Job openings in Program 3
Biocatalytic processes for sustainable synthesis
PhD student positions
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Enzymes are highly powerful and potent tools in nature. In this project we want to repurpose ROS producing enzymes for potential use in degradation of synthetic polymers. Candidate enzymes will be thoroughly studied to understand their structure function relationship to the fullest in order to have a solid basis for engineering approaches that ultimately yield highly efficient and stable “blockbuster” enzymes.
BackgroundThe degradation of biopolymers requires a suite of specific enzymes secreted by plant biomass degrading microorganisms. For synthetic polymers, especially the difficult to depolymerize polyolefines, like polyethylene or polypropylene, such specific enzymes have not been evolved by organisms yet. Instead of combining a series of enzymes with different activities, the proposed strategy involves enzymes producing reactive compounds that start depolymerization reactions of recalcitrant polymers. Bacterial ROS producing oxidoreductases will act as a starting point in this project.
Aims
In this project, enzymes producing ROS species, hypohalous acids and other radicals will be screened, produced, characterized and engineered. Special focus will be put on the thermal and turnover stability of these “blockbuster” enzymes and various methods will be used to engineer stable producers of highly reactive species. The produced enzymes will be distributed in the COE to be studied with biopolymers in Program 1 and polyolefines in Program 3.
Methods
Genomic-, microorganism- and activity screening methods
Enzyme expression and purification
Biochemical characterization (protein analysis and kinetic measurements)
Protein engineering methods
Application in processes and process engineering
Main supervisor: Assistant Prof. Stefan Hofbauer
Co-supervisor: Associate Prof. Roland Ludwig
Location: BOKU University (Vienna)
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Description of project
Enzymes will be engineered by fusion with metal-binding peptides or protein binding modules to immobilize them on electrode materials (e.g. platinum, gold, carbon). For this purpose, metal-binding peptides are screened by phage display and naturally occurring protein binding modules are engineered. Candidate peptides and proteins will be tagged to the bioelectrocatalysts for oriented immobilization and the reactions electrochemically investigated.
Background
Enzymes as bioelectrocatalysts need to be connected to an electrode. Chemical immobilization methods lead to random orientations of the enzyme on the electrode and deactivation. The oriented immobilization of enzymes in a monolayer can be achieved by peptide or protein sequences/modules that bring the enzymes in productive contact with the electrode.
Research Objectives
In silico and in vitro screening of peptides and protein binding to electrode materials
Protein modelling and engineering for fusion proteins, production of fusion proteins
Biochemical characterization and electrochemical testing
Methods
Affinity screening (fluorescence microscopy, SPR)
Phage display screening of metal-binding peptides using model metal surfaces
Protein engineering (Rational design) of protein binding modules
Recombinant protein expression and purification
Biochemical and electrochemical characterization
Main supervisor: Priv.-Doz. Dr. Doris Ribitsch
Co-supervisor: Associate Prof. Roland Ludwig
Location: BOKU University (UFT Tulln)
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Description of project
Development of efficient bio-electrocatalytic systems based on advanced understanding, and engineering, of the functional interactions between enzymes and electrode surfaces; design of enzymes and surfaces for optimized interaction for mediated or direct electron transfer with electrodes
Background
Bio-electrocatalysis is promising to perform chemical transformations with minimal use of reagents and low waste produced. The design of electrochemical reactors often requires that enzyme catalysts are immobilized on the electroactive surfaces of electrodes. Electrode materials (e.g., metals, carbon) are often poorly suitable to provide an interface for interaction with the enzyme catalysts for immobilization. The project aims to deepen the understanding of enzyme interactions with electrode materials in order to enable more efficient engineering of functional bio-interfaces in, and for, electrochemical transformations.
Research Objectives
Exploring and optimizing enzyme interactions with carbon-based electron surfaces
Designing enzymes for improved active adsorption on electrodes
Engineering of enzyme-surface interactions for direct electron transfer
Characterization of enzyme electrodes for mediated and direct electron transfer
Methods
Electrochemical analysis and characterization (e.g., cyclic voltammetry, impedance spectroscopy); characterization of enzyme-surface interactions (e.g., atomic force microscopy, fluorescence microscopy); enzyme function assessment on surface and in solution; enzyme engineering (e.g., development of fusion proteins); analysis and characterization of enzyme binding to electrode surfaces; protein biochemistry (expression, purification, stability).
Main supervisor: Univ.-Prof. Bernd Nidetzky
Co-supervisor: Associate Prof. Roland Ludwig
Location: TU Graz
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Description of project
The goal of this project is to find a new and better way to deal with plastic and PFAS pollution. Right now, we often dispose of plastic in ways that harm the environment. The project suggests a new method to recycle plastics by creating a special enzyme that uses light, and air to break down plastics and PFAS in water. The primary aim of this project is to discover an improved method for upcycling these plastics and PFAS into valuable materials, aligning with the concept of a sustainable and closed-loop society. The innovative aspect of this initiative involves the utilization of specialized proteins capable of generating reactive oxygen species (ROS) upon light exposure. These proteins are affixed to additional elements to facilitate sticking to plastic surfaces. This unique approach targets microplastics and aims to solve the pollution problem.
Background
The group has experience with flavin enzymes and with the analysis of reactive oxygen species. Additionally the group has gained experience in surface analytics of plastics and the analysis of degradation products by NMR and MS/MS methods.
Research Objectives
Design and production of plastic and PFAS degrading enzymes.
Analysis of the degradation products and elucidation of degradation mechanism.
Utilization of the degradation products for the productions of novel chemicals.
Methods
Selection of potential enzyme candidates for the degradation of plastic and PFAS.
Cloning and expression in Escherichia coli and subsequent isolation, purification and characterization of these enzymes.
Testing on their degradation activities.
Main supervisor: Associate Prof. Florian Rudroff
Co-supervisor: Univ.-Prof. Katharina Schröder
Location: TU Wien (Vienna)
Postdoc positions
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Background
Hydrophobic pockets often play a decisive part in the mechanisms underlying the selectivity of enzymes. Yet, the interactions between hydrophobic substrates and the highly dynamic hydrophobic surfaces of these catalytic motifs are still poorly understood, making a control of selectivity by rational design exceedingly difficult. The project deals with the role of hydrophobic pockets in the catalytic mechanism of a membrane-bound monooxygenase.
Structure elucidation of membrane enzymes used to be exceedingly difficult, which was a considerable challenge for their enzyme engineering. The advent of CryEM and de novo structure prediction methods greatly facilitated structure-based enzyme engineering approaches. Bacterial alkane monooxygenase (AlkB) catalyzes the terminal hydroxylation of alkanes. The Kourist group showed a 6-fold activity increase of an AlkB-based whole-cell biocatalysts in the synthesis of precursor of the biobased monomer Tulipalin A.
Aims / Hypotheses
The project aims to characterize AlkB in a cell-free system in order to investigate the effect of amino acid substitutions in the hydrophobic active-site cavities, and to analyze the molecular basis of a side-reactivity of the enzyme. Furthermore, the influence of peripheral amino acids on catalysis is investigated. The evolutionary emergency of the acceptance of different substrates such as alkanes and aromates will be analyzed by ancestral sequence reconstruction.
Method
Phylogeny and ancestor reconstruction
Kinetic investigation of membrane-enzymes
Collaboration with Oostenbrink will focus on MD simulations of membrane-enzymes. The feasibility of mechanistic modeling will be tested.
In the long term, we plan to develop a methodology to characterize fitness landscapes of these enzymes by coupling of high-throughput screens and deep sequencing of libraries.
Main supervisor: Univ.-Prof. Robert Kourist
Co-supervisors: Univ.-Prof. Ruth Birner-Gruenberger, Univ.-Prof. Chris Oostenbrink
Location: TU Graz
Duration: 30 months
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Description of project
The identification of novel biocatalysts and development of bioprocesses for industrial applications has been significantly advanced by omics technologies, bioinformatics, and engineering. Redox-stress can be a relevant limiting factor with regards to yield and product quality. However, a global, comprehensive and systematic analysis of redox-stress with molecular resolution of different hosts, promoters, products and process parameters is lacking and one major aim of this project, which will be supported by a PhD student and performed in collaboration with Oliver Spadiut, Robert Kourist, Wolfgang Kroutil, Matthias Steiger and Florian Rudroff (program 3). The second major aim is to identify novel enzymes including oxidoreductases and hydrolases accepting selected substrates, e.g., lignocellulose, without prior information about their sequence or structure through functional proteomics approaches, including secretomics, thermal proteome profiling and activity-based proteomics of selected microorganisms and environments such as rumen or elephant faeces, which will be supported by a PhD student and performed in collaboration with Doris Ribitsch (programs 1 and 3). A third aim will be to perform subcellular proteomics as part of developing compartmentalized multi-omics workflows in collaboration with Gunda Koellensperger, Brigitte Gasser and Matthias Steiger (program 2).
Background
The working group has experience in functional proteomics, such as redox-proteomics and -metabolite analysis [1-3], activity-based proteomics [4-7], secretomics and enzyme discovery [8,9].
Research Objectives
Elucidation of redox-stress mechanisms and pathways in diverse hosts
Identification of critical bioprocess parameters causing redox-stress
Identification of new biocatalysts for decomposition of natural and synthetic polymers
Methods
Establishment of redox-proteomics and -metabolite analysis of diverse hosts including E. coli, P. pastoris, cyanobacteria and archaea
Redox-proteomics and -metabolite analyses
Pathway analysis, gene ontology enrichments
Product analysis by mass spectrometry
Establishment of functional proteomics screening assays with target substrates (secretomics, thermal proteome profiling)
Establishment of activity-based proteomics of hydrolases and oxidoreductases
Establishment of habitat specific metaproteomics workflows
Screening of strains (anaerobe, aerobe) and microbial communities from underexplored sources for new enzyme activities
Job requirements
The ideal candidate should hold a PhD degree in biotechnology, biochemistry, chemistry, or equivalent and have international experience, proven publication and presentation activity and experience in proteomics and bioinformatics. Experience in metabolomics, recombinant expression in different hosts and characterization of enzymes will be an added advantage. The candidate is ready to dive quickly into this project, has strong communication skills in English and is motivated to work in an active and interdisciplinary team at TU Wien.
References
Tomin T, Honeder S, Liesinger L, Gremel D, Retzl B, Lindenmann J, Brcic L, Schittmayer M*, Birner-Gruenberger R. (2025) Increased antioxidative defense and reduced advanced glycation end-product formation by metabolic adaptation in NSCLC patients. Nat Commun, accepted; preprint on Research Square 2024; doi: 10.21203/rs.3.rs-4535848/v1 (*co-corresponding author))
Tomin T, Schittmayer M, Sedej S, Bugger H, Gollmer J, Honeder S, Darnhofer B, Liesinger L, Zuckermann A, Rainer PP and Birner-Gruenberger R. (2021) Mass spectrometry-based redox proteome profiling of failing human hearts. Int. J. Mol. Sci. 2021, 22, 1787. doi:10.3390/ijms22041787
Tomin T, Schittmayer M, Birner-Gruenberger R. (2020) Addressing glutathione redox-status in clinical samples by two step alkylation with N-ethylmaleimide isotopologues. Metabolites. 2020, 10(2):71. doi: 10.3390/metabo10020071.
Krammer L, Darnhofer B#, Kljajic M, Liesinger L, Schittmayer M, Neshchadin D, Gescheidt G, Kollau A, Mayer B, Fischer RC, Wallner S, Macheroux P, Birner-Gruenberger R*, Breinbauer R. (2025) A general approach for activity-based protein profiling of oxidoreductases with redox-differentiated diarylhalonium warheads. Chem Sci; doi: 10.1039/d4sc08454c. Epub ahead of print. PMID: 40103729; PMCID: PMC11912224. (#co-first author, *co-corresponding author)
Honeder SE, Tomin T, Schinagl M, Pfleger R, Hoehlschen J, Darnhofer B, Schittmayer M, Birner-Gruenberger R. (2023) Research advances through activity-based lipid hydrolase profiling. Israel Journal of Chemistry; doi: 10.1002/ijch.202200078
Schittmayer, M., Vujic, N., Darnhofer, B., Korbelius, M., Honeder, S., Kratky, D., Birner-Gruenberger, R. (2020) Spatially Resolved Activity-based Proteomic Profiles of the Murine Small Intestinal Lipases. Molecular & Cellular Proteomics, 19:2104-2115. DOI:10.1074/mcp.RA120.002171
Wallace, P. W., Haernvall, K., Ribitsch, D., Zitzenbacher, S., Schittmayer, M., Steinkellner, G., Gruber, K., Guebitz, G. M., Birner-Gruenberger, R. (2017) PpEst is a novel PBAT degrading polyesterase identified by proteomic screening of Pseudomonas pseudoalcaligenes. Applied Microbiology and Biotechnology, 101:2291–2303. DOI:10.1007/s00253-016-7992-8
Sturmberger, L., Wallace, P. W., Glieder, A., Birner-Gruenberger, R. (2016) Synergism of proteomics and mRNA sequencing for enzyme discovery. Journal of Biotechnology, 235:132-138. DOI:10.1016/j.jbiotec.2015.12.015
Main supervisor: Univ.-Prof. Ruth Birner-Gruenberger
Co-supervisor: Univ.-Prof. Oliver Spadiut, Priv.-Doz. Dr. Doris Ribitsch
Location: TU Wien, Research Group Bioanalytics: https://www.tuwien.at/en/tch/bioanalytics
Duration: 12 months (40 h/week, with option to prolong to 36 months)
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Description of project
This postdoctoral project aims to develop an integrated, sustainable approach to biomass valorization by leveraging alternative solvent systems and catalytic processes. The research focuses on three interconnected objectives:
Selective Extraction of Biomass Using Alternative Solvents
Develop and optimize protocols for extracting valuable fine chemicals from lignocellulosic biomass using green solvents such as supercritical CO₂, ionic liquids, and subcritical water. The goal is to recover bioactive compounds with potential applications in pharmaceuticals, cosmetics, and nutraceuticals.
Delignification and Conversion to Fermentable Acidic Building Blocks
Investigate novel methods for extracting and fractionating lignin to isolate functionalized aromatic acids and other depolymerization products. These molecules will serve as precursors for microbial fermentation to produce sustainable chemicals and biofuels.
Functionalization of Biomass Residue for Catalytic CO₂ Conversion
Modify the porous residual biomass framework post-extraction to incorporate heterogeneous catalysts, transforming it into an active support for continuous CO₂ conversion. The aim is to create integrated systems for producing bulk chemicals such as methanol or formic acid, leveraging the structural and chemical properties of the biomass-derived support.
Background
The project aligns with the goals of Program 3: Biocatalytic Processes for Sustainable Synthesis, focusing on innovative strategies for biomass utilization and CO₂ conversion. By integrating green chemistry principles and circular economy concepts, this research seeks to minimize waste and environmental impact while maximizing the value derived from biomass resources.
Research Objectives
Develop and optimize green solvent-based extraction methods for biomass.
Characterize and fractionate lignin into fermentable building blocks.
Engineer biomass-derived materials as catalysts for CO₂ conversion.
Integrate the above processes into a cohesive, sustainable biomass valorization pathway
Methods
Solvent extraction techniques (supercritical CO₂, ionic liquids, subcritical water).
Catalyst synthesis and characterization.
Continuous-flow chemistry and reaction engineering
Analytical tools: GC-MS, HPLC, NMR, BET, FTIR.
Main supervisor: Univ.-Prof. Katharina Schröder
Co-supervisor: Univ.-Prof. Oliver Spadiut, Associate Prof. Robert Woodward
Location: TU Wien (Vienna)
Duration: 36 months
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Description of project
This postdoctoral project targets the circular recovery of fluorine from poly- and perfluorinated alkyl substances (PFAS)—a class of persistent, toxic environmental pollutants. PFAS are extensively used in industry and consumer products, leading to their widespread presence in water and soil. Their strong carbon–fluorine bonds make them exceptionally resistant to degradation. The project proposes an innovative closed-loop PFAS valorization strategy that integrates advanced defluorination with reuse of fluorine-rich intermediates in pharmaceutical and fine chemical synthesis. It builds on the following objectives:
Photocatalytic and Biocatalytic Degradation of PFAS
Develop and apply photocatalytic and photobiocatalytic approaches to break down PFAS compounds into smaller, less harmful fluorinated fragments. Emphasis will be placed on technologies such as UV/sulfite systems, electrochemical oxidation, and enzymatic transformations (e.g., fluorinase- or aldolase-based systems).
Analytical Characterization of PFAS Degradation Products
Utilize advanced analytical methods (e.g., LC-MS/MS, NMR) to monitor PFAS degradation pathways and characterize the generated fluorinated intermediates. Special focus will be on identifying valuable fragments that retain fluorine atoms suitable for further synthetic applications.
Fluorine Recovery via Chemical and Enzymatic Synthesis
Transform the fluorinated degradation products into high-value compounds through tailored chemical or enzymatic fluorination strategies. This includes applying known fluorinases or engineering novel enzymatic routes to build reusable fluorinated building blocks, aligning with the principles of green chemistry and circular fluorine economy.
Background
The project supports the mission of Program 1 and 3 by promoting green materials cycles and biocatalytic synthesis routes. It addresses a critical environmental and regulatory challenge—PFAS contamination—while simultaneously proposing innovative recycling of fluorine for use in drug discovery and specialty chemistry.
Research Objectives
Develop novel photocatalytic/biocatalytic systems for PFAS degradation.
Elucidate transformation pathways and characterize fluorinated intermediates.
Explore enzymatic methods to incorporate recovered fluorine into value-added chemicals.
Integrate degradation and synthesis in a holistic fluorine recovery platform.
Methods
Experience with homogenous and heterogenous photocatalysis
Advanced Oxidation Processes
Hands-on expertise in LC-MS/MS and NMR for structural elucidation of degradation products
LC/MS, NMR, FTIR for molecular characterization
Flow Chemistry or Microreactor systems
Main supervisor: Univ.-Prof. Katharina Schröder
Co-supervisor: Associate Prof. Florian Rudroff
Location: TU Wien (Vienna)
Duration: 36 months