Characterisation of CYP102A25 from Bacillus marmarensis and CYP102A26 from Pontibacillus halophilus: P450 Homologues of BM3 with Preference towards Hydroxylation of Medium‐Chain Fatty Acids

Cytochrome P450 monooxygenases are highly desired biocatalysts owing to their ability to catalyse a wide variety of chemically challenging C?H activation reactions. The CYP102A subfamily of enzymes are natural catalytically self‐sufficient proteins consisting of a haem and FMN‐FAD reductase domain fused in a single‐component system. They catalyse the oxygenation of saturated and unsaturated fatty acids to produce primarily ω?1, ω?2 and ω?3 hydroxy acids. These monooxygenases have potential applications in biotechnology; however, their substrate range is still limited and there is a continued need to add diversity to this class of biocatalysts. Herein, we present the characterisation of two new members of this class of enzymes, CYP102A25 (BMar) from Bacillus marmarensis and CYP102A26 (PHal) from Pontibacillus halophilus, both of which express readily in a recombinant bacterial host. BMar exhibits the highest activity toward myristic acid and shows moderate activity towards unsaturated fatty acids. PHal exhibits broader activity towards mid‐chain‐saturated (C₁₄–C₁₈) and unsaturated fatty acids. Furthermore, PHal shows good regioselectivity for the hydroxylation of myristic acid, targeting the ω?2 position for C?H activation.     

Decoupled Roles for the Atypical,Bifurcated Binding Pocket of the ybfF Hydrolase

Serine hydrolases have diverse intracellular substrates, biological functions, and structural plasticity, and are thus important for biocatalyst design. Amongst serine hydrolases, the recently described ybfF enzyme family are promising novel biocatalysts with an unusual bifurcated substrate‐binding cleft and the ability to recognize commercially relevant substrates. We characterized in detail the substrate selectivity of a novel ybfF enzyme from Vibrio cholerae (Vc‐ybfF) by using a 21‐member library of fluorogenic ester substrates. We assigned the roles of the two substrate‐binding clefts in controlling the substrate selectivity and folded stability of Vc‐ybfF by comprehensive substitution analysis. The overall substrate preference of Vc‐ybfF was for short polar chains, but it retained significant activity with a range of cyclic and extended esters. This broad substrate specificity combined with the substitutional analysis demonstrates that the larger binding cleft controls the substrate specificity of Vc‐ybfF. Key selectivity residues (Tyr116, Arg120, Tyr209) are also located at the larger binding pocket and control the substrate specificity profile. In the structure of ybfF the narrower binding cleft contains water molecules prepositioned for hydrolysis, but based on substitution this cleft showed only minimal contribution to catalysis. Instead, the residues surrounding the narrow binding cleft and at the entrance to the binding pocket contributed significantly to the folded stability of Vc‐ybfF. The relative contributions of each cleft of the binding pocket to the catalytic activity and folded stability of Vc‐ybfF provide a valuable map for designing future biocatalysts based on the ybfF scaffold.     

Modular biocatalysts

Modularity is a highly sought after feature in engineering design. A modular catalyst is a multi‐component system whose parts can be predictably interchanged for functional flexibility and variety. Over the past two decades, much of the research in our laboratory has focused on understanding the modularity of a class of multifunctional enzymes called polyketide synthases (PKSs). PKSs catalyze the biosynthesis of a broad range of complex natural products in microorganisms, including many well‐known and emerging antibiotics. A better understanding of the fundamental principles governing their modular chemistry promises to create powerful opportunities for engineering new medicines, and may even open the door to radically new catalytic processes for functionally dense, chiral synthons. © 2009 American Institute of Chemical Engineers AIChE J, 2009     

Effect of a double‐structured microporous polymer support on the catalytic activity,stability and aggregation behavior of immobilized enzymes

A double‐structured microporous polymer composite support consisting of a microporous skeleton for protection of immobilized enzymes and a gel‐like polymer bearing different functionalities has been synthesized for immobilization of various enzymes. Among three approaches based on two types of interactions (physical and chemical), we found that under our experimental conditions the covalent bonding between amine moieties of enzymes and epoxide groups of the support was the best, with enzyme leaching being reduced to as low as zero for nine enzymes and catalytic activities increased by factors of 1–4 for two lipases. The improvement in catalytic activity could be attributed to the amphiphilic soft gel which might create a kind of lipid–water interface or microenvironment in aqueous solution, favoring the interfacial activation of certain lipases. Furthermore, the thermal and operational stability, and reusability of all the enzymes could be enhanced to varying degrees. We also found that enzyme aggregates of different sizes could be formed on the spherical support surface at quite low enzyme concentrations, which might also influence the final catalytic activities of the immobilized enzymes. © 2015 Society of Chemical Industry     

Vypal2: A Versatile Peptide Ligase for Precision Tailoring of Proteins

The last two decades have seen an increasing demand for new protein-modification methods from the biotech industry and biomedical research communities. Owing to their mild aqueous reaction conditions, enzymatic methods based on the use of peptide ligases are particularly desirable. In this regard, the recently discovered peptidyl Asx-specific ligases (PALs) have emerged as powerful biotechnological tools in recent years. However, as a new class of peptide ligases, their scope and application remain underexplored. Herein, we report the use of a new PAL, VyPAL2, for a diverse range of protein modifications. We successfully showed that VyPAL2 was an efficient biocatalyst for protein labelling, inter-protein ligation, and protein cyclization. The labelled or cyclized protein ligands remained functionally active in binding to their target receptors. We also demonstrated on-cell labelling of protein ligands pre-bound to cellular receptors and cell-surface engineering via modifying a covalently anchored peptide substrate pre-installed on cell-surface glycans. Together, these examples firmly establish Asx-specific ligases, such as VyPAL2, as the biocatalysts of the future for site-specific protein modification, with a myriad of applications in basic research and drug discovery.     

Multifunctional Poly‐N‐Isopropylacrylamide/DNAzyme Microgels as Highly Efficient and Recyclable Catalysts for Biosensing

The development of highly efficient, recyclable, and multifunctional biocatalysts is of great importance for various applications, especially in biosensing. In this study, highly catalytic and recyclable DNAzyme functionalized poly‐N‐isopropylacrylamide (pNIPAM) microgels are prepared via one‐step precipitation polymerization. The pNIPAM/DNAzyme microgels exhibit highly catalytic activities in aqueous solution at room temperature, and become hydrophobic and separable from the reaction mixture at temperature higher than the lower critical solution temperature of pNIPAM, which facilitate the recyclable utilization of these catalysts. Different kinds of DNAzyme functionalized catalytic microgels can be facilely prepared via the one‐step synthesis procedure. Two typical catalytic DNA structures, the Mg²⁺‐dependent DNAzyme and the hemin‐G‐quadruplex horseradish peroxidase (HRP)‐mimicking DNAzyme, are chosen as model systems to validate the feasibility. These pNIPAM/DNAzyme microgel catalysts maintain 80% to 91% initial catalytic activity after eight times of catalysis recycling. Furthermore, the pNIPAM microgels by themselves provide additional interfaces to capturing an enzyme, glucose oxidase, which can cascade with the linked HRP mimicking DNAzymes, to form recyclable bi‐enzyme cascading system for the sensing of glucose.     

Surface‐Layer Lattices as Patterning Element for Multimeric Extremozymes

A promising new approach for the production of biocatalysts comprises the use of surface‐layer (S‐layer) lattices that present functional multimeric enzymes on their surface, thereby guaranteeing most accurate spatial distribution and orientation, as well as maximal effectiveness and stability of these enzymes. For proof of concept, a tetrameric and a trimeric extremozyme are chosen for the construction of S‐layer/extremozyme fusion proteins. By using a flexible peptide linker, either one monomer of the tetrameric xylose isomerase XylA from the thermophilic Thermoanaerobacterium strain JW/SL‐YS 489 or, in another approach, one monomer of the trimeric carbonic anhydrase from the methanogenic archaeon Methanosarcina thermophila are genetically linked to one monomer of the S‐layer protein SbpA of Lysinibacillus sphaericus CCM 2177. After isolation and purification, the self‐assembly properties of both S‐layer fusion proteins as well as the specific activity of the fused enzymes are confirmed, thus indicating that the S‐layer protein moiety does not influence the nature of the multimeric enzymes and vice versa. By recrystallization of the S‐layer/extremozyme fusion proteins on solid supports, the active enzyme multimers are exposed on the surface of the square S‐layer lattice with 13.1 nm spacing.