Research
In the focus of our research are enzymes, which are elaborate proteins that catalyse cellular reactions with high specificity and efficiency.
Model system
Our preferred model system is the (βα)8-barrel family of enzymes, which is the most frequently encountered protein fold. (βα)8-barrel enzymes catalyse a large variety of mechanistically diverse reactions. The fold of the canonical (βα)8-barrel consists of a central barrel of eight parallel β-strands, which are surrounded by eight external α-helices. Connecting loops are located at both the N-terminal (α-β loops) and the C-terminal (β-α loops) face of the barrel. Due to the spatial separation of structural elements that are important for stability and catalytic activity, (βα)8-barrels provide an ideal scaffold for the study of enzyme evolution and the design of new enzymatic activities.
Projects
We are using rational design and directed evolution to engineer the stability and catalytic activity of enzymes, experimentally reconstruct the natural evolution of enzymes, assign functions to uncharacterised enzymes, and characterize allosteric interactions within multi-enzyme complexes. To this end, we apply a broad range of experimental and computational methods.
Team-Leaders
Alumni
Dr. Silke Beissmann-Driemeier |
Jan 1998 - Jan 2001 |
Vera Röhlich |
Juli 2000 - Juni 2001 |
Dr. Martina Henn-Sax |
Sept 1998 - Dez 2001 |
Dr. Andreas Ivens |
Jan 2000 - Juni 2002 |
Dr. Stefan Hettwer |
Apr 1998 - Sept 2002 |
Dr. Satoshi Akanuma |
Juli 2001 - Feb 2003 |
Dr. Birte Höcker |
Nov 1998 - Juni 2003 |
Dr. Manal Bosnali |
Okt 2002 - März 2004 |
Natalie Heuer |
Okt 2002 - März 2004 |
Simona Jansen |
Juli 2000 - April 2004 |
Iris Lambeck |
Dez 2003 - Dez 2004 |
Dr. Catharina Dönges |
März 2000 - Jan 2005 |
Susanne Marquardt |
April 2004 - März 2005 |
Birgit Schwarz |
Dez 2003 - April 2005 |
Dr. Michaela Häger |
Feb 2001 - Juni 2005 |
Dr. Karin Babinger |
Juni 2005 - Okt 2005 |
Dr. Sonja Leopoldseder |
2001 - Jan 2006 |
Christian Bolz |
Jan 2006 - Nov 2006 |
Maximilian Plank |
Juni 2006 - Aug 2007 |
Lorella Ungar |
Jan 2004 - Aug 2007 |
Matthias Zwick |
Sep 2006 - Dez 2007 |
Dr. Markus Richter |
Mai 2004 - Aug 2008 |
Dr. Jörg Claren |
Nov 2004 - Dez 2008 |
Ulrike Eßlinger |
Juni 2008 - Mai 2009 |
Daniel Roderer |
Sep 2008 - Aug 2009 |
Bettina Sommer |
Feb 2009 - Nov 2009 |
Dr. Felix List |
Nov 2004 - März 2010 |
Dr. Alexander Ehrmann |
Okt 2005 - Aug 2010 |
Dr. Tobias Seitz |
April 2006 - Sept 2010 |
Nadine Borst |
Jan 2010 - Sept 2010 |
Dr. Thomas Schwab |
Jan 2006 - Dez 2010 |
Dr. Susanne Dietrich |
Okt 2005 - Dez 2010 |
Dr. Harald Guldan |
Feb 2007 - Juni 2011 |
Dr. Marco Bocola |
Okt 2006 - Juli 2011 |
Dr. Hermann Zellner |
April 2007 - Okt 2011 |
Barbara Beer |
Mai 2011 - Mai 2012 |
Dr. Daniel Schneider |
Dez 2006 - Mai 2012 |
Dr. Linn Carstensen |
Okt 2008 - Juni 2012 |
Veronika Schmid |
Jan 2012 - Sept 2012 |
Bastian Groitl |
Jan 2012 - Sept 2012 |
Dr. Monika Meier |
Feb 2008 - Jan 2013 |
Dr. Dietmar Birzer |
März 2009 - Aug 2013 |
Dr. Josef Sperl |
Aug 2009 - Aug 2013 |
Dr. David Peterhoff |
Aug 2009 - Okt 2013 |
Dr. Bernd Reisinger |
Aug 2009 - Juli 2014 |
Dr. Florian Busch |
Jan 2010 - Aug 2015 |
Dr. Alexandra Holinski |
Nov 2011 - Apr 2017 |
Dr. Patrick Löffler |
Dez 2012 - Mai 2017 |
Dr. Wolfgang Kaiser | Jan 2013 - Sept 2017 |
Publications
The following list summarizes all contributions of the scientific employees
2018 - 2017
Schlee, S., Klein, T., Schumacher, M., Nazet J., Merkl, R., Steinhoff, H.J. & Sterner, R. (2018). Relationship of catalysis and active site loop dynamics in the (βα)8-barrel enzyme indole-3-glycerol phyosphate synthase. Biochemistry doi: 10.1021/acs.biochem.8b00167 [Epub ahead of print].
Löffler, P., Schmitz, S., Hupfeld, E., Sterner, R. & Merkl, R. (2017). Rosetta: MSF: a modular framework for multi-state computational protein design. PLoS Comput Biol 13, e1005600.
Holinski, A., Heyn, K., Merkl, R. & Sterner, R. (2017). Combining ancestral sequence reconstruction with protein design to identify an interface hotspot in a key metabolic enzyme complex. Proteins 85, 312-321.
2014 - 2013
Janda, J. O., Meier, A. & Merkl, R. (2013). CLIPS-4D: a classifier that distinguishes structurally and functionally important residue-positions based on sequence and 3D data. Bioinformatics 29, 3029-3035.
Sperl, J. M., Rohweder, B., Rajendran, C. & Sterner, R. (2013). Establishing catalytic activity on an artificial (βα)8-barrel protein designed from identical half-barrels. FEBS Lett.. 587, 2798-2805.
Meier, M.M., Rajendran, C., Malisi, C., Fox, N.G., Xu, C., Schlee, S., Barondeau, D.P. Hoecker, B., Sterner, R. & Raushel, F.M. (2013). Molecular engineering of organophosphate hydrolysis activity from a weak promiscuous lactonase template. J. Am. Chem. Soc. 135, 11670-11677.
Hauptmann, J., Dueck, A., Harlander, S., Pfaff, J., Merkl, R. & Meister, G. (2013). Turning catalytically inactive human Argonaute proteins into active slicer enzymes. Nat. Struct. Mol. Biol. 20, 814-817.
2012 - 2011
Carstensen, L., Sperl, J. M., Bocola, M., List, F., Schmid, F. X. & Sterner, R. (2012). Conservation of the folding mechanism between designed primordial (βα)8-barrel proteins and their modern descendant. J. Am. Chem. Soc. 134, 12786-12791.
Dietrich, S., Borst, N., Schlee, S., Schneider, D., Janda, J. O., Sterner, R. & Merkl, R. (2012). Experimental assessment of the importance of amino acid positions identified by an entropy-based correlation analysis of multiple sequence alignments. Biochemistry 51, 5633-5641.
molecules of β-galactosidase. Biochem. Cell Biol. 90, 540-547.
Carstensen, L., Zoldák, G., Schmid, F. X. & Sterner, R. (2012). Folding mechanism of an extremely thermostable (βα)8-barrel enzyme: a high kinetic barrier protects the protein from denaturation. Biochemistry 51, 3420-3432.
Guldan, H., Matysik, F. M., Bocola, M., Sterner, R. & Babinger, P. (2011). Functional assignment of an enzyme that catalyzes the synthesis of an archaea-type ether lipid in bacteria. Angew. Chem. Int. Ed. Engl. 50, 8188-8191.
2010 - 2009
B Mandach, C. & Merkl R. (2010) Genes optimized by evolution for accurate and fast translation encode in Archaea and Bacteria a braod and characteristic spectrum of protein functions. MC Genomics 11, 617.
Richter, M., Bosnali, M., Carstensen, L., Seitz, T., Durchschlag, H., Blanquart, S., Merkl, R. & Sterner, R. (2010). Computational and experimental evidence for the evolution of a (βα)8-barrel protein from an ancestral quarter-barrel stabilised by disulfide bonds. J. Mol. Biol. 398, 763-773.
Drzewiecki, K., Angelov, A., Ballschmiter, M. Tiefenbach, K.-J., Sterner, R. & Liebl, W. (2010) Hyperthermostable acetyl xylan esterase. Microbial Biotechnol. 3, 84-92.
Schlee, S., Deuss, M., Bruning, M., Ivens, A., Schwab, T., Hellmann, N., Mayans, O. & Sterner, R. (2009). Activation of anthranilate phosphoribosyl transferase from Sulfolobus solfataricus by removal of Mg-inhibition and acceleration of product release. Biochemistry 48, 5199-5209.
Claren, J., Malisi, C., Höcker, B. & Sterner, R. (2009). Establishing wild-type levels of catalytic activity on natural and artificial (βα)8-barrel protein scaffolds. Proc. Natl. Acad. Sci. USA 106, 3704-3709.
Fischer, A., Enkler, N., Neudert, G., Bocola, M., Sterner, R. & Merkl, R. (2009). TransCent: Computational enzyme design by transferring active sites and considering constraints relevant for catalysis. BMC Bioinformatics 10, 54.
Seitz, T., Thoma, R., Schoch, G.A., Stihle, M., Benz, J., D'Arcy, B., Wiget, A., Ruf, A., Hennig, M. & Sterner, R. (2010). Enhancing the stability and solubility of the glucocorticoid receptor ligand-binding domain by high-throughput library screening. J. Mol. Biol. 403, 562-577.
Höcker, B., Lochner, A., Seitz, T., Claren, J. & Sterner, R. (2009). High-resolution crystal structure of an artificial (βα)8-barrel protein designed from identical half-barrels. Biochemistry 48, 1145-1147.
2008 - 2006
Guldan, H., Sterner, R. & Babinger, P. (2008). Identification and Characterization of a Bacterial Glycerol-1-phosphate Dehydrogenase: Ni2+ -Dependent AraM from Bacillus subtilis. Biochemistry 47, 7376-7384.
Merkl, R. & Zwick, M. (2008). H2r:Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments. BMC Bioinformatics 9, 151.
Merkl, R. (2007). Modelling the evolution of the archeal tryptophan synthase. BMC Evol Biol. 7, 59.
Merkl, R. (2006). AMIGOS: a method for the inspection of genomic organisation or structure and its application to characterise conserved gene arrangements. In Silico Biol. 6, 281-306.
Waack, S., Keller, O., Asper, R., Brodag, T., Damm, C., Fricke, W. F., Surovcik, K., Meinicke, P. & Merkl, R. (2006). Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models. BMC Bioinformatics 7, 142.
Merkl, R. (2006). A comparative categorization of protein function encoded in bacterial or archeal genomic islands. J Mol Evol. 62, 1-14.
2005 - 2003
Schneider, B., Knöchel, T., Darimont, B., Hennig, M., Dietrich, S., Babinger, K., Kirschner, K. & Sterner, R. (2005). Role of the N-terminal Extension of the (βα)8-Barrel Enzyme Indole-3-Glycerol Phosphate Synthase for its Fold, Stability and Catalytic Activity. Biochemistry 44, 16405-16412.
Wiezer, A. & Merkl, R. (2005). A comparative categorization of gene flux in diverse microbial species. Genomics 86, 462-475.
Höcker, B., Claren, J. & Sterner, R. (2004). Mimicking enzyme evolution by generating new (βα)8-barrels from (βα)4-half-barrels. Proc. Natl. Acad. Sci. USA 101, 16448-16453.
Meinicke, P., Tech, M., Morgenstern, B. & Merkl, R. (2004). Oligo kernels for datamining on biological sequences: a case study on prokaryotic translation initiation sites. BMC Bioinformatics 5, 169.
Veith, B., Herzberg, C., Steckel, S., Feesche, J., Maurer, K. H., Ehrenreich, P., Bäumer, S., Henne, A., Liesegang, H., Merkl, R., Ehrenreich, A. & Gottschalk, G. (2004). The complete genome sequence of Bacillus licheniformis DSM13, an organism with great industrial potential. J Mol Microbiol Biotechnol. 7, 204-211.
Merkl, R. (2004). SIGI: score-based identification of genomic islands. BMC Bioinformatics 5, 22.
Henne, A., Brüggemann, H., Raasch, C., Wiezer, A., Hartsch, T., Liesegang, H., Johann, A., Lienard, T., Gohl, O., Martinez-Arias, R., Jacobi, C., Starkuviene, V., Schlenczeck, S., Dencker, S., Huber, R., Klenk, H. P., Kramer W., Merkl, R., Gottschalk, G., & Fritz, H.J.(2004). The genome sequence of the extreme thermophile Thermus thermophilus. Nat. Biotechnol. 22, 547-553.
Helmstaedt, K., Heinrich, G., Merkl, R. & Braus, G. H. (2004). Chorismate mutase of Thermus thermophilus is a monofunctional AroH class enzyme inhibited by tyrosine. Arch Microbiol. 181, 195-203.
Tech, M. & Merkl, R. (2003). YACOP: Enhanced gene prediction obtained by a combination of existing methods. In Silico Biol. 3, 441-451.
Merkl, R. (2003). A survey of codon and amino acid frequency bias in microbial genomes focusing on translational efficiency. J Mol Evol. 57, 453-466.
Wiezer, A. & Merkl, R. (2003). secureBLAST. In Silico Biol. 3, 405-409.
Bruggemann, H., Baumer, S., Fricke, W. F., Wiezer, A., Liesegang, H., Decker, I., Herzber, C., Martinez-Arias, R., Merkl, R., Henne, A. & Gottschalk, G. (2003). The genome sequence of Clostridium tetani, the causative agent of tetanus disease. Proc Natl Acad Sci U S A 100, 1316-1321.
2002 - 2000
Henn-Sax, M., Thoma, R., Schmidt, S., Hennig, M., Kirschner, K. & Sterner, R. (2002). Two (βα)8-barrel enzymes of histidine and tryptophan biosynthesis have similar reaction mechanisms and common strategies for protecting their labile substrates. Biochemistry 41, 12032-12042.
Douangamath, A., Walker, M., Beismann-Driemeyer, S., Vega-Fernandez, M.C., Sterner, S. & Wilmanns, M. (2002). Structural evidence for ammonia tunnelling across the (βα)8-barrel of the imidazole glycerol phosphate synthase bienzyme complex. Structure 10, 185-193.
Larbig, K. D., Christmann, A., Johann, A., Klockgether, J., Hartsch, T., Merkl, R., Wiehlmann, L., Fritz, H. J. & Tümmler, B. (2002). Gene islands integrated into tRNA(Gly) genes confer genome diversity on a Pseudomonas aeruginosa clone. J Bacteriol. 184, 6665-6680.
Deppenmeier, U., Johann, A., Hartsch, T., Merkl, R., Schmitz, R. A., Martinez-Arias, R., Henne, A., Wiezer, A., Bäumer, S., Jacobi, C., Brüggemann, H., Lienard, T., Christmann, A., Bömeke, M., Steckel, S., Bhattacharyya, A., Lykidis, A., Overbeek, R., Klenk, H. P., Gunsalus, R. P., Fritz, H. J. & Gottschalk, G. (2002). The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. J Mol Microbiol Biotechnol. 4, 453-461.
Höcker, B., Beismann-Driemeyer, S., Hettwer, S., Lustig, A. & Sterner, R. (2001). Dissection of a (βα)8-barrel enzyme into two folded halves. Nat. Struct. Biol. 8, 32-36.
Reviews
Sterner, R. & Brunner, E. The relationship between catalytic activity, structural flexibility and conformational stability as deduced from the analysis of mesophilic - thermophilic enzyme pairs and protein engineering studies. In: F. Robb et al., eds., Thermophiles - Biology and Technology at High Temperatures, CRC Press, Boca Raton, London, New York, pp. 25-38, 2008.
Sterner, R. (2001). 4Fe-4S ferredoxin from Thermotoga maritima. Meth. Enzymol. 334, 23-30.
Höcker, B., Jürgens, C., Wilmanns, M. & Sterner, R. (2001). Stability, catalytic versatility and evolution of the (βα)8-barrel fold. Curr. Opin. Biotechnol. 12, 376-381.
Henn-Sax, M., Höcker, B., Wilmanns, M. & Sterner, R. (2001). Divergent evolution of (βα)8-barrel enzymes. Biol. Chem. 382, 1315-1317.
Others
Meeting reports, books, book reviews, guest editorials
Claren, J., Schwab, T. & Sterner, R. (2018). Library generation and auxotrophic selection assays in Escherichia coli and Thermus thermophilus. Methods Mol Biol, 1685, 333-345.
Merkl, R. (2015) Bioinformatik: Grundlagen, Algorithmen, Anwendungen. Wiley-VCH, Weinheim.
Sterner, R. (2011). Directed evolution: a powerful approach to optimising and understanding enzymes. ChemBioChem 12, 1439-1440.
Merkl, R. & Waack, Stephan (2009) Bioinformatik Interaktiv: Algorithmen und Praxis. Wiley-Blackwell, Weinheim.
Sterner, R. & Skerra, A. (2007). Design von Enzymen und anderen Proteinen: Einblicke aus Natur, Labor und Computersimulationen. Biospektrum 07, 814.
Sterner, R. & Schmid, F.X. (2004). De novo design of an enzyme. Science 304, 1916-1917.
Schmid, F.X. & Sterner, R. (2004). Protein Design. ChemBioChem 5, 143-144.
contact
Prof. Dr. Reinhard Sterner
Institute of Biophysics and Physical Biochemistry
Room Nr. E3_1.313
Address:
University of Regensburg
Universitätsstrasse 31
93053 Regensburg
Postal Address:
University of Regensburg
93040 Regensburg
Secretary:
Claudia Pauer
Room Nr. E3_1.311
Phone +49-941-943 3004
Fax +49-941-943 2813