Active site titration as a tool for the evaluation of immobilization procedures of penicillin acylase

Putting precision and elegance in enzyme immobilisation with bio-orthogonal chemistry

The covalent immobilisation of enzymes generally involves the use of highly reactive crosslinkers, such as glutaraldehyde, to couple enzyme molecules to each other or to carriers through, for example, the free amino groups of lysine residues, on the enzyme surface. Unfortunately, such methods suffer from a lack of precision. Random formation of covalent linkages with reactive functional groups in the enzyme leads to disruption of the three dimensional structure and accompanying activity losses. This review focuses on recent advances in the use of bio-orthogonal chemistry in conjunction with rec-DNA to affect highly precise immobilisation of enzymes. In this way, cost-effective combination of production, purification and immobilisation of an enzyme is achieved, in a single unit operation with a high degree of precision. Various bio-orthogonal techniques for putting this precision and elegance into enzyme immobilisation are elaborated. These include, for example, fusing (grafting) peptide or protein tags to the target enzyme that enable its immobilisation in cell lysate or incorporating non-standard amino acids that enable the application of bio-orthogonal chemistry.

Research progress and the biotechnological applications of multienzyme complex

The multienzyme complex system has become a research focus in synthetic biology due to its highly efficient overall catalytic ability and has been applied to various fields. Multienzyme complexes are formed by cascading complexes, which are multiple functionally related enzymes that continuously and efficiently catalyze the production of substrates. Compared with current mainstream microbial cell catalytic systems, in vitro multienzyme molecular machines have many advantages, such as fewer side reactions, a high product yield, a fast reaction speed, easy product separation, a tolerable toxic environment, and robust system operability, showing increasing competitiveness in the field of biomanufacturing. In this review, the research progress of multienzyme complexes in nature and multienzyme cascades in vivo or in vitro will be introduced, and the discovered enzyme cascades concerning scaffolding proteins will also be discussed. This review is expected to provide a more theoretical basis for the modification of multienzyme complexes and broaden their application in the field of synthetic biology. KEY POINTS: • The cascade reactions of some natural multienzyme complexes are reviewed. • The main approaches of constructing artificial multienzyme complexes are summarized. • The structure and application of cellulosomes are discussed and prospected.

On the relationship between structure and catalytic effectiveness in solid surface-immobilized enzymes: Advances in methodology and the quest for a single-molecule perspective

The integration of enzymes with solid materials is important in many biotechnological applications, including the use of immobilized enzymes for biocatalytic synthesis. The development of functional enzyme-material composites is restrained by the lack of molecular-level insight into the behavior of enzymes in confined, surface-near environments. Here, we review recent advances in surface-sensitive spectroscopic techniques that push boundaries for the determination of enzyme structure and orientation at the solid-liquid interface. We discuss recent evidence from single-molecule studies showing that analyses sensitive to the temporal and spatial heterogeneities in immobilized enzymes can succeed in disentangling the effects of conformational stability and active-site accessibility on activity. Different immobilization methods involve distinct trade-off between these effects, thus emphasizing the need for a holistic (systems) view of immobilized enzymes for the rational development of practical biocatalysts.

Lipolytic proteomics

Activity-based proteomics (ABP) employs small molecular probes to specifically label sets of enzymes based on their shared catalytic mechanism. Given that the vast majority of lipases belong to the family of serine hydrolases and share a nucleophilic active-site serine as part of a catalytic triad, activity-based probes are ideal tools to study lipases and lipolysis. Moreover, the ability of ABP to highlight or isolate specific subproteomes results in a massive decrease of sample complexity. Thereby, in-depth analysis of enzymes of interest with mass spectrometry becomes feasible. In this review, we cover probe design, technological developments, and applications of ABP of lipases, as well as give an overview of relevant identified proteins.

A novel and efficient method for the immobilization of thermolysin using sodium chloride salting-in and consecutive microwave irradiation

Sodium chloride salting-in and microwave irradiation were combined to drive thermolysin molecules into mesoporous support to obtain efficiently immobilized enzyme. When the concentration of sodium chloride was 3 M and microwave power was 40 W, 93.2% of the enzyme was coupled to the support by 3 min, and the maximum specific activity of the immobilized enzyme was 17,925.1 U mg(-1). This was a 4.5-fold increase in activity versus enzyme immobilized using conventional techniques, and a 1.6-fold increase versus free enzyme. Additionally, the thermal stability of the immobilized thermolysin was significantly improved. When incubated at 70°C, there was no reduction in activity by 3.5h, whereas free thermolysin lost most of its activity by 3h. Immobilization also protected the thermolysin against organic solvent denaturation. The microwave-assisted immobilization technique, combined with sodium chloride salting-in, could be applied to other sparsely soluble enzymes immobilization because of its simplicity and high efficiency.

Substrate channeling and enzyme complexes for biotechnological applications

Substrate channeling is a process of transferring the product of one enzyme to an adjacent cascade enzyme or cell without complete mixing with the bulk phase. Such phenomena can occur in vivo, in vitro, or ex vivo. Enzyme-enzyme or enzyme-cell complexes may be static or transient. In addition to enhanced reaction rates through substrate channeling in complexes, numerous potential benefits of such complexes are protection of unstable substrates, circumvention of unfavorable equilibrium and kinetics imposed, forestallment of substrate competition among different pathways, regulation of metabolic fluxes, mitigation of toxic metabolite inhibition, and so on. Here we review numerous examples of natural and synthetic complexes featuring substrate channeling. Constructing synthetic in vivo, in vitro or ex vivo complexes for substrate channeling would have great biotechnological potentials in metabolic engineering, multi-enzyme-mediated biocatalysis, and cell-free synthetic pathway biotransformation (SyPaB).

Enhancement of microwave-assisted covalent immobilization of penicillin acylase using macromolecular crowding and glycine quenching

In order to create macromolecular crowding resembling cells in mesopores and improve the covalent immobilization of penicillin acylase (PA), macromolecular reagents were covalently assembled on the walls of mesocellular silica foams (MCFs) and paralleled enzyme molecules under microwave irradiation at low temperatures. The effects of kind and content of macromolecules on immobilization and the characteristics of the immobilized enzyme were investigated carefully. The maximum specific activities of PA assembled with Dex 10 (Dextran, Mw 10000) (85.3 U/mg) and BSA (Bovine Serum Albumin) (112.7 U/mg) in MCFs under microwave irradiation were 1.73 and 1.31 times, respectively, that of PA solely immobilized by the conventional method. The optimum reaction temperature rose from 45-55 degrees C. Moreover, amino acids were used to quench excess activated groups in order to improve the thermostability of the immobilized enzyme. PA coassembled with Dex 10 in mesopores retained 88% of its initial catalytic activity after heating at 50 degrees C for 6 h, as a result of glycine quenching the excess activated groups. This biomolecule enhanced the thermostability of the enzyme preparation by 2-fold. A crowding environment resembling cells made from macromolecular reagents would be suitable for stabilizing the structure of PA and improving its catalytic activity. Glycine, a small biocompatible molecule, quenched the excess activated groups and modified the surface chemical properties of the mesoporous support, which would further favor the stability of PA at higher temperatures. Combining macromolecular crowding with glycine quenching was one of the efficient strategies adopted to improve microwave-assisted covalent PA immobilization.

Improving enzyme immobilization in mesocellular siliceous foams by microwave irradiation

Microwave irradiation was used to immobilize papain and penicillin acylase in mesocellular siliceous foams (MCFs) at low temperature. The maximum loading of papain reached 984.1 mg/g, 1.26 times that obtained using the conventional, non-microwave-assisted method. The half-life (t(0.5)) of papain immobilized in MCFs by microwave irradiation at 80 degrees C was 17 h, 5.21 times that of papain immobilized by conventional means. The activities of papain and penicillin acylase immobilized with the microwave-assisted method were 779.6 U/mg and 141.8 U/mg respectively, 1.86 and 1.39 times of those obtained without microwave immobilization. Using microwave irradiation it only took 140 s for penicillin acylase, an enzyme of large dimensions, to be immobilized in MCFs. In contrast, it took 15 h to do the same using the conventional method. The results showed that microwave irradiation improved the adsorption and immobilization of enzymes in mesocellular siliceous foams.

Determination of active enzyme concentration using activity-based probes and direct mass spectrometric readout

Activity-based probes (ABPs) are specific covalent inhibitors developed for different classes of enzymes. We have titrated a serine protease and a lipase with their specific ABPs and measured the extent of inhibition using nanoelectrospray mass spectrometry (nanoESI-MS). Because ABPs only interact with the active enzyme form, the approach allows to accurately measure the active enzyme concentration in solution. This is even possible in the presence of contaminants. The concentrations of the two enzymes were also investigated by UV spectroscopy, which appears to give higher concentrations than those measured with the active site titration method.

A rapid and direct method for the determination of active site accessibility in proteins based on ESI-MS and active site titrations

We have developed an electrospray ionisation mass spectrometry (ESI-MS) technique that can be applied to rapidly determine the number of intact active sites in proteins. The methodology relies on inhibiting the protein with an active-site irreversible inhibitor and then using ESI-MS to determine the extent of inhibition. We have applied this methodology to a test system: a serine protease, subtilisin Carlsberg, and monitored the extent of inhibition by phenylmethylsulfonyl fluoride (PMSF), an irreversible serine hydrolase inhibitor as a function of the changes in immobilisation and hydration conditions. Two types of enzyme preparation were investigated, lyophilised enzymes and protein-coated microcrystals (PCMC).

A new, mild cross-linking methodology to prepare cross-linked enzyme aggregates

Cross-linked enzyme aggregates (CLEAs) were prepared from several enzymes (penicillin G acylase, hydroxynitrile lyase, alcohol dehydrogenase, and two different nitrilases) by precipitation and subsequent cross-linking using dextran polyaldehyde. In most cases, higher immobilization yields were obtained using the latter cross-linker as compared with the commonly used glutaraldehyde. Active site titration of penicillin acylase CLEAs showed that the higher activity originated from a significantly lower loss in active sites using dextran polyaldehyde as a cross-linking agent. It is proposed that macromolecular cross-linkers are too large to penetrate the protein active site and react with catalytically essential amino acid residues.

Production of a fully functional, permuted single-chain penicillin G acylase

Penicillin G acylase (PGA) is a heterodimeric enzyme synthesized as a single-polypeptide precursor that undergoes an autocatalytic processing to remove an internal spacer peptide to produce the active enzyme. We constructed a single-chain PGA not dependent on autoproteolytic processing. The mature sequence of the beta-domain was expressed as the N terminus of a new polypeptide, connected by a random tetra-peptide to the alpha-domain, to afford a permuted protein. We found several active enzymes among variants differing in their linker peptides. Protein expression analysis showed that the functional single-chain variants were produced when using a Sec-dependent leader peptide, or when expressed inside the bacterial cytoplasm. Active-site titration experiments showed that the single-chain proteins displayed similar k(cat) values to the ones obtained with the wild-type enzyme. Interestingly, the single-chain proteins also displayed close to 100% of functional active sites compared to 40% to 70% functional yield usually obtained with the heterodimeric protein.

Preparation, optimization, and structures of cross-linked enzyme aggregates (CLEAs)

The broad applicability of the cross-linking of enzyme aggregates to the effective immobilisation of enzymes is demonstrated and the influence of many parameters on the properties of the resulting CLEAs is determined. The relative simplicity of the operation ideally lends itself to high-throughput methodologies. The aggregation method was improved up to 100% activity yield for any enzyme. For the first time, the physical structures of CLEAs are elucidated.