Click, Compute, Create: A Review of Web-based Tools for Enzyme Engineering.

Enzyme engineering, though pivotal across various biotechnological domains, is often plagued by its time-consuming and labor-intensive nature. This review aims to offer an overview of supportive in silico methodologies for this demanding endeavor. Starting from methods to predict protein structures, to classification of their activity and even the discovery of new enzymes we continue with describing tools used to increase thermostability and production yields of selected targets. Subsequently, we discuss computational methods to modulate both, the activity as well as selectivity of enzymes. Last, we present recent approaches based on cutting-edge machine learning methods to redesign enzymes. With exception of the last chapter, there is a strong focus on methods easily accessible via web-interfaces or simple Python-scripts, therefore readily useable for a diverse and broad community.

The catalytic machinery of the FAD-dependent AtBBE-like protein 15 for alcohol oxidation: Y193 and Y479 form a catalytic base, Q438 and R292 an alkoxide binding site.

Monolignol oxidoreductases are members of the berberine bridge enzyme-like (BBE-like) protein family (pfam 08031) that oxidize monolignols to the corresponding aldehydes. They are FAD-dependent enzymes that exhibit the para-cresolmethylhydroxylase-topology, also known as vanillyl oxidase-topology. Recently, we have reported the structural and biochemical characterization of two monolignol oxidoreductases from Arabidopsis thaliana, AtBBE13 and AtBBE15. Now, we have conducted a comprehensive site directed mutagenesis study for AtBBE15, to expand our understanding of the catalytic mechanism of this enzyme class. Based on the kinetic properties of active site variants and molecular dynamics simulations, we propose a refined, structure-guided reaction mechanism for the family of monolignol oxidoreductases. Here, we propose that this reaction is facilitated stepwise by the deprotonation of the allylic alcohol and a subsequent hydride transfer from the Cα-atom of the alkoxide to the flavin. We describe an excessive hydrogen bond network that enables the catalytic mechanism of the enzyme. Within this network Tyr479 and Tyr193 act concertedly as active catalytic bases to facilitate the proton abstraction. Lys436 is indirectly involved in the deprotonation as this residue determines the position of Tyr193 via a cation-π interaction. The enzyme forms a hydrophilic cavity to accommodate the alkoxide intermediate and to stabilize the transition state from the alkoxide to the aldehyde. By means of molecular dynamics simulations, we have identified two different and distinct binding modes for the substrate in the alcohol and alkoxide state. The alcohol interacts with Tyr193 and Tyr479 while Arg292, Gln438 and Tyr193 form an alkoxide binding site to accommodate this intermediate. The pH-dependency of the activity of the active site variants revealed that the integrity of the alkoxide binding site is also crucial for the fine tuning of the pKa of Tyr193 and Tyr479. Sequence alignments showed that key residues for the mechanism are highly conserved, indicating that our proposed mechanism is not only relevant for AtBBE15 but for the majority of BBE-like proteins.

Face, content, construct and concurrent validity of dry laboratory exercises for robotic training using a global assessment tool.

OBJECTIVES: To evaluate robotic dry laboratory (dry lab) exercises in terms of their face, content, construct and concurrent validities. To evaluate the applicability of the Global Evaluative Assessment of Robotic Skills (GEARS) tool to assess dry lab performance. MATERIALS AND METHODS: Participants were prospectively categorized into two groups: robotic novice (no cases as primary surgeon) and robotic expert (≥30 cases). Participants completed three virtual reality (VR) exercises using the da Vinci Skills Simulator (Intuitive Surgical, Sunnyvale, CA, USA), as well as corresponding dry lab versions of each exercise (Mimic Technologies, Seattle, WA, USA) on the da Vinci Surgical System. Simulator performance was assessed by metrics measured on the simulator. Dry lab performance was blindly video-evaluated by expert review using the six-metric GEARS tool. Participants completed a post-study questionnaire (to evaluate face and content validity). A Wilcoxon non-parametric test was used to compare performance between groups (construct validity) and Spearman's correlation coefficient was used to assess simulation to dry lab performance (concurrent validity). RESULTS: The mean number of robotic cases experienced for novices was 0 and for experts the mean (range) was 200 (30-2000) cases. Expert surgeons found the dry lab exercises both 'realistic' (median [range] score 8 [4-10] out of 10) and 'very useful' for training of residents (median [range] score 9 [5-10] out of 10). Overall, expert surgeons completed all dry lab tasks more efficiently (P < 0.001) and effectively (GEARS total score P < 0.001) than novices. In addition, experts outperformed novices in each individual GEARS metric (P < 0.001). Finally, in comparing dry lab with simulator performance, there was a moderate correlation overall (r = 0.54, P < 0.001). Most simulator metrics correlated moderately to strongly with corresponding GEARS metrics (r = 0.54, P < 0.001). CONCLUSIONS: The robotic dry lab exercises in the present study have face, content, construct and concurrent validity with the corresponding VR tasks. Until now, the assessment of dry lab exercises has been limited to basic metrics (i.e. time to completion and error avoidance). For the first time, we have shown it is feasibile to apply a global assessment tool (GEARS) to dry lab training.

Structure of the Reductase Domain of a Fungal Carboxylic Acid Reductase and Its Substrate Scope in Thioester and Aldehyde Reduction.

The synthesis of aldehydes from carboxylic acids has long been a challenge in chemistry. In contrast to the harsh chemically driven reduction, enzymes such as carboxylic acid reductases (CARs) are considered appealing biocatalysts for aldehyde production. Although structures of single- and didomains of microbial CARs have been reported, to date no full-length protein structure has been elucidated. In this study, we aimed to obtain structural and functional information regarding the reductase (R) domain of a CAR from the fungus Neurospora crassa (Nc). The NcCAR R-domain revealed activity for N-acetylcysteamine thioester (S-(2-acetamidoethyl) benzothioate), which mimics the phosphopantetheinylacyl-intermediate and can be anticipated as the minimal substrate for thioester reduction by CARs. The determined crystal structure of the NcCAR R-domain reveals a tunnel that putatively harbors the phosphopantetheinylacyl-intermediate, which is in good agreement with docking experiments performed with the minimal substrate. In vitro studies were performed with this highly purified R-domain and NADPH, demonstrating carbonyl reduction activity. The R-domain was able to accept not only a simple aromatic ketone but also benzaldehyde and octanal, which are typically considered to be the final product of carboxylic acid reduction by CAR. Also, the full-length NcCAR reduced aldehydes to primary alcohols. In conclusion, aldehyde overreduction can no longer be attributed exclusively to the host background.