A method for the systematic selection of enzyme panel candidates by solving the maximum diversity problem

Enzymes are being increasingly exploited for their potential as industrial biocatalysts. Establishing a portfolio of useful biocatalysts from large and diverse protein family is challenging and a systematic method for candidate selection promises to aid in this task. Moreover, accurate enzyme functional annotation can only be confidently guaranteed through experimental characterisation in the laboratory. The selection of catalytically diverse enzyme panels for experimental characterisation is also an important step for shedding light on the currently unannotated proteins in enzyme families. Current selection methods often lack efficiency and scalability, and are usually non-systematic. We present a novel algorithm for the automatic selection of subsets from enzyme families. A tabu search algorithm solving the maximum diversity problem for sequence identity was designed and implemented, and applied to three diverse enzyme families. We show that this approach automatically selects panels of enzymes that contain high richness and relative abundance of the known catalytic functions, and outperforms other methods such as k-medoids.

Regioselective Radical Alkylation of Arenes Using Evolved Photoenzymes

Substituted arenes are ubiquitous in molecules with medicinal functions, making their synthesis a critical consideration when designing synthetic routes. ^1,2 Regioselective C-H functionalization reactions are attractive for preparing alkylated arenes, ^3-5 however, the selectivity of existing methods is modest and primarily governed by substrate electronic properties. ^6,7 Here, we demonstrate a biocatalyst-controlled method for the regioselective alkylation of electron-rich and electron-deficient heteroarenes. Starting from an unselective 'ene'-reductase (ERED) (GluER-T36A), we evolved a variant that selectively alkylates the C4 position of indole, an elusive position using prior technologies. Mechanistic studies across the evolutionary series indicate that changes to the protein active site alter the electronic character of the charge transfer (CT) complex responsible for radical formation. This resulted in a variant with a significant degree of ground state change transfer in the CT complex. Mechanistic studies on a C2 selective ERED suggest that the evolution of GluER-T36A helps disfavor a competing mechanistic pathway. Additional protein engineering campaigns were carried out for a C8 selective quinoline alkylation. This study highlights the opportunity to use enzymes for regioselective reactions where small molecule catalysts struggle to alter selectivity.

Cascade enzymatic synthesis of l-homoserine – mathematical modelling as a tool for process optimisation and design

Mathematical modelling enabled cascade reaction optimisation; 100% increase in product concentration and 18% increase in volume productivity compared to previous work.

nanoDSF as screening tool for enzyme libraries and biotechnology development

Enzymes are attractive tools for synthetic applications. To be viable for industrial use, enzymes need sufficient stability towards the desired reaction conditions such as high substrate and cosolvent concentration, non-neutral pH and elevated temperatures. Thermal stability is an attractive feature not only because it allows for protein purification by thermal treatment and higher process temperatures but also due to the associated higher stability against other destabilising factors. Therefore, high-throughput screening (HTS) methods are desirable for the identification of thermostable biocatalysts by discovery from nature or by protein engineering but current methods have low throughput and require time-demanding purification of protein samples. We found that nanoscale differential scanning fluorimetry (nanoDSF) is a valuable tool to rapidly and reliably determine melting points of native proteins. To avoid intrinsic problems posed by crude protein extracts, hypotonic extraction of overexpressed protein from bacterial host cells resulted in higher sample quality and accurate manual determination of several hundred melting temperatures per day. We have probed the use of nanoDSF for HTS of a phylogenetically diverse aldolase library to identify novel thermostable enzymes from metagenomic sources and for the rapid measurements of variants from saturation mutagenesis. The feasibility of nanoDSF for the screening of synthetic reaction conditions was proved by studies of cosolvent tolerance, which showed protein melting temperature to decrease linearly with increasing cosolvent concentration for all combinations of six enzymes and eight water-miscible cosolvents investigated, and of substrate affinity, which showed stabilisation of hexokinase by sugars in the absence of ATP cofactor. ENZYMES: Alcohol dehydrogenase (NADP⁺ ) (EC 1.1.1.2), transketolase (EC 2.2.1.1), hexokinase (EC 2.7.1.1), 2-deoxyribose-5-phosphate aldolase (EC 4.1.2.4), fructose-6-phosphate aldolase (EC 4.1.2.n).

A community based programme to improve access to dental services for drug users

In 1999 South Lancashire Health Authority published their Oral Health Improvement Plan in which they specifically identified drug users as a target group. In this paper the authors outline the development of a project, which aimed to improve access to dental services for this group. Essential to the relative success of the project was the inclusion of drug users and service providers at the outset. In addition perceived barriers, which exist between drug users and the profession have started to be broken down.