Bettina Bommarius

Bettina Bommarius
Georgia Institute of Technology | GT · School of Chemical & Biomolecular Engineering

PhD

About

49
Publications
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1,939
Citations

Publications

Publications (49)
Article
Despite the benefits of aqueous two-phase extraction (ATPE) for purification of high-value biomolecules, phase-formers that are used to generate the aqueous two-phase system (ATPS) often reduce the stability and solubility of the biomolecule. Within this work, we thus evaluated the use of suitable excipients to increase the biomolecule stability an...
Article
Enzymes used as biocatalysts in evolving green processes have already reached industrial competitiveness to classical chemical catalysts. After production of these enzymes, aqueous two-phase extraction using an aqueous two-phase system (ATPS) has been shown a promising and sustainable alternative to common cost-intense chromatographic purification....
Article
We investigate in detail both the deracemization reaction rate and maximum conversion of (R,S)-1-phenylethanol in a bubble column and the deactivation rates of both enzymes involved, alcohol dehydrogenase (ADH) and NADH oxidase (nox2). Instead of the predicted ellipsoidal shape of the bubbles, we observe a spherical shape in all our experiments. Ca...
Article
Full-text available
Widespread testing for the presence of the novel coronavirus SARS-CoV-2 in individuals remains vital for controlling the COVID-19 pandemic prior to the advent of an effective treatment. Challenges in testing can be traced to an initial shortage of supplies, expertise and/or instrumentation necessary to detect the virus by quantitative reverse trans...
Article
A continuous flow packed bed reactor system was developed for the asymmetric reductive amination of 5-methyl-2-hexanone with a chimeric amine dehydrogenase (AmDH) and the formate dehydrogenase (FDH) from Candida boidinii. Both enzymes were co-immobilized onto the Nuvia® IMAC resin from Bio-Rad which employs the well-established binding chemistry be...
Preprint
Full-text available
Widespread testing for the presence novel coronavirus SARS-CoV-2 in patients remains vital for controlling the COVID-19 pandemic prior to the advent of an effective treatment. The early testing shortfall in some parts of the US can be traced to an initial shortage of supplies, expertise and/or instrumentation necessary to detect the virus by quanti...
Article
Full-text available
Immobilization of enzymes provides many benefits, including facile separation and recovery of enzymes from reaction mixtures, enhanced stability, and co‐localization of multiple enzymes. Calcium‐phosphate‐protein supraparticles imbued with a leucine zipper binding domain (ZR) serve as a modular immobilization platform for enzymes fused to the compl...
Article
Full-text available
Amine dehydrogenases (AmDHs) catalyze the enzymatic reduction of ketones to amines, serving as a suitable biocatalytic route for amine synthesis. A limited number of experimentally validated native AmDHs (nat‐AmDHs) have been reported recently, expanding the sequences with this function to complement the small set of engineered enzymes. Since resea...
Article
Full-text available
FOx News: Formate oxidase from Aspergillus oryzae (AoFOx) also oxidises methanol and formaldehyde producing one equivalent of H2O2 in each oxidation step. Thus, AoFOx is a promising catalyst for the in situ generation of H2O2 to drive peroxygenase‐catalysed oxyfunctionalisation reactions. The preparative usefulness of AoFOx is demonstrated in combi...
Article
Full-text available
Mutations were introduced into the leucine amine dehydrogenase (L‐AmDH) derived from G. stearothermophilus leucine dehydrogenase (LeuDH) with the goals of increased activity and expanded substrate acceptance. A triple variant (L‐AmDH‐TV) including D32A, F101S, and C290V showed an average of 2.5‐fold higher activity toward aliphatic ketones and an 8...
Article
Obverse Cover: The cover image is based on the Research Article The Short‐chain Dehydrogenase/Reductase Engineering Database (SDRED): A classification and analysis system for a highly diverse enzyme family by Maike Gräff et al., DOI: 10.1002/prot.25694.
Article
The inside cover picture, provided by Andreas Bommarius, John Woodley, and co‐workers, illustrates how oxygen transfer into an enzyme‐containing solution and enzyme stability are often at odds with each other. A vigorously sparged and stirred tank is best for oxygen transfer but worst for enzyme stability, while a quiescent solution shows the oppos...
Article
Full-text available
An increasing number of biocatalytic oxidation reactions rely on H2O2 as clean oxidant. The poor robustness of most enzymes towards H2O2, however, necessitates more efficient in situ H2O2 generation systems. In analogy to the well‐known formate dehydrogenase to promote NADH‐dependent reactions, we here propose employing formate oxidase (FOx) to pro...
Article
Full-text available
An increasing number of biocatalytic oxidation reactions rely on H2O2 as a clean oxidant. The poor robustness of most enzymes towards H2O2, however, necessitates more efficient systems for in situ H2O2 generation. In analogy to the well‐known formate dehydrogenase to promote NADH‐dependent reactions, we here propose employing formate oxidase (FOx)...
Article
Full-text available
The E-factor has become an important measure for the environmental impact of (bio)chemical reactions. However, summing up the obvious wastes generated in the laboratory neglects energy-related wastes (mostly greenhouse gases) which are generated elsewhere. To estimate these wastes, we propose to extend the E-factor by an energy-term (E⁺-factor). At...
Article
Full-text available
One of the major drawbacks for many biocatalysts is their poor stability under industrial process conditions. A particularly interesting example is the supply of oxygen to biooxidation reactions, catalyzed by oxidases, oxygenases or alcohol dehydrogenases coupled with NAD(P)H (reduced nicotinamide adenine dinucleotide phosphate) oxidases, which all...
Article
The Short‐chain Dehydrogenases/Reductases Engineering Database (SDRED) covers one of the largest known protein families (168,150 proteins). Assignment to the superfamilies of Classical and Extended SDRs was achieved by global sequence similarity and by identification of family‐specific sequence motifs. Two standard numbering schemes were establishe...
Chapter
Protein engineering reflects the active design of protein properties by changing its amino acid sequence. This goal can be approached via rational design, combinatorial design, or a combination, termed data-driven protein engineering. Among the two principal strategies of tackling the huge size of protein sequence space, this chapter focuses on res...
Article
Full-text available
Tuberculosis (TB) is a major public health concern worldwide with over 2 billion people currently infected. The rise of strains of Mycobacterium tuberculosis (Mtb) that are resistant to some or all first and second line antibiotics, including multidrug-resistant (MDR), extensively drug resistant (XDR) and totally drug resistant (TDR) strains, is of...
Conference Paper
The novel amine dehydrogenase (AmDH) has been recently developed1 and further characterized. Through protein engineering of the amino acid dehydrogenase scaffold, the amine dehydrogenase now catalyzes the reduction of prochiral ketones to chiral amines. Further protein engineering to the phenylalanine amine dehydrogenase (F-AmDH) to expand the bind...
Conference Paper
We have recently developed several amine dehydrogenases (AmDHs) that are of interest for production of enantiomerically pure amines as precursors for active pharmaceutical ingredients (Abrahamson et al. 2012 and 2013, Bommarius B et al, submitted). Their potential as synthetically interesting enzymes led us to develop a scalable, cost-effective pil...
Article
A novel amine dehydrogenase, “F-AmDH”, catalyzes the reversible reduction of prochiral ketones to chiral amines. However, many targeted hydrophobic substrates of F-AmDH show little to no solubility in an aqueous medium. The introduction of water-miscible organic solvents was unsuccessful because of AmDH deactivation. In a biphasic aqueous–organic s...
Article
We created a novel chimeric amine dehydrogenase (AmDH) via domain shuffling of two parent AmDHs (‘L- and F-AmDH’), which in turn had been generated from leucine and phenylalanine DH, respectively. Unlike the parent proteins, the chimeric AmDH (‘cFL-AmDH’) catalyzes the amination of acetophenone to (R)-methylbenzylamine and adamantly-methylketone to...
Patent
Full-text available
Non-naturally occurring amine dehydrogenases (AmDH) and methods of use thereof the produce chiral amines are disclosed. The AmDH are variants of amino acid dehydrogenases. AmDH based on phenylalanine, leucine, and valine scaffolds are provided. The AmDH typically have one, two, three, four, or more amino acid alterations relative to the scaffold. T...
Article
Recently, we obtained the first amine dehydrogenases, termed L‐AmDH and F‐AmDH, from leucine DH [1] and phenylalanine DH [2], respectively, allowing direct reductive amination of ketones to chiral amines. Starting from a scaffold devoid of such activity, a robust AmDH has been evolved with a single two‐site library allowing for the direct productio...
Article
Fluorescence microscopy is a widely used non-invasive tool for investigating intracellular structure and processes. Although the palette of fluorescent proteins has revolutionized detection and dynamics in molecular and cellular biology, the limited brightness, low spectral discrimination, and high cellular autofluorescence continue to limit applic...
Conference Paper
The cellulose-binding domain (CBD) has long been recognized as a key moiety in cellulolytic enzymes to bring the full-length enzyme to a close proximity of the cellulose substrate. As one of the most efficient exoglucanases, T. reesei Cel7A has attracted enormous interest. The cellulose-binding domain of Cel7A has been reported to be capable of dec...
Conference Paper
To produce biofuels from cellulosic materials, the materials are pretreated and then subsequently hydrolyzed with cellulolytic enzymes for conversion to simple fermentable sugars. However, due to its partially crystalline structure, the complete hydrolysis of cellulose often requires a prohibitively large quantity of hydrolytic enzymes, which is on...
Conference Paper
The reductive amination of ketones to produce chiral amines is an important transformation in the production of pharmaceutical intermediates. Recently, we obtained the first amine dehydrogenases (L-AmDH) from a leucine dehydrogenase [1] and from phenylalanine dehydrogenase (F-AmDH).[2] Here, we report on successful domain shuffling efforts to creat...
Conference Paper
Title: Development of a Biphasic Organic Solvent System to Broaden the Substrate Range of the Phenylalanine Amine Dehydrogenase Authors: Samantha K. Au, Bettina Bommarius, Andreas Bommarius The novel enzyme amine dehydrogenase (AmDH) derived through introduction of mutations to the phenylalanine dehydrogenase gene and thus termed F-AmDH, cataly...
Article
Blue fluorescent proteins (BFPs) offer visualization of protein location and behavior, but often suffer from high autofluorescent background and poor signal discrimination. Through dual-laser excitation of bright and photoinduced dark states, mutations to the residues surrounding the BFP chromophore enable long-wavelength optical modulation of BFP...
Patent
The present disclosure relates generally to bacterial NADH oxidases and, more particularly, to novel NADH oxidases obtained from Lactobacillus plantarum, and derivatives thereof that demonstrate enzymatic activity for NADH, NADPH, or both NADH and NADPH. The compositions comprising an NADH oxidase obtained from L. plantarum or derivatives thereof i...
Article
Full-text available
Enteropathogenic Escherichia coli (EPEC), enterohemorrhagic E. coli (EHEC) and enteroaggregative E. coli (EAEC) are intestinal pathogens that cause food and water-borne disease in humans. Using biochemical methods and NMR-based comparative metabolomics in conjunction with the nematode Caenorhabditis elegans, we developed a bioassay to identify secr...
Data
Structures of natural and commercially available synthetic indole derivatives used for structure-activity profile. (TIF)
Data
Identification of indole as an E. coli toxin. (a) Survival curves of C. elegans N2 and various mutants upon exposure to 3.5 mM indole in agar plates. Similar results were obtained upon exposure of C. elegans in broth. No adjustment for strain differences was made to these data. (b) E. coli strains kill C. elegans. C. elegans N2 animals were exposed...
Data
(a) Western analysis of Tir expression in EPEC treated with low concentrations of indole, ICA or IAA. Note that indole and ICA induce Tir expression at low concentrations, but all three compounds (indole, ICA and IAA) suppress Ler and Tir at high concentrations. The band recognized by the DnaK pAb served as a loading control. (b) Growth curves of E...
Data
(a) Overlay of UV-HPLC chromatograms (absorption at 260 nm) of the EPEC and EPECΔtnaA extracts as well as of synthetic standards of ICOOH, ICA, IAA, and indole, obtained using a reverse phase HPLC column. Effects of indole derivatives on C. elegans and on infection of mammalian cells. (b) Neither ICA, nor IAA, nor ICOOH alone at the indicated conce...
Article
Cationic antimicrobial host defense peptides (HDPs) combat infection by directly killing a wide variety of microbes, and/or modulating host immunity. HDPs have great therapeutic potential against antibiotic-resistant bacteria, viruses and even parasites, but there are substantial roadblocks to their therapeutic application. High manufacturing costs...
Article
The concept of using antimicrobial peptides (AMPs) and host defense peptides (HDPs) as therapeutics was first introduced in the late 1990s. However, an AMP drug has yet to reach the market. AMPs and HDPs have intriguing potential as therapeutics: the peptides are evolutionary conserved, and are critical components of the innate immune system of all...
Article
Full-text available
Enteropathogenic Escherichia coli, enterohemorrhagic E. coli, and Citrobacter rodentium are classified as attaching and effacing pathogens based on their ability to adhere to intestinal epithelium via actin-filled membranous protrusions (pedestals). Infection of mice with C. rodentium causes breach of the colonic epithelial barrier, a vigorous Th1...
Article
Enteropathogenic Escherichia coli (EPEC) cause intestinal inflammation, severe diarrhoea and mortality, particularly among children in developing nations. Upon attachment to intestinal epithelial cells, EPEC induces actin-filled membrane protrusions called 'pedestals' and disrupts microvilli to form attaching and effacing (A/E) lesions. EPEC also d...
Article
Full-text available
The Poxviridae family members vaccinia and variola virus enter mammalian cells, replicate outside the nucleus and produce virions that travel to the cell surface along microtubules, fuse with the plasma membrane and egress from infected cells toward apposing cells on actin-filled membranous protrusions. We show that cell-associated enveloped virion...
Article
Full-text available
Enteropathogenic Escherichia coli (EPEC) are deadly contaminants in water and food and induce protrusion of actin-rich membrane pedestals beneath themselves upon attachment to intestinal epithelia. EPEC then causes intestinal inflammation, diarrhea, and, among children, death. Here, we show that EPEC uses multiple tyrosine kinases for formation of...
Article
Reactive oxygen species (ROS) appear to play an important role in regulating growth and survival of prostate cancer. However, the sources for ROS production in prostate cancer cells have not been determined. We report that ROS are generated by intact American Type Culture Collection DU 145 cells and by their membranes through a mechanism blocked by...

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