Methods

Lorenz Adrian Johann Heider Jürgen Moser Carola Schulzke
Matthias Boll Gunhild Layer Constanze Pinske Günter Schwarz
Holger Dobbek Silke Leimkühler Antonio J. Pierik Seigo Shima
Oliver Einsle Roland Lill Gary Sawers Basem Soboh
Thorsten Friedrich Ralf R. Mendel Raffael Schaffrath Matthias Ullmann
Ute Krämer Franc Meyer Volker Schünemann
Günter Fritz /
Julia Fritz-Steuber
Serena DeBeer /
Frank Neese
Carsten Berndt /
Christopher Lillig
Oliver Lenz /
Ingo Zebger

 

Name Expertise Methodology provided
Adrian, Lorenz  Microbiology, biochemistry and genomics of organohalide respiration (anaerobic respiration with halogenated organics). Isolation and cultivation of slow-growing anaerobic microorganisms. Chloroflexi in marine and terrestrial sediments. Anaerobic biochemistry: isolation and characterization of respiratory metallo-complexes; mass spectrometry; stable isotope labelling approaches for metabolic tracing, enzymatic and abiotic Anaerobic cultivation in small and medium scale up to 80 l reactors, anaerobic biochemistry (activity tests, enzyme complex membrane solubilization, and purification via chromatography, FPLC and native gel electrophoresis).

The department Isotope Biogeochemistry provides ICP-MS for the metal analysis from cell preparations or subcellular fractions or protein preparations. Nano-SIMS with a lateral resolution down to about 100 nm is available for the analysis of microbial single cell analysis or image generation in eukaryotic structures. nLC-high-resolution MS/MS is available for protein identification, shotgun proteomics and cofactor identification. For structure identification FT-ICR is accessible. Helium microscopy

Berndt, Carsten Thiol redox signaling by thio- and glutaredoxins (redoxins), especially during cellular differentiation, embryonic development and neurological disorders; biochemistry  and biophysics of redoxins; structure-function relationship of iron-sulfur cluster coordinating glutaredoxins Primary cell cultures (neuronal and glial cells), differentiation of primary progenitor cells and cell lines, organotypic slice cultures, zebrafish (e.g. as model for vertebrate development), experimental models (cells, slice cultures, animals) for neurological diseases based on inflammation, immunological methods, determination of protein redox state, in vitro reconstitution of Fe2S2 and Fe4S4 clusters
Boll, Matthias   Large scale cultivation of microorganisms (200-L-scale), protein biochemistry, molecular biology (cloning, site-directed mutagenesis, genetic system of E. coli, G. metallireducens and T. aromatica, qPCR), UPLC/HPLC/IC/LC-MS (Q-TOF)-analysis of metabolites (CoA-esters, nucleotides etc.), protein expression in E. coli, G. metallireducens, and T. aromatica, protein purification and characterization of metalloenzymes/oxygen-sensitive enzymes, enzyme kinetics, anaerobic techniques, elucidation of novel metabolic pathways 
DeBeer, Serena The development and application of X-ray spectroscopic methods to understand fundamental processes of biological nitrogen reduction, methane to methanol conversion, hydrogen production and water oxidation. – X-ray absorption spectroscopy (XAS)
– Extended X-ray absorption fine structure (EXAFS)
– X-ray emission spectroscopy (XES)
– Two-dimensional X-ray spectroscopic methods for enhanced selectivity.
Dobbek, Holger Enzymology of the reductive acetyl-CoA pathway, nickel and iron-containing enzymes and their maturation, carbon monoxide dehydrogenases, structure and function of molybdo-enzymes – production of metalloenzymes with complex metal sites
– production and handling of O2-sensitive iron/sulfur-cluster containing enzymes
– crystallization and structure determination of O2-sensitive enzymes
– stopped-flow (UV/fluorescence) spectroscopy, quenched flow-kinetics under aerobic and strictly anoxic conditions ([O2] < 0.5 ppm)
– isothermal titration calorimetry under strictly anoxic conditions ([O2] < 0.5 ppm)
– kinetic monitoring of conformational changes (stopped-flow FRET kinetics)
Einsle, Oliver Structural and functional analysis of metalloproteins and membrane proteins, bioinorganic chemistry, enzymology of the biogeochemical cycles of nitrogen and sulfur, biological nitrogen fixation, nitrous oxide reductase, multiheme cytochromes c, maturation and assembly of metal centers  – isolation of metalloproteins from     native and recombinant sources
– anoxic protein biochemistry
– crystallization and structure solution by X-ray diffraction under excluion of O2
– fast kinetics (stopped-flow) with UV/vis and fluorescence detection

– isothermal titration calorimetry
– UV/vis spectroscopy in microvolumes and on single crystals
– EPR spectroscopy (cw, X- and Q-band)
-Analytical size-exclusion chromatography with UV/vis, refractory index and right-angle light scattering
thermofluor protein stability assays 
Friedrich, Thorsten Enzyme complexes of respiratory chains, kinetic and functional characterization of enzyme complexes of respiratory chains, characterization of electron transfer reactions involving several cofactors, genetic manipulation of enzyme complexes, modeling of human pathogenic mutations in bacteria, ESR-spectroscopy of FeS clusters, FeS cluster biosynthesis, molecular chaperones assisting FeS cluster and heme biosynthesis, regulation of catalytic activity by FeS clusters The Friedrich lab will provide long-standing expertise on the recombinant production and functional characterization of membraneous metalloproteins and proteins involved in the biosynthesis of FeS clusters. This includes cloning, and manipulation of genes involved as well as heterologous production, and purification of the enzyme complexes and putative chaperones in E. coli. The analytical methods include enzyme kinetics (e.g. ESR-spectroscopy, stopped flow, UV-Vis spectrometry, fluorescence, diode array and dual-beam techniques), protein stability analysis by thermoFAD, protein electrochemistry, functional protein-protein interaction (isothermal titration calorimetry, split-GFP, cross-linking coupled to mass spectrometry, native PAGE) and cellular localization of proteins (FP-fusion proteins). 
Fritz, Günter FeS, heme, flavin, Calcium, Zinc containing proteins and enzymes; X-ray crystallography of proteins and complexes and analysis at low resolution; protein-protein interaction; spectroscopic analysis including e.g. CD, MCD, SAXS. – Recombinant expression of multi protein complexes in coli or insect cells.
– Isolation of proteins under exclusion of oxygen.
– Determination of redox potential of redox cofactors
– Crystallization and X-ray analysis of proteins
Fritz-Steuber, Julia We use the Na+-translocating NADH:quinone oxidoreductase from Vibrio cholerae as a model to apply and develop techniques for functional characterization of large membrane protein complexes in native membranes, or with purified complexes in detergent-solubilized state and after reconstitution in liposomes. Devices and techniques for bacterial cell growth, bacterial mutagenesis, cell rupture and membrane protein purification in S1 laboratories. In addition, we offer access to laboratories with biological safety level 2 for growth, storage, manipulation and lysis of bacteria classified as S2. The S2 laboratories are fully equipped with an autoclave, several incubators and shakers, a safety cabinet for biological cultures, centrifuges, an Emulsiflex system for cell lysis, a spectrophotometer, freezer and a fridge for storage of bacterial strains.
Heider, Johann Molybdenum and tungsten enzymes, iron sulfur enzymes, radical reactions, kinetic and functional characterization of metalloenzymes, regulation of synthesis of molybdoenzymes. The Heider lab will provide expertise on the biochemistry of molybdo- and tungstoenzymes and proteins involved in the biosynthesis of the cofactors, as well as on molecular biological and genetic methods with E. coli and other bacteria. This includes cloning, overexpression, and purification of genes/functional enzymes from various bacterial organisms. The laboratory is equipped with a fermentation unit allowing the large scale cultivation of wild type and recombinant bacteria up to 200 l. The repertoire further includes detailed enzyme kinetics assays (e.g. stopped flow, UV-Vis spectrometry, anaerobic assays) and analytic methods (HPLC, GC).  
Krämer, Ute Physiological analysis of cellular and whole-plant metal homeostasis and its dynamics under a variety of metal imbalance conditions, physiological and regulatory cross-talk between Fe and other metals in plants (Zn, Cu), the use of metal-regulated transcripts and metalloenzyme protein levels and activities as metal status markers, metal-dependent spatio-termporal dynamics, e.g. of circadian clock output. The Krämer lab provides expertise on the physiological analysis of metal homeostasis at the cellular and supra-cellular level in model organisms, especially in Arabidopsis thaliana. This includes the implementation of a variety of metal stati in plants and their in-depth phenotypic analysis, a large panel of general and plant molecular biology and molecular genetics techniques including the heterologous screening of plant cDNA libraries in Saccharomyces cerevisiae and forward and reverse genetics in both yeast and Arabidopsis, sequencing- and microarray-based transcriptomics and targeted transcript quantification, metalloenzyme assays, (fluorophore-based) in vivo metal imaging and GFP-based protein localization, multi-element analysis of plant and soil samples by ICP-OES, protein purification, protein immunodetection. 
Layer, Gunhild Enzymes involved in tetrapyrrole biosynthesis, iron-sulfur cluster containing enzymes, Radical SAM enzymes, iron-sulfur cluster biosynthesis in prokaryotes, protein biochemistry and enzymology. Our lab is well equipped for all kinds of work in the fields of protein biochemistry, molecular biology and microbiology. This includes protein production and purification under aerobic and anaerobic conditions, cloning and heterologous gene expression. Enzyme kinetics are measured using UV-Visible absorption spectroscopy and HPLC analysis. We have a long-standing expertise in the anaerobic handling and crystallization of oxygen-labile iron-sulfur cluster proteins.
Leimkühler, Silke Molybdenum enzymes and molybdenum cofactor biosynthesis, kinetic and functional characterization of metalloenzymes, mechanism of Moco-assembly and insertion into apo-enzymes by molecular chaperones, cross-talk of molybdenum cofactor biosynthesis and iron sulfur clusters in the cell, analysis of the regulation of synthesis of molybdoenzymes, detection of sulfur-containing molecules and cofactors (Moco, thionucleosides in tRNA, thimin, FeS containg enzymes). The Leimkühler lab will provide long-standing expertise on the recombinant production and functional characterization of molybdoenzymes and proteins involved in the biosynthesis of the molybdenum cofactor. This includes cloning, heterologous overexpression, and purification of genes/functional enzymes from various organisms, including humans, SF9 cells and E. coli. The repertoire further includes detailed enzyme kinetics (e.g. stopped flow, UV-Vis spectrometry, anaerobic assays), protein stability analysis by thermofluor. The lab is well equiped for functional protein-protein interaction studies (Biacore,isothernal titration calorimetry, Biolayer interferometry, thermophorese), and metal detection (ICP-OES). Subcellular localization of proteins (transfection, GFP-fusion proteins) and splitGFP as molecular probe for the intracellular interaction of proteins have been established. Additional genetic methods involve RT-PCR and gene expression analysis.
Lenz, Oliver The group of Oliver Lenz is well-experienced in the molecular genetics, biochemistry and biotechnological application of hydrogenases that oxidize and produce molecular hydrogen in the presence of dioxygen. The activities of the group are embedded in the multidisciplinary environment of the Cluster of Excellence “Unifying Concepts in Catalysis” headed by the TU Berlin. Recently, the molecular basis for the striking oxygen-tolerance of the membrane-bound [NiFe] hydrogenase from the β-proteobacterium Ralstonia eutropha has been elucidated in a joint effort involving molecular and structural biology, spectroscopy, electrochemistry and theory. The novel insights into the factors/genes involved in cofactor assembly and catalytic mechanism of this functional O2-tolerant hydrogenase provide the basis of the current project.  Microbiology, molecular biology, protein biochemistry, and genetic engineering. Gas handling for fermentation with explosive H2/O2 mixtures. Mutagenesis, homologous and heterologous protein-overproduction and purification (FPLC). UV-Vis spectrometry. Gas quantification by amperometry (inverted Clark electrode), gas chromatography and mass spectrometry
Lillig, Christopher

Thiol redox signaling by thio- and glutaredoxins, especially during cellular de-differentiation, hypoxia, and related human diseases; biochemistry and biophysics of glutaredoxins; structure-function relationship of iron-sulfur cluster coordinating glutaredoxins.

Primary and stable cell cultures, RNAi and CrispR/Cas9 targeting glutaredoxins and other proteins/genes. Mouse models of human diseases (e.g. Ischemia-reperfusion injury and cardiac hypertrophy), immunological methods, determination of protein redox states on single protein and protemic level, reconstitution and spectroscopic analysis of FeS clusters and cluster transfer between proteins.

 

Lill, Roland

The Lill group uses the yeast Saccharomyces cerevisiae and human cell culture as main experimental systems. In some cases the group has worked on human patient material. The general expertise is in yeast molecular genetics and cell biology, protein biochemistry, metal biology and metal protein analysis, protein spectroscopy, protein crystallization, proteomic and genomic analysis of physiological changes after alterations in Fe/S protein or iron metabolism, metabolite transport into and out of mitochondria, cell culture analyses and RNAi technology.

Yeast molecular genetics, human cell culture, RNAi technology, cell biological and biochemical analysis of Fe/S protein biogenesis (anaerobic reconstitution) and iron metabolism, protein biochemistry and spectroscopy (UV/Vis, EPR, CD, fluorescence), protein interaction studies (thermophoresis, plasmon resonance, immunoprecipitation, NMR), metal detection (ICP-MS), molecular biology (site-directed mutagenesis and protein expression-purification in yeast and E. coli), 3D structural analysis of proteins, proteomic and genomic analyses, metabolite transport into and out of mitochondria.

 

Mendel, Ralf

Molybdenum enzymes and molybdenum cofactor biosynthesis, kinetic and functional characterization of metalloenzymes, mechanism of Moco-assembly and insertion into apo-enzymes, cross-talk of molybdenum cofactor biosynthesis and iron sulfur clusters in the cell, analysis of the regulation of synthesis of molybdoenzymes, detection of protein-protein interactions in vivo.

The Mendel lab will provide long-standing expertise on the recombinant production and functional characterization of molybdoenzymes and proteins involved in the biosynthesis of the molybdenum cofactor. This includes cloning, heterologous overexpression, and purification of genes/functional enzymes from various organisms, including humans, yeast, Neurospora crassa and E. coli. The lab is well equipped for functional protein-protein interaction studies (Biacore, ITC, thermophorese), and metal detection (ICP-MS). Subcellular localization of proteins (transfection, GFP-fusion proteins) and splitGFP / splitLuciferase as molecular probe for the intracellular interaction of proteins have been established. Additional genetic methods involve RT-PCR, gene expression analysis and generation of knockouts in N. crassa.

 

Meyer, Franc

Synthetic (bio)inorganic and organometallic chemistry, specifically biomimetic coordination chemistry and bioinspired catalysis; small molecule activation and characterization of active intermediates; magnetochemistry; synthesis and spectroscopy under anaerobic conditions. Organic and inorganic synthesis of model complexes; analysis and spectroscopy of small molecules including IR, Raman, UV-vis, EPR (X-band) and multinuclear NMR spectroscopies (all at variable temperatures); zero-field 57Fe Mössbauer spectroscopy; SQUID magnetometry; mass spectrometry (various ionization methods); electrochemistry; single crystal X-ray diffractometry.

 

Moser, Jürgen

Large scale protein production, partially automated protein purification, protein crystallography and structural biology, enzyme kinetics of metalloenzymes, substrate analog and inhibitor studies, HPLC, investigation of dynamic protein-protein interaction. All techniques for crystal growth in the absence of molecular oxygen, crystal manipulation and shock freezing of crystals are established in our laboratory. More sophisticated instruments (e.g. for X-ray diffraction analysis) are directly accessible at the closely located Helmholtz Centre for Infection Research in Braunschweig.

Neese, Frank

Development and application of quantum chemical methods for understanding fundamental processes in biological catalysis. Experimental molecular spectroscopyand the theoretical interpretation of spectra.

– Electronic structure calculations
– Spectral calculations
– X-ray magnetic circular dichroism (XMCD)

Pierik,
Antonio J.

Iron sulfur proteins, iron sulfur protein biosynthesis, bioinformatic analysis, yeast genetics, in vivo interaction studies, enzyme kinetics, synthesis and application of isotopically labelled compounds, microbial biochemical pathways, anaerobic methods, redox chemistry, radical enzymes, application of spectroscopic methods for the functional and quantitative analysis of (multi-cofactor containing) metalloproteins: (parallel-mode) EPR, FTIR, NMR, UV-Vis, fluorescence and Mössbauer spectroscopies, elemental analysis (AAS, ICP-MS, PIXE, INAA).

The Pierik laboratory has facilities and experience to produce and handle proteins under anaerobic conditions. For protein production in E. coli and genetic studies of yeast large scale variable temperature shakers and a French Press are available. For functional analysis an anaerobic tent, a wide range of UV-Vis and fluorescence spectrometers and a pulsed X-band EPR spectrometer with various cavities and helium transfer lines are present. Equally important is the local networking of the Pierik lab with other groups in the chemistry and directly adjacent biology and physics departments at the campus of the Technical University Kaiserslautern. This allows on site access to Resonance Raman, (high field) Mössbauer (Diller, Schünemann), FTIR (Gerhards) and CD spectroscopy (Keller).

Pinske, Constanze

[NiFe]-hydrogenase characterization and purification, generation of chromosomal mutants and variants, fermentative and anaerobic respiratory growth and enzyme activity characterization (UV/Vis, native PAGE with activity staining), metabolite analysis (gas chromatography, HPLC), handling of category 2 organisms/S2 (Salmonella enterica), aerobic and anaerobic protein purification of multi-protein complexes, working with gases and gas mixtures for analysis and activity of enzymes.  

The lab has an extensive knowledge in genetic manipulation of E. coli strains and general molecular biology and aims at investigation of effects under normal protein expression levels. This allows to analyse gene expression by RT-PCR and effects on protein and enzyme maturation by western blotting. In addition, activity analysis by Native-PAGE with activity staining, enzyme assays via UV-Vis and fluorescence spectrometers is possible for both native level proteins and purified proteins. We can perform affinity and native purification under aerobic and anaerobic conditions and have an in house X-ray facility, NMR and MS analysis. We perform ITC, 2D-PAGE, metabolite analysis by HPLC or assays  and also have access to the ICP-MS of Prof. Dietrich Nies group.

Sawers, Gary

Biochemistry and physiology of molybdenum-selenium enzymes and nickel-iron hydrogenases; characterization of biosynthesis of metalloenzymes; mechanism of NiFe-cofactor assembly and insertion into apo-hydrogenase by molecular chaperones; biosynthesis of iron sulfur clusters and insertion into electron-transport proteins.

Our lab has expertise in anaerobic protein biochemistry, microbial physiology, molecular biology and molecular genetics of metalloenzyme biosynthesis and function. These techniques include cloning, heterologous protein-overproduction, anaerobic purification of oxygen-sensitive enzymes and cofactors using mainly E. coli as host. We also have extensive expertise in the analysis of membrane proteins and protein-protein interaction. The lab equipped for functional anaerobic protein purification (anaerobic glove box with protein-purification facility), the study of protein-protein interaction (e.g. ITC) and we have access to metal analysis (ICP-MS – group of Dietrich Nies). The lab also has considerable expertise in all aspects of molecular biology and analysis of gene expression. We also have an excellent collaboration with the group of Andrea Sinz in Halle who is a world-leader in mass spectrometry.

Schaffrath, Raffael

Molecular genetics, biology, biochemistry & cell biology of conventional and non-conventional yeast models (Saccharomyces, Kluyveromyes, Pichia). Cell growth control and signaling in eukaryotes through low molecular weight antifungals (sordarin; rapamycin) and microbial protein toxins (corynebacterial ADP ribosylase and yeast tRNase toxins). The Schaffrath lab has expertise in the physiological and pathological roles of pathways for tRNA and protein diphthamide modifications in cell proliferation control. Using methodologies based on molecular, cell biological and biochemical tools, they analyse post-transcriptional modifications of tRNA anticodons (tRNA purification, tRNA modification profiling, EMSA). A second focus is on post-translational protein modifications (de-/phosphorylation, diphthamide synthesis and ubiquitin-like protein urmylation) and involves various protocols for protein-protein and protein-RNA interactions (yeast-two-hybrid, co-immune precipitation, thermophoresis, plasmon resonance, ITC, EMSA etc) in cooperation with on-site campus groups from Biochemistry, Biophysics & Developmental Genetics. Additional expertise accessible to the SPP1927 are site-directed mutagenesis and protein expression in yeast and E. coli using TAP and related purification protocols. In collaboration with SPP1784 Chemical Biology of Native Nucleic Acid Modifications, the Schaffrath lab may make in-depth tRNA modification profiling via LC-MS/MS available to interested members of the SPP1927.

Schulzke, Carola

Inorganic (i.e. complex) and organic synthesis; in particular: molybdenum,
tungsten and vanadium complex synthesis, synthesis of ligands and ligand precursors mimicking aspects of molybdopterin, non-innocent ligands; synthesis and characterization under inert gas conditions; crystallography; NMR-spectroscopy (1H, 13C, 31P, 51V); electrochemistry; optical spectroscopy (UV-vis, IR); oxo-transfer catalysis; model complex kinetics
The Schulzke lab is ready to provide long-standing expertise in the field of bioinorganic synthetic chemistry including the development of active site mimics as well as the design of models for natural ligand systems as for instance molybdopterin. The focus (and expertise) lies on the metals molybdenum, tungsten and vanadium but synthetic work also frequently involves for instance nickel and zinc complexes. The preparation of bioinorganic model compounds may be needed by other participants of the SPP for the comparison with enzymes and interpretation of enzymatic spectroscopic data (in particular EXAFS data).

Further expertise and readily available methods include small molecule crystallography (as opposed to protein crystallography), electrochemistry, NMR-spectroscopy (1H, 13C, 31P, 51V; other nuclei are possible), catalysis and kinetics of biomimetic processes and optical spectroscopy (UV-vis and IR). All methods can be provided under inert gas conditions (either sample preparation or execution of the whole experiments can be done for instance in a glove box with no water and no oxygen {< 0.1 ppm} present in the atmosphere).

Schünemann, Volker Molecular biophysics; electronic and dynamical properties of iron centers in proteins and corresponding chemical models; reaction intermediates; spin crossover complexes; nanostructures of spincrossover complexes; iron containing nanoparticles; heterogeneous catalysis.

Field and temperature dependent Mössbauer Spectroscopy;  synchrotron techniques based on the Mössbauer effect: Nuclear Forward and Nuclear Inelastic scattering, Application of density functional theory (DFT); electron paramagnetic resonance (EPR) spectroscopy; Infrared and Raman-spectroscopy; Freeze-Quench techniques for the study of reaction intermediates by Mössbauer and EPR spectroscopy.

Schwarz, Günter

In the field of molybdenum cofactor and molybdenum enzymes we study the biosynthesis of the molybdenum cofactor in humans. We express proteins in E. coli or animal cells and characterize their function in vitro and in vivo. We investigate their cellular distribution and subcellular targeting mechanisms. We generated an animal model for molybdenum cofactor deficiency, developed a therapy and currently study the molecular mechanism of the disease using cellular and animal models. We are interested in the structure-function relation in animal sulfite oxidase. We apply steady-state and pre-steady-state kinetics to investigate different activities in sulfite oxidase including nitrite reduction and NO synthesis. In plants, we investigate the structure and function of nitrate reductase including their posttranslational regulation by phosphorylation and 14-3-3 protein binding. In another research area we study the formation of inhibitory synapses in the central nervous system. We apply cellular and biochemical tools to understand the underlying mechanism leading to the formation of postsynaptic scaffold, their stability and plasticity.

Molecular biology, biochemistry and cell biology; recombinant expression, purification and characterization of proteins using E. coli, Pichia pastoris, insect cells, and human cells as host system; biochemical and biophysical characterization of proteins (CD spectroscopy, dynamic light scattering, differential scanning calorimetry), protein interaction studies in vitro (cosedimentation, isothermal titratrion calorimetry, surface plamon resonance spectroscopy) and in vivo (expression in animal cells including in culture neurons); protein crystallography and structural biology; enzymology (steady state and pre-steady state); studies in mice (animal facility, animal models and in collaboration AAV-mediate gene therapy); neurobiology (culture of hippocampal and cortical neurons, cell viability studies, synaptogenesis); targeting and function of mitochondrial proteins.

Shima, Seigo Cultivation of methanogenic archaea. Purification and characterization of enzymes involved in methanogenesis and anaerobic oxidation of methane including [Fe]-hydrogenase, F420-reducing [NiFe]-hydrogenase and methyl-coenzyme M reductase. Crystallization of the metaloproteins. We solved many crystal structures of the proteins in collaboration with U. Ermler (MPI of Biophysics). Analysis of the [Fe]-hydrogenase cofactor (the FeGP cofactor) biosynthesis by using stable-isotope labeling. Chemical and spectroscopic analyses of the FeGP cofactor and its biosynthetic precursors. Molecular cloning of genes and heterologous expression in Escherichia coli. We elucidated structure of the FeGP cofactor and the related compounds with NMR, ESI-MS, MALDI-TOF-MS), circular dichroism spectroscopy, Mössbauer spectroscopy, X-ray absorption spectroscopy in collabolations. Gene knock out of M. maripaludis in collaboration with Michael Rother (Technisch Universität Dresden).

The Shima lab has long-standing expertise on the anaerobic purification and characterization of oxygen-sensitive enzymes. The enzymes can be anaerobically crystallized in anaerobic conditions. We are familiar with recombinant production and functional characterization of proteins. This includes gene cloning, heterologous overexpression of the genes in Escherichia coli and purification of proteins.

Soboh, Basem

In vitro biosynthesis and assembly of complex Fe-S cofactors of [NiFe]-hydrogenase and FeMo-Nitrogenase. Isolation of active maturation machinery and follow the stepwise synthesis and assembly of cofactor biochemically and spectroscopically. Cloning, overexpression, anaerobic purification and analysis of the compositions of functional complexes and membrane proteins. Protein refolding and reconstitution of FeS cluster in vitro.

Our lab will provide expertise on the biochemical-genetic strategy of in vitro reconstitution of pathways for assembly and maturation of Fe-S cofactor containing proteins. Our concept involves a broad range of methodologies. This includes manipulation of genes, overexpression (E. coli as host) and anaerobic isolation of protein complexes and intermediates, that bound cofactor precursors in preparative amounts. The analytical methods include anoxic enzyme kinetics, UV-vis spectroscopy, FPLC, functional protein-protein interaction (thermophoresis), metal detection (ICP-MS), and native gel electrophoresis. Spectroscopic methods like infrared spectroscopy, surface-enhanced IR absorption spectroscopy (SEIRAS), and Raman spectroscopy are well established in our Lab (Sven Stripp). All methods are performed in a glove box including isotope editing of the carbonyl ligands of cofactor.

Ullmann, Matthias In our research, we investigate the function of proteins by various computational methods on the basis of structural models of the proteins. Mainly we are interested in proteins that are involved in various biological energy transduction pathways. Many of these proteins are metalloproteins or cofactor-containing proteins. To study these proteins and processes, we apply a variety of theoretical methods including continuum electrostatics calculations, elastic network models, molecular dynamics simulations and quantum chemical calculations. Moreover, we develop methods to analyze and simulate the energetics and kinetics of charge and exciton transfer processes.

We use a large variety of structure-based modelling techniques to understand enzymatic mechanisms. We can analyze electrostatic potentials of proteins, calculate protonation probabilities, relative pKa values and relative redox potentials. Moreover, we can determine reaction paths of enzymatic mechanism on the basis of crystal structures.

Zebger, Ingo

The group has a long standing experience in the vibrational spectroscopic characterization of metalloproteins, including the type of proteins that are in the center of the project, i.e., hydrogenases, iron-sulfur proteins, non-heme iron proteins, and heme proteins. In the past decades the group has made substantial contributions to the elucidation of structure-function relationships in metalloenzymes, in many cases in tight collaboration with groups in the field of theory, and molecular and structural biology. Furthermore, substantial methodological developments have been made in our group that are particularly advantageous for the project and the entire consortium. These are the adaptation of IR and RR spectroscopy to immobilized enzymes on electrodes coated with model membranes models (SEIRA, SERR spectroscopy), extension of SERR and SEIRA spectroscopy to the time-resolved domain, application of the freeze-quench to RR and EPR spectroscopy, RR spectroscopy analysis of protein crystals, IR/SEIRA spectroscopy under strictly anaerobic conditions, IR and EPR spectroscopy of enzymes in whole cells, and the development of integral theoretical/spectroscopic approaches for determining cofactor structures (in collaboration).

We will make the advanced vibrational spectroscopic techniques described in the “Methods” and “Expertise” sections available to all projects in the consortium.

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