Engineering of Biomolecular Energy Conversion and Transport Modules for the Assembly of Molecular Factories

  • Schematic representation of a ‘simple’ biomolecular factory: The reactor is a nanocontainer (made of lipid or block copolymer) equipped with light-driven proton pumps (in red; energizing modules), proton-driven solute transporters (in blue; translocating modules) and metabolizing enzymes (in brown; metabolizing modules). Such light powered nanoreactors will import specific solutes from a solution and degrade them inside. Possible application: decontamination of water/solutions from toxic compounds or pollutant.
    Schematic representation of a ‘simple’ biomolecular factory: The reactor is a nanocontainer (made of lipid or block copolymer) equipped with light-driven proton pumps (in red; energizing modules), proton-driven solute transporters (in blue; translocating modules) and metabolizing enzymes (in brown; metabolizing modules). Such light powered nanoreactors will import specific solutes from a solution and degrade them inside. Possible application: decontamination of water/solutions from toxic compounds or pollutant.

Building autonomous synthetic organelles and cells with a defined function using a repertoire of functional modules (toolkit) and containing inside a minimal metabolism for survival, represents the ultimate goal of this project group.

Such complex processors will open a wide variety of possibilities ranging from environmental to medical applications. One of the most important challenges will be to provide a large repertoire of engineered and modular biomolecular-transport and -energy conversion systems for assembly of nanoreactors with diverse functionalities in lipid bilayers and block copolymers.

Initially, modules will include light-­driven proton pumps and proton-driven solute transporters in the membrane, and metabolizing enzymes inside the container. Next, more complex powering systems will be explored such as combinations of light-­driven proton pumps with sodium/proton antiporters with the objective: to energise sodium-driven solute transporters. This will significantly increase the repertoire and specificity of translocating modules.

The availability of numerous, highly specialized membrane proteins in milligram amounts offers the unique opportunity to use them as building blocks and toolkit to assemble molecular factories in the form of nanoreactors and functional surfaces using bottom-up approaches.

This project group has a strong expertise and knowledge in biochemistry, function and structure of membrane proteins. Furthermore, the group already possesses a significant number of recombinant transport proteins for different solutes such as peptides, sugars, amino acids and antibiotics that can be used as modules for engineering and assembly of nanoreactors.

Articles

P. R. Laskowski, M. Pfreundschuh, M. Stauffer, Z. Ucurum, D. FotiadisD. J. MüllerHigh-Resolution Imaging and Multiparametric Characterization of Native Membranes by Combining Confocal Microscopy and Atomic Force Microscopy-Based Multifunctional Toolbox“ ACS Nano (2017). [Link]
N. Ritzmann, J. Thoma, S. Hirschi, D. Kalbermatter, D. FotiadisD. J. MüllerFusion Domains Guide the Oriented Insertion of Light-Driven Proton Pumps into Liposomes“ Biophys J. (2017). [Link]
D. Kalbermatter, P. Chiu, J. Jeckelmann, Z. Ucurum, T. Walz, D. FotiadisElectron crystallography reveals that substrate release from the PTS IIC glucose transporter is coupled to a subtle conformational change“ J. Struct. Biol. (2017). [Link]
M. Pfreundschuh, D. Harder, Z. Ucurum, D. FotiadisD. J. MüllerDetecting Ligand-Binding Events and Free Energy Landscape while Imaging Membrane Receptors at Subnanometer Resolution“ Nano Lett. 17, 5, 3261-69 (2017). [Link]
D. Harder, S. Hirschi, Z. Ucurum, R. Goers, W. MeierD. J. MüllerD. FotiadisEngineering a Chemical Switch into the Light-driven Proton Pump Proteorhodopsin by Cysteine Mutagenesis and Thiol Modification“ Angew. Chem. Int. Ed.  55, 8846 (2016). [Link]
S. HirschiM. Stauffer, D. Harder, D. J. MüllerW. MeierD. FotiadisEngineering and Assembly of Protein Modules into Functional Molecular Systems“ Chimia 6, 398 (2016). [Link]
R. Boggavarapu, S. Hirschi, D. Harder, M. Meury, Z. Ucurum, M. J. Bergeron, D. FotiadisPurification of Human and Mammalian Membrane Proteins Expressed in Xenopus laevis Frog Oocytes for Structural Studies“ Heterologous Expression of Membrane Proteins 1432, 223-42 (2016). [Link]
D. Kalbermatter, J. Jeckelmann, P. Chiu, Z. Ucurum, T. Walz, D. Fotiadis2D and 3D crystallization of the wild-type IIC domain of the glucose PTS transporter from Escherichia coli“ J. Struct. Biol. 191, 376-80 (2015). [Link]
R. Boggavarapu, J. Jeckelmann, D. Harder, Z. Ucurum, D. FotiadisRole of electrostatic interactions for ligand recognition and specificity of peptide transporters“ BMC Biol. 13, DOI: 10.1186/s12915-015-0167-8 (2015). [Link] [More Information]
D. Fotiadis, A. Engel “Two‐Dimensional Crystallisation of Membrane Proteins and Structural Assessment“ eLS, 1-10 (2015). [Link]
R. Petrosyan, C. A. Bippes, S. Walheim, D. Harder, D. Fotiadis, T. Schimmel, D. Alsteens, D. J. MüllerSingle-Molecule Force Spectroscopy of Membrane Proteins from Membranes Freely Spanning Across Nanoscopic Pores“ Nano Lett. 15, 3624 (2015). [Link]
P. D. Bosshart, A. Engel, D. FotiadisHigh-Resolution Atomic Force Microscopy Imaging of Rhodopsin in Rod Outer Segment Disk Membranes“ Rhodopsin, 189-203 (2015). [Link]

Who works with whom?

Prof. Dimitrios Fotiadis from the University of Berne (Institute of Biochemistry and Molecular Medicine) leads this project and works in close collaboration with Stephan Hirschi and Mirko Stauffer (PhD-students).

Group

Read more about the Fotiadis-Group here.

Collaborations

Biophysical and structural characterization of engineered modules is being performed in collaboration with the groups of Daniel Müller and Gebhard Schertler, and assembly of modules into block copolymers in collaboration with Wolfgang Meier and Cornelia Palivan. Interactions with Urs Dürg and Sven Panke are and will be crucial for the development of functional surfaces and minimal metabolisms of nanocells, respectively. We are supporting with our expertise in membrane proteins projects from Richard Kammerer and Thomas Ward.