Partner 4

Biotransformation and Biocatalysis, and Protein Crystallography, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen (RUG), the Netherlands

Both RUG research groups participating in the P4FIFTY RTN project belong to GBB. This university institute performs research in the field of biomolecular sciences, with a focus on proteins and molecular microbiology. We aim to understand the structure and dynamics of proteins in relation to their function and activity; to unravel the functional role of proteins in living cells; and to obtain insight in the fundamental properties of proteins that are relevant for application in health and the emerging bio-based economy. As a graduate school, GBB provides an attractive research and training environment for (under)graduate students and postdoctoral fellows.

Biocatalysis is a strong research topic in GBB.  The institute attracts funding from programmes supported by the Dutch Government, industries and the EU. In this area, the three major research lines at GBB are engineering of enzymes for the production of antibiotics, the discovery and redesign of oxidative biocatalysis for efficient synthesis of fine chemicals, and the identification, characterization, and engineering of carbohydrate-acting enzymes. Metagenomics, directed evolution, and protein engineering are combined with high-throughput screening approaches to select for new and improved enzyme activities. Much of the enzyme engineering research is supported by mechanistic and functional insight obtained by protein crystallography. The unique close interaction between crystallography, organic chemistry and biochemistry contributes to the training of PhD students and post docs.

Biotransformation and Biocatalysis
Head: Prof. dr. D.B. Janssen and Prof. Dr. M.W. Fraaije

The Biotransformation and Biocatalysis group has a key position in GBB's efforts in enzyme discovery and engineering. The group investigates the enzymology of the microbial transformation of synthetic compounds, and the development of improved biocatalysts for such transformations. We study catalytic mechanisms, kinetic properties, and structure-function relationships in enzymes that can be used for regio- and enantioselective synthesis reactions for preparing fine chemicals. We also investigate enzymes involved in the biodegradation of environmental pollutants by microorganisms. Obtaining new enzymes by enrichment, genome mining, and high-throughput screening as well as their improvement by structure-inspired directed evolution are important parts of this work. Applications are developed in various projects with external partners, including industry.

Enzyme discovery, characterization and engineering for new applications

Protein crystallography: structure-function relationship of proteins
Head: Prof. dr. B.W. Dijkstra

The goal of the research in the Protein Crystallography group is to gain insight into the functioning of proteins at the atomic level. Structure-function relationships of proteins are determined via the high-resolution analysis of structures and active sites of enzymes and larger protein complexes using protein X-ray crystallography, in combination with other biochemical and biophysical tools. Proteins under investigation are enzymes involved in carbohydrate bioprocessing and biotransformation of synthetic compounds, as well as transporters and membrane membrane protein complexes.

Some α/β-hydrolase fold enzymes of which the structures were solved in the Protein Crystallography group

Examples of proteins of which structures were solved by this research group are dehalogenases, epoxide hydrolase, aminotransferases, amino esterases, and other enzymes involved in microbial detoxification or important for industrial biocatalysis. Several of the research projects are directed towards the elucidation of reaction mechanisms of novel enzymes and protein engineering of enzymes to make them more suitable for application in biotechnology. Due to its front-end position in the crystallographic analysis of enzymes, the group plays a central role in GBB's research in enzyme engineering.

Recent publications

Augustyniak W, Brzezinska AA, Pijning T, Wienk H, Boelens R, Dijkstra BW, Reetz MT. Biophysical characterization of mutants of Bacillus subtilis lipase evolved for thermostability: factors contributing to increased activity retention. Protein Sci 2012, 21:487-97.
 
Pijning T, Anwar MA, Böger M, Dobruchowska JM, Leemhuis H, Kralj S, Dijkhuizen L, Dijkstra BW. Crystal structure of inulosucrase from Lactobacillus: insightsinto the substrate specificity and product specificity of GH68 fructansucrases. J Mol Biol 2011 412:80-93.
 
Schallmey A, den Besten G, Teune IG, Kembaren RF, Janssen DB. Characterization of cytochrome P450 monooxygenase CYP154H1 from the thermophilic soil bacterium Thermobifida fusca. Appl Microbiol Biotechnol 2011 89:1475-85
 
Szymański W, Westerbeek A, Janssen DB, Feringa BL. A simple enantioconvergent and chemoenzymatic synthesis of optically active α-substituted amides. Angew Chem Int Ed Engl 2011 50:10712-5.
 
van Leeuwen JG, Wijma HJ, Floor RJ, van der Laan JM, Janssen DB. Directed evolution strategies for enantiocomplementary haloalkane dehalogenases: from chemical waste to enantiopure building blocks. Chembiochem 2012 13:137-48.
 
Wu B, Szymański W, Wybenga GG, Heberling MM, Bartsch S, de Wildeman S, Poelarends GJ, Feringa BL, Dijkstra BW, Janssen DB. Mechanism-inspired engineering of phenylalanine aminomutase for enhanced β-regioselective asymmetric amination of cinnamates. Angew Chem Int Ed Engl 2012, 51:482-6.