Annotation of metabolites remains a major challenge in liquid chromatography–mass spectrometry (LC–MS) based untargeted metabolomics. The current gold standard for metabolite identification is to match the detected feature with an authentic analyzed on same equipment and using method as experimental samples. However, there are substantial practical challenges applying this approach large data sets. One widely used annotation search spectral libraries reference databases matching metabolites;...

Abstract Motivation While traditionally utilized for identifying site-specific metabolic activity within a compound to alter its interaction with metabolizing enzyme, predicting the site-of-metabolism (SOM) is essential in analyzing promiscuity of enzymes on substrates. The successful prediction SOMs and relevant promiscuous products has wide range applications that include creating extended models (EMMs) account enzyme construction novel heterologous synthesis pathways. There therefore need...

Lactiplantibacillus plantarum is known to utilize exogenous small molecule quinone mediators perform extracellular electron transfer (EET), allowing it produce a detectable current in bioelectrochemical system (BES). Utilization of by L. requires type-II NADH dehydrogenase (Ndh2); however, structural variations the core 1,4-naphthoquinone EET have shown yield significantly different outputs. Herein, we assembled library 40 quinone-based probe important physicochemical properties and...

Abstract Lactiplantibacillus plantarum is known to utilize exogenous small molecule quinone mediators perform extracellular electron transfer (EET), allowing it produce a detectable current in bioelectrochemical system (BES). Utilization of by L. requires type‐II NADH dehydrogenase (Ndh2); however, structural variations the core 1,4‐naphthoquinone EET have shown yield significantly different outputs. Herein, we assembled library 40 quinone‐based probe important physicochemical properties and...

Metabolic models are indispensable in guiding cellular engineering and advancing our understanding of systems biology. As not all enzymatic activities fully known and/or annotated, metabolic remain incomplete, resulting suboptimal computational analysis leading to unexpected experimental results. We posit that one major source unaccounted metabolism is promiscuous activity. It now well-accepted most, if all, enzymes promiscuous-i.e., they transform substrates other than their primary...

Lactiplantibacillus plantarum is known to utilize exogenous small molecule quinone mediators perform extracellular electron transfer (EET), which allows it produce a detectable current in bioelectrochemical system. Utilization of by L. requires type-II NADH dehydrogenase (Ndh2), however structural variations the core 1,4-naphthoquinone EET yields significantly different outputs. Herein, we assembled library 30 naphthoquinone-based order probe important physicochemical properties and...

Increasing understanding of metabolic and regulatory networks underlying microbial physiology has enabled creation progressively more complex synthetic biological systems for biochemical, biomedical, agricultural, environmental applications. However, despite best efforts, confounding phenotypes still emerge from unforeseen interplay between parts, the design robust modular remains elusive. Such interactions are difficult to predict when designing may manifest during experimental testing as...

Abstract Biological engineering aims to enhance biological systems by designing proteins with improved catalytic properties or ligands enhanced function. Typically, applications permit proteins, e.g., an enzyme in a biodegradation reaction, drug for target receptor, but not both. Yet, some can benefit from more flexible approach where both the protein and ligand be designed modified together desired property. To meet need this co-design capability, we introduce novel paradigm demon- strate...

Reduction/Oxidation (redox) potential of small organic compounds is a key property that drives innumerable chemical and biological electron transfer reactions. However, experimental measurement redox time-consuming expensive, yielding few measured datasets. Computational methods have previously been applied to create predictors applicable only specific dataset. In this work, we investigate the effectiveness various descriptors, including structural functional properties, molecular energies,...

Lactiplantibacillus plantarum is known to utilize exogenous small molecule quinone mediators perform extracellular electron transfer (EET), allowing it produce a detectable current in bioelectrochemical system (BES). Utilization of by L. requires type-II NADH dehydrogenase (Ndh2), however structural variations the core 1,4-naphthoquinone EET has shown yield significantly different outputs. Herein, we assembled library 40 quinone-based probe important physicochemical properties and...

Metabolomics-based studies have provided critical insights across many applications and now offer researchers an opportunity to collect information about thousands of small molecules in-bulk through untargeted metabolomics. However, taking advantage this new development requires accurate identification metabolites their biological significance in a given sample, which unfortunately remains difficult. Pathway enrichment is powerful method that can aid addressing those tasks, but existing...

Abstract Background Increasing understanding of metabolic and regulatory networks underlying microbial physiology has enabled creation progressively more complex synthetic biological systems for biochemical, biomedical, agricultural, environmental applications. However, despite best efforts, confounding phenotypes still emerge from unforeseen interplay between parts, the design robust modular remains elusive. Such interactions are difficult to predict when designing may manifest during...