FKKT

Bologna 1st Cycle Study Programmes

Chemistry

• Molecular Fundamentals of Life Sciences (also Chemical Engineering; Marko Novinec)
• Biological Chemistry (Gregor Gunčar)

Biochemistry

• Biochemistry Fundamentals (Miha Pavšič)
• Practical Course in Biochemistry (Miha Pavšič)
• Biochemistry (Gregor Gunčar)
• Molecular Biology (Marko Dolinar)
• Biochemical Informatics ( Miha Pavšič)
• Molecular Cloning (Marko Dolinar)
• Protein Structure (Miha Pavšič)
• Enzymology (Marko Novinec)
• Cellular and Molecular Immunology (Gregor Gunčar)
• Biomacromolecules in Industry and Medicine (Miha Pavšič)
• Molecular Evolution and Development (Vera Župunski)

Bologna 2nd Cycle Study Programmes

Biochemistry

• DNA Technology  (Marko Dolinar)
• Methods of Macromolecular 3D Structure Determination (Kristina Djinović Carugo, Janez Plavec)
• Molecular Human Genetics (Vera Župunski, Boris Rogelj)
• Synthetic Biology (Marko Dolinar)
• Biochemistry of Multicellular Systems (Marko Novinec)
• Interactions of Biological Molecules (Marko Novinec)   
• Bionanotechnology (Gregor Gunčar)
• Selected Topics in Biomedical Chemistry (Boris Turk)
• Modern and Complementary Approaches in Structural Biology (Janez Plavec, Kristina Djinović Carugo)
• Molecular Biotechnology (Marko Dolinar)

Bologna 3rd Cycle Doctoral Study Programme in Chemical Sciences

• Modern Methods and Techniques in Biochemistry (Marko Dolinar)
• Selected Topics in Biochemistry (Miha Pavšič)
• Modern Computational Methods in Biochemistry (Marko Novinec)
• Biological Drugs (Gregor Gunčar)
• Modern NMR Approaches to Compound Characterization (Janez Plavec)

Extramural Courses

Bologna 1st Cycle Study Programmes (Biotechnical Faculty)   

• Enzyme Technology (Boris Turk)

Bologna 3rd Cycle Doctoral Study Programme in Biomedicine

• Principles and Techniques in Biochemistry and Molecular Biology (Miha Pavšič)
• Experimental Methods in Studies of Nucleic Acid Structure (Janez Plavec)
• Nuclear Magnetic Resonance in Research of Biological Macromolecules (Janez Plavec)
• Recombinant Proteins (Marko Dolinar)
• Protein Structure (Gregor Gunčar)
• Protein Glycosylation (Gregor Gunčar)

Chair members were engaged in seven research projects and in three different research programmes (mainly involving Jožef Stefan Institute staff): Toxins and Biomembranes, Proteolysis and its Regulation, and Structural Biology.
We are investigating structure-function relationship of transmembrane protein EpCAM (epithelial cell adhesion molecule) and the related molecule Trop-2 which participate in cell-cell contacts and signalling. To get insight into the structure of different parts of both molecules we combined the results obtained by X-ray crystallography and nuclear magnetic resonance with computer simulations of molecular dynamics. In addition, both molecules already serve as diagnostic and therapeutic targets due to their increased expression on the surface of carcinoma cells. In this field we are collaborating with the group of Prof. Plückthun from Switzerland who developed EpCAM-targetting DARPin molecules. Specifically, we are interested in mapping the surface of EpCAM recognized by DARPins and to use this knowledge for developing enchanced therapies.
We are studying the function of human extracellular calcium-binding protein SMOC-1 (Secreted MOdular Calcium-binding protein-1). Recombinant full-length protein, as well as its individual domains, have been prepared to obtain structural and functional data for determining its roles in the extracellular matrix. We have identified a heparan sulfate-binding region on SMOC-1 which mediates the adhesion and spreading of epithelial cells on SMOC-1.
We continued with investigations of structural and functional properties of α-actinin 1. We have also started studying interactions between α–actinin 2, myotilin and filamin C, which are Z-disc proteins of the sarcomere. Our goal is to determine three-dimensional structure of this protein and to elucidate structural changes that result from binding of calcium ions. In addition, we would like to study structural elucidation of the C-terminal portion of myotilin in complex with selected binding partners.

In 2012, we continued our research on the interactions between the cysteine peptidase cathepsin K and collagen at the molecular level. The results of this study will explain the roles of this enzyme in the mechanisms of bone resorption and development of osteoporosis. We have also identified the glycoprotein clusterin as an extracellular chaperone for cathepsin K and continued our work on the development of novel regulators of cathepsin K for use in vitro and in vivo.

Recently, large expansion of GGGGCC repeat has been discovered in the first intron of the C9orf72 gene, causing ALS and FTD. In patients, over 1,000 repeats were shown while normal population carries up to 22 repeats. Restriction analysis of the large expansion has shown that the repeat is not uniform, therefore we would like to determine the sequence of the expansion. Furthermore, we are looking for GGGGCC repeatsin interacting partners.

The research on toxinology continues to focus on the evolution, dynamics and mechanisms of transposition elements and on structure – function investigations of toxin proteins.

APOBEC3 proteins are cytidine deaminases, potent host restriction factors acting against various exogenous and endogenous retroviruses including retrotransposons. We are studying the mechanisms of APOBECs inhibition of retrotransposition in mammalian cell models, in vivo, and by genome analyses. Our studies reveal that various mammalian and non-mammalian APOBEC proteins are able to inhibit the pre-integration step of retrotransposition, and that the mechanism of retrotransposition is evolutionary conserved.

We started some experiments on cyanobacteria which will be used in biotechnological processes. Our major point of interest are intrinsic toxin – antitoxin systems and their suitability for increased biological safety.
Part of our research activities is focused on the proteins that are involved in immune response. In particular, we are interested in human MLKL protein, which we have expressed in bacteria. We have recorded NMR spectra of its structurally unknown N-terminal domain. The structure of this domain might help us to elucidate its biological role in necroptosis.

We are also developing nanobiosensors that are based on the hyper-variable domain of cameloid antibodies (nanobody). Target specific nanobody has been expressed in bacteria and the crystals of the nanobody in complex with small molecule antibody have been grown for structural studies.

• Refrigerated Floor and Tabletop Centrifuges
• Refrigerated Microcentrifuges
• Spectrophotometers UV / VIS with Computer Support
• Fluorimeter Perkin-Elmer LS 50 with Computer Support
• Fluorimeter Aminco
• Stopped-Flow Enzyme Kinetics Apparatus
• Incubator for Crystallization Trays Molecular Dimensions
• Crystallization Robot (96 Channels) Crystal Gryphon
• Microtiter Plate Readers
• PCR Apparatuses
• Spectrophotometer for Small Sample Volumes (NanoDrop)
• Rotation Homogenizer
• Ultrasound Homogenizer
• Electroporator
• Instruments for Electrophoretic Separations of Proteins and Western Blotting
• Phast Electrophoresis System
• Instruments for DNA Agarose Gel Electrophoresis
• Transilluminators
• Electrophoresis Documentation System
• Shakers
• Cooled Incubators/Shakers
• CO₂ Incubator
• Stereo Microscope M7.5 Leica
• Inverted Microscope CKX-41 Olympus
• Mixers and Shakers
• Analytical Balances
• Clean Chambers
• pH Meter
• Fast Protein Liquid Chromatograpy (FPLC)
• Acta Prime Protein Liquid Chromatography System
• High Performance Liquid Chromatography (HPLC)
• Fraction Collectors
• Flaked Ice Machines
• Thermostated Water Bath
• Dry steriliser
• Autoclaves
• Freezers -80 °C
• Ultrapure Water System Milli-Q