Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Hydrocarbon Synthesis via Photoenzymatic Decarboxylation of Carboxylic Acids
Zhang, Wuyuan ; Ma, Ming ; Huijbers, Mieke M.E. ; Filonenko, Georgy A. ; Pidko, Evgeny A. ; Schie, Morten van; Boer, Sabrina de; Burek, Bastien O. ; Bloh, Jonathan Z. ; Berkel, Willem J.H. van; Smith, Wilson A. ; Hollmann, Frank - \ 2019
Journal of the American Chemical Society 141 (2019)7. - ISSN 0002-7863 - p. 3116 - 3120.

A recently discovered photodecarboxylase from Chlorella variabilis NC64A ( CvFAP) bears the promise for the efficient and selective synthesis of hydrocarbons from carboxylic acids. CvFAP, however, exhibits a clear preference for long-chain fatty acids thereby limiting its broad applicability. In this contribution, we demonstrate that the decoy molecule approach enables conversion of a broad range of carboxylic acids by filling up the vacant substrate access channel of the photodecarboxylase. These results not only demonstrate a practical application of a unique, photoactivated enzyme but also pave the way to selective production of short-chain alkanes from waste carboxylic acids under mild reaction conditions.

Photoenzymatic epoxidation of styrenes
Schie, Morten M.C.H. Van; Paul, Caroline E. ; Arends, Isabel W.C.E. ; Hollmann, Frank - \ 2019
Chemical Communications 55 (2019)12. - ISSN 1359-7345 - p. 1790 - 1792.

Two-component-diffusible-flavomonooxygenases are versatile biocatalysts for selective epoxidation-, hydroxylation- or halogenation reactions. Their complicated molecular architecture can be simplified using photochemical regeneration of the catalytically active, reduced FADH 2 prosthetic group. In this contribution we provide the proof-of-concept and characterization for the direct regeneration of the styrene monooxygenase from Pseudomonas.

Straightforward Regeneration of Reduced Flavin Adenine Dinucleotide Required for Enzymatic Tryptophan Halogenation
Ismail, Mohamed ; Schroeder, Lea ; Frese, Marcel ; Kottke, Tilman ; Hollmann, Frank ; Paul, Caroline E. ; Sewald, Norbert - \ 2019
ACS Catalysis 9 (2019)2. - ISSN 2155-5435 - p. 1389 - 1395.
enzymatic cofactor regeneration - FADH - flavin-dependent halogenases - hydride transfer - NADH mimics - regioselective chlorination

Flavin-dependent halogenases are known to regioselectively introduce halide substituents into aromatic moieties, for example, the indole ring of tryptophan. The process requires halide salts and oxygen instead of molecular halogen in the chemical halogenation. However, the reduced cofactor flavin adenine dinucleotide (FADH2) has to be regenerated using a flavin reductase. Consequently, coupled biocatalytic steps are usually applied for cofactor regeneration. Nicotinamide adenine dinucleotide (NADH) mimics can be employed stoichiometrically to replace enzymatic cofactor regeneration in biocatalytic halogenation. Chlorination of l-tryptophan is successfully performed using such NADH mimics. The efficiency of this approach has been compared to the previously established enzymatic regeneration system using the two auxiliary enzymes flavin reductase (PrnF) and alcohol dehydrogenase (ADH). The reaction rates of some of the tested mimics were found to exceed that of the enzymatic system. Continuous enzymatic halogenation reaction for reaction scale-up is also possible.

Biocatalytic C=C Bond Reduction through Carbon Nanodot-Sensitized Regeneration of NADH Analogues
Kim, Jinhyun ; Lee, Sahng Ha ; Tieves, Florian ; Choi, Da Som ; Hollmann, Frank ; Paul, Caroline E. ; Park, Chan Beum - \ 2018
Angewandte Chemie-International Edition 57 (2018)42. - ISSN 1433-7851 - p. 13825 - 13828.
alkene hydrogenation - asymmetric catalysis - carbon nanodot - NADH analogues - photobiocatalysis

Light-driven activation of redox enzymes is an emerging route for sustainable chemical synthesis. Among redox enzymes, the family of Old Yellow Enzyme (OYE) dependent on the nicotinamide adenine dinucleotide cofactor (NADH) catalyzes the stereoselective reduction of α,β-unsaturated hydrocarbons. Here, we report OYE-catalyzed asymmetric hydrogenation through light-driven regeneration of NADH and its analogues (mNADHs) by N-doped carbon nanodots (N-CDs), a zero-dimensional photocatalyst. Our spectroscopic and photoelectrochemical analyses verified the transfer of photo-induced electrons from N-CDs to an organometallic electron mediator (M) for highly regioselective regeneration of cofactors. Light triggered the reduction of NAD+ and mNAD+s with the cooperation of N-CDs and M, and the reduction behaviors of cofactors were dependent on their own reduction peak potentials. The regenerated cofactors subsequently delivered hydrides to OYE for stereoselective conversions of a broad range of substrates with excellent biocatalytic efficiencies.

Deazaflavins as photocatalysts for the direct reductive regeneration of flavoenzymes
Schie, M.M.C.H. van; Younes, S.H.H. ; Rauch, M.C.R. ; Pesic, M. ; Paul, C.E. ; Arends, I.W.C.E. ; Hollmann, F. - \ 2018
Molecular Catalysis 452 (2018). - ISSN 2468-8231 - p. 277 - 283.
Biocatalysis - Flavin - Old yellow enzyme - Oxygen dilemma - Photochemistry
Deazaflavins are potentially useful redox mediators for the direct, nicotinamide-independent regeneration of oxidoreductases. Especially the O2-stability of their reduced forms have attracted significant interest for the regeneration of monooxygenases. In this contribution we further investigate the photochemical properties of deazaflavins and investigate the scope and limitations of deazaflavin-based photoenzymatic reaction systems.
Special issue OxiZymes 2016
Berkel, Willem van; Fraaije, Marco ; Hollmann, Frank - \ 2016
Journal of Molecular Catalysis. B, Enzymatic 134 (2016). - ISSN 1381-1177 - p. 273 - 273.
Strategies for structuring interdisciplinary education in Systems Biology: an European perspective
Cvijovic, Marija ; Höfer, Thomas ; Acimovic, Jure ; Alberghina, Lilia ; Almaas, Eivind ; Besozzi, Daniela ; Blomberg, Anders ; Bretschneider, Till ; Cascante, Marta ; Collin, Olivier ; Atauri, Pedro de; Depner, Cornelia ; Dickinson, Robert ; Dobrzynski, Maciej ; Fleck, C. ; Garcia-Ojalvo, Jordi ; Gonze, Didier ; Hahn, Jens ; Hess, Heide Marie ; Hollmann, Susanne ; Krantz, Marcus ; Kummer, Ursula ; Lundh, Torbjörn ; Martial, Gifta ; Martins dos Santos, V.A.P. ; Mauer-Oberthür, Angela ; Regierer, Babette ; Skene, Barbara ; Stalidzans, Egils ; Stelling, Jörg ; Teusink, Bas ; Workman, Christopher T. ; Hohmann, Stefan - \ 2016
npj Systems Biology and Applications 2 (2016). - ISSN 2056-7189 - 7 p.
Systems Biology is an approach to biology and medicine that has the potential to lead to a better understanding of how biological properties emerge from the interaction of genes, proteins, molecules, cells and organisms. The approach aims at elucidating how these interactions govern biological function by employing experimental data, mathematical models and computational simulations. As Systems Biology is inherently multidisciplinary, education within this field meets numerous hurdles including departmental barriers, availability of all required expertise locally, appropriate teaching material and example curricula. As university education at the Bachelor’s level is traditionally built upon disciplinary degrees, we believe that the most effective way to implement education in Systems Biology would be at the Master’s level, as it offers a more flexible framework. Our team of experts and active performers of Systems Biology education suggest here (i) a definition of the skills that students should acquire within a Master’s programme in Systems Biology, (ii) a possible basic educational curriculum with flexibility to adjust to different application areas and local research strengths, (iii) a description of possible career paths for students who undergo such an education, (iv) conditions that should improve the recruitment of students to such programmes and (v) mechanisms for collaboration and excellence spreading among education professionals. With the growing interest of industry in applying Systems Biology approaches in their fields, a concerted action between academia and industry is needed to build this expertise. Here we present a reflection of the European situation and expertise, where most of the challenges we discuss are universal, anticipating that our suggestions will be useful internationally. We believe that one of the overriding goals of any Systems Biology education should be a student’s ability to phrase and communicate research questions in such a manner that they can be solved by the integration of experiments and modelling, as well as to communicate and collaborate productively across different experimental and theoretical disciplines in research and development.
Peroxygenase-Catalyzed Oxyfunctionalization Reactions Promoted by the Complete Oxidation of Methanol
Ni, Yan ; Fernández-Fueyo, Elena ; Baraibar, Alvaro Gomez ; Ullrich, René ; Hofrichter, Martin ; Yanase, Hideshi ; Alcalde, Miguel ; Berkel, W.J.H. van; Hollmann, Frank - \ 2016
Angewandte Chemie-International Edition 55 (2016)2. - ISSN 1433-7851 - p. 798 - 801.
Heme proteins - Hydrogen peroxide - Hydroxylation - Oxidation - Peroxygenases

Peroxygenases catalyze a broad range of (stereo)selective oxyfunctionalization reactions. However, to access their full catalytic potential, peroxygenases need a balanced provision of hydrogen peroxide to achieve high catalytic activity while minimizing oxidative inactivation. Herein, we report an enzymatic cascade process that employs methanol as a sacrificial electron donor for the reductive activation of molecular oxygen. Full oxidation of methanol is achieved, generating three equivalents of hydrogen peroxide that can be used completely for the stereoselective hydroxylation of ethylbenzene as a model reaction. Overall we propose and demonstrate an atom-efficient and easily applicable alternative to established hydrogen peroxide generation methods, which enables the efficient use of peroxygenases for oxyfunctionalization reactions.

Complete enzymatic oxidation of methanol to carbon dioxide: towards more eco-efficient regeneration systems for reduced nicotinamide cofactors
Kara, S. ; Schrittwieser, J.H. ; Gargiulo, S. ; Ni, Y. ; Yanase, H. ; Opperman, D.J. ; Berkel, W.J.H. van; Hollmann, F. - \ 2015
Advanced Synthesis and Catalysis 357 (2015)8. - ISSN 1615-4150 - p. 1687 - 1691.
pseudomonas-putida f61 - formaldehyde dismutase - biocatalysis - reductions - aldehydes - reductase
A novel system for in situ regeneration of reduced nicotinamide cofactors (NADH) is proposed: through a cascade of alcohol dehydrogenase (ADH), formaldehyde dismutase (FDM) and formate dehydrogenase (FDH) complete oxidation of methanol to carbon dioxide (CO2) is coupled to the regeneration of NADH. As a consequence, from one equivalent of methanol three equivalents of NADH can be obtained. The feasibility of this cascade is demonstrated at the examples of an NADH-dependent reduction of conjugated C[DOUBLE BOND]C-double bonds (catalysed by an enoate reductase) and the NADH-dependent hydroxylation of phenols (catalysed by a monooxygenase). The major limitation of the current regeneration system is the comparably poor catalytic efficiency of the methanol oxidation step (low kcat and high KM value of the ADH used) necessitating higher than theoretical methanol concentrations.
ISBE – set out for a Systems Biology Infrastructure for Europe
Hollmann, S. ; Martins dos Santos, V.A.P. ; Regierer, Babette - \ 2013
EMBnet.journal 19 (2013)1. - ISSN 2226-6089 - p. 3 - 4.
Systems biology requires the availability, co-ordination and simultaneous interaction of a large number of diverse facilities and activities. These cover an entire spectrum, from mathematical modelling, through biological, biomedical and clinical experiments, to dedicated technology development. The systems biology community needs close cooperation with data-generation groups and bioinformaticians to define a strategy for producing life-science data of sufficiently high quality for model generation. For each medical, biological or biotechnological problem addressed, the optimal combination of facilities and activities is likely to be different. The complexity of biological systems, and the diversity and dynamics of their processes, means that a full analysis is far too complex to be handled by a single entity, industry or country – a variety of specialist expertise and facilities are typically necessary to achieve results suitable for modelling. Systems-level approaches for tackling the complexity of life-science data provide a profound conceptual advance compared to reductionist biological research methods of the past. Rather than focusing on individual laboratories, specialising in a limited number of research technologies, the Infrastructure for Systems Biology in Europe (ISBE) will facilitate the synergistic application of a wide range of research techniques and technologies to problems of major medical and biotechnological importance.
More efficient redox biocatalysis by utilizing 1,4-butanediol as a ‘smart cosubstrate'
Kara, S. ; Spickermann, D. ; Schrittwieser, J.H. ; Leggewie, C. ; Berkel, W.J.H. van; Arends, I.W.C.E. ; Hollmann, F. - \ 2013
Green Chemistry 15 (2013)2. - ISSN 1463-9262 - p. 330 - 335.
liver-alcohol-dehydrogenase - old yellow enzyme - organic-synthesis - catalyzed oxidations - asymmetric bioreduction - activated alkenes - nadh regeneration - chiral lactones - meso diols - enantioselective reduction
1,4-Butanediol is shown to be an efficient cosubstrate to promote NAD(P)H-dependent redox biocatalysis. The thermodynamically and kinetically inert lactone coproduct makes the regeneration reaction irreversible. Thereby not only the molar surplus of cosubstrate is dramatically reduced but also faster reaction rates are obtained
Instrumental and sensory analysis of the flavour of French beans (Phaseolus vulgaris) after different rehydration conditions.
Ruth, S.M. van; Roozen, J.P. ; Hollmann, M.E. ; Posthumus, M.A. - \ 1996
Zeitschrift für Lebensmittel-Untersuchung und -Forschung. A, Food research and technology 203 (1996). - p. 7 - 13.
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