and isolated by preparative HPLC in 28.8% yield and 95.8% purity. The structure of the asymmetric product was fully characterized by NMR and high-resolution mass spectrometry. This work demonstrates that selective enzymatic hydrolysis provides a simple and effective preparative route to asymmetric Rhodamine 110 derivatives, offering a practical alternative to conventional multistep synthetic approaches and enabling improved substrate design for kinetic studies.

Enzymes are powerful catalysts for selective transformations but often suffer from limited stability under operational conditions such as elevated temperature or the presence of organic cosolvents. While sequence‐based strategies have been widely used to improve stability, chemical protein engineering enables modifications beyond the natural amino acid repertoire thereby offering complementary routes to tailor enzyme function and robustness. Here, we apply the in situ cyclization of proteins (INCYPRO) to a D‐stereospecific hydrolase with low intrinsic thermal stability. Site‐specific macrocyclization substantially improved resilience to heat and cosolvent stress. Unexpectedly, we discovered a cross‐linked protein dimer with enhanced activity and thermal stability. The complex structure was confirmed by x‐ray crystallography. Extending the INCYPRO approach, we engineered a multicyclic enzyme dimer with a total of four cross‐linking sites, which not only retained high activity under benign conditions but also outperformed the wild‐type under stress. Our findings establish protein macrocyclization as a versatile strategy to stabilize both monomeric and multimeric enzymes, providing a powerful route to robust biocatalysts.

Enzymes are powerful catalysts for selective transformations but often suffer from limited stability under operational conditions such as elevated temperature or the presence of organic cosolvents. While sequence‐based strategies have been widely used to improve stability, chemical protein engineering enables modifications beyond the natural amino acid repertoire thereby offering complementary routes to tailor enzyme function and robustness. Here, we apply the in situ cyclization of proteins (INCYPRO) to a D‐stereospecific hydrolase with low intrinsic thermal stability. Site‐specific macrocyclization substantially improved resilience to heat and cosolvent stress. Unexpectedly, we discovered a cross‐linked protein dimer with enhanced activity and thermal stability. The complex structure was confirmed by x‐ray crystallography. Extending the INCYPRO approach, we engineered a multicyclic enzyme dimer with a total of four cross‐linking sites, which not only retained high activity under benign conditions but also outperformed the wild‐type under stress. Our findings establish protein macrocyclization as a versatile strategy to stabilize both monomeric and multimeric enzymes, providing a powerful route to robust biocatalysts.

For protein evaluation of feedstuffs for ruminants, the Streptomyces griseus protease test provides a solely enzymatic method for estimating ruminal protein degradation. Since plant proteins are often structured in carbohydrate complexes, the use of carbohydrase during the test might improve its accuracy. It is advisable to co-incubate protease and carbohydrase, risking that the carbohydrase activity is reduced under the influence of the protease. The present study was conducted to investigate this impact by using α-amylase or the multi-enzyme complex Viscozym^® L as carbohydrase. The detection of active protease was determined fluorescence photometrically using internally quenched fluorogenic substrates (IQFS). Cellulose, pectin, and starch degradation were determined spectrophotometrically using 3,5-dinitro salicylic acid as a colorimetric agent. The Streptomyces griseus protease mixture proved to be active for the selected IQFS immediately after the start of measurements (p < 0.05). Starch hydrolysis catalyzed by α-amylase or Viscozym^® L, respectively, was decreased by co-incubation with protease mixture by maximal 3% or 37%, respectively, at 5 h incubation time (p > 0.05). Pectin and cellulose hydrolysis catalyzed by Viscozym^® L, respectively, was not significantly influenced by co-incubation with a protease mixture (p > 0.05). Although a decrease in carbohydrase activity during co-incubation with Streptomyces griseus protease occurred, it was only numerical and might be counteracted by an adapted carbohydrase activity.

Trypsin is a long-known serine protease widely used in biochemical, analytical, biotechnological, or biocatalytic applications. The high biotechnological potential is based on its high catalytic activity, substrate specificity, and catalytic robustness in non-physiological reaction conditions. The latter is mainly due to its stable protein fold, to which six intramolecular disulfide bridges make a significant contribution. Although trypsin does not depend on cofactors, it essentially requires the binding of calcium ions to its calcium-binding site to obtain complete enzymatic activity and stability. This behavior is inevitably associated with a limitation of the enzyme’s applicability. To make trypsin intrinsically calcium-independent, we removed the native calcium-binding site and replaced it with another disulfide bridge. The resulting stabilized apo-trypsin (aTn) retains full catalytic activity as proven by enzyme kinetics. Studies using Ellmann’s reagent further prove that the two inserted cysteines at positions Glu70 and Glu80 are in their oxidized state, creating the desired functional disulfide bond. Furthermore, aTn is independent of calcium ions, possesses increased thermal and functional stability, and significantly reduced autolysis compared to wildtype trypsin. Finally, we confirmed our experimental data by solving the X-ray crystal structure of aTn.

Bispecific antibodies (bsAbs) were first developed in the 1960s and are now emerging as a leading class of immunotherapies for cancer treatment with the potential to further improve clinical efficacy and safety. Many different formats of bsAbs have been established in the last few years, mainly generated genetically. Here we report on a novel, flexible, and fast chemo–enzymatic, as well as purely enzymatic strategies, for generating bispecific antibody fragments by covalent fusion of two functional antibody Fab fragments (Fabs). For the chemo–enzymatic approach, we first modified the single Fabs site-specifically with click anchors using an enhanced Trypsiligase variant (eTl) and afterward converted the modified Fabs into the final heterodimers via click chemistry. Regarding the latter, we used the strain-promoted alkyne-azide cycloaddition (SPAAC) and inverse electron-demand Diels–Alder reaction (IEDDA) click approaches well known for their fast reaction kinetics and fewer side reactions. For applications where the non-natural linkages or hydrophobic click chemistry products might interfere, we developed two purely enzymatic alternatives enabling C- to C- and C- to N-terminal coupling of the two Fabs via a native peptide bond. This simple system could be expanded into a modular system, eliminating the need for extensive genetic engineering. The bispecific Fab fragments (bsFabs) produced here to bind the growth factors ErbB2 and ErbB3 with similar K_D values, such as the sole Fabs. Tested in breast cancer cell lines, we obtained biologically active bsFabs with improved properties compared to its single Fab counterparts.

Fluorescent fusion proteins are powerful tools for studying biological processes in living cells, but universal application is limited due to the voluminous size of those tags, which might have an impact on the folding, localization or even the biological function of the target protein. The designed biocatalyst trypsiligase enables site‐directed linkage of small‐sized fluorescence dyes on the N terminus of integral target proteins located in the outer membrane of living cells through a stable native peptide bond. The function of the approach was tested by using the examples of covalent derivatization of the transmembrane proteins CD147 as well as the EGF receptor, both presented on human HeLa cells. Specific trypsiligase recognition of the site of linkage was mediated by the dipeptide sequence Arg‐His added to the proteins’ native N termini, pointing outside the cell membrane. The labeling procedure takes only about 5 minutes, as demonstrated for couplings of the fluorescence dye tetramethyl rhodamine and the affinity label biotin as well.

Liquid and HR-MAS NMR spectroscopy at two magnetic field strengths was employed to investigate the dynamics of ([C₁C₁IM][(CH₃)₂PO₄]).

Site-specific incorporation of artificial functionalities into protein targets is an important tool in both basic and applied research and can be a major challenge to protein chemists. Chemical labeling methods often targeting multiple positions within a protein and therefore suffer from lack of specificity. Enzymatic protein modification is an attractive alternative due to the inherent regioselectivity and stereoselectivity of enzymes. In this contribution we describe the application of the highly specific trypsin variant named trypsiligase for the site-specific modification of virtual any target protein. We present two general routes of modification resulting in either N- or C-terminal functionalized protein products. Both reaction regimes proceed under mild and bioorthogonal conditions in a short period of time which result in homogeneously modified proteins bearing the artificial functionality exclusively at the desired position. We detail protocols for the expression and purification of trypsiligase as well as the construction of peptide or acyl donor ester probes used as substrates for the biocatalyst. In addition, we provide instructions how to perform the ultimate bioconjugation reactions and finally render assistance for the qualitative and quantitative analysis of the reaction course and outcome.

Site-specific incorporation of nonproteinogenic functionalities into protein targets is an important tool in both basic and applied research and represents a major challenge to protein chemists. Chemical labeling methods often target multiple positions within a protein and therefore suffer from a lack of specificity. Enzymatic protein modification is an attractive alternative due to the inherent regioselectivity and stereoselectivity of enzymes. In this chapter we describe the application of the highly specific trypsin variant trypsiligase for the site-specific modification of virtual any target protein. We present two general routes of modification resulting in either N- or C-terminal functionalized protein products. Reactions rapidly proceed under mild conditions and result in homogeneously modified proteins bearing the artificial functionality exclusively at the desired position. We detail protocols for the expression and purification of trypsiligase as well as the synthesis of peptide (ester) substrates. In addition, we provide instructions for the bioconjugation reactions and for the qualitative and quantitative analysis of reaction progress and efficiency.