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Research projects of the CIPKeBiP Centre of Excellence

The Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins brings together and connects the best Slovenian research groups in the fields of biomedicine, biotechnology and understanding life under extreme conditions.

The main research targets of CIPKeBiP are proteins together with their DNA and RNA. Together they form the basis for all molecular processes in living organisms and cells. The transfer of knowledge in the industrial environment is integrated into the research of the Centre of Excellence. 

The research work at the Centre of Excellence is organized in a single research program under the leadership of Prof. Dr. Dušan Turk, ARIS code 2990-001, and is carried out in the form of funded research projects and the infrastructure program based on successful applications to calls for proposals published, for example, by the Slovenian Research and Innovation Agency ARIS. 

ONGOING PROJECTS

Infrastructural Program: Analysis and protein production and biologically active molecules of medical importance

ARIS Code: IO―0048
Coordinator: Prof. Dr. Dušan Turk, CIPKeBiP
Duration: 2013-2014, 2015-2021, 2022-2027
Infrastructural program IO-0048

Research project: MicroBeast: Understanding microbial degradation for advanced sustainable materials and biodegradation techniques for tackling plastic pollution

ARIS Code: J4-50148 (C)
Coordinator: Dr. Miša Mojca Cajnko, National Institute of Chemistry
Duration: 2023-2026
Research project J4-50148

Research project: Human cathepsin F: An unusual cysteine protease involved in neurodegeneration

ARIS Code: J1-2473 (D)
Coordinator: Prof. Dr. Veronika Stoka, Jožef Stefan Institute
Duration: 2020-2023 + 2024
Research project J1-2473

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Completed Funding of Early Stage Researchers (2011-2017)

The training of the early stage researchers was financially supported by the Slovenian Research and Innovation Agency.

1. Early stage researcher Dr. Piotr Sosnowski finished on 4 May 2016,
Mentor Prof. Dr. Dušan Turk, duration from 1 November 2011 until 30 April 2016. ARIS code: 34422. Piotr Sosnowski received Krka award in 2016 for PhD thesis titled "Structural insight in the substrate specificity of cathepsins".

2. Early stage researcher Maša Černič,
Mentor Prof. Dr. Dušan Turk, duration from 1 December 2012 until 31 May 2017. ARIS code: 35500

3. Early stage researcher Dr. Štefan Možina finished on 22 June 2017,
Mentor Prof. Dr. Stojan Stavber, duration from 1 November 2013 until 31 March 2017. ARIS code: 36492

4. Early stage researcher Klara Čebular,
Mentor Prof. Dr. Stojan Stavber, duration from 1 November 2014 until 30 April 2018. ARIS code: 37542. Klara Čebular received an award for the best poster entitled "Direct metal-free dehydrative cross-coupling of alcohols and alkenes catalysed by molecular iodine under solvent-free reaction conditions" at the 6th International IUPAC Conference on Green Chemistry in September 2016 in Venice, Italy.

5. CIPKeBiP as institution is no longer eligible for applying for ARIS "Early stage researcher funding" due to new ARIS regulations.

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CIPKeBiP research areas in the period between 2010 to 2013

The European Regional Development Fund (85% co-financing) and the Slovenian Ministry of Science (15% co-financing) have co-financed the development of the CIPKeBiP Centre of Excellence with an operation code OP13.1.1.2.02.0005. The funding period was from 2010 to 2013. 

The research was carried out within the framework of the four research areas:

Mechanisms and Pathways of Immune Response

Principal investigator: Prof. Dr. Maja Rupnik

The focuss of the research work was to investigate molecular mechanisms of the immune response. The objectives were:mhc2
• Investigation of specific ways and molecules involved in infectious and communicable diseases,
• Identification of potential targets for diagnostics and treatment of infections,
• Investigation of infections with microorganisms,
• Investigations of autoimmune diseases,
• The study of mechanisms of introduction of pathogens into the cell and the immune response (immune response, infectious disease, cancer, ...),
• Investigation of intermolecular interactions from different point of view including biochemical and structural analysis and microscopy of cells and tissues.

Intra and intercellular communication

Principal investigator: Dr. Enej Kuščer

celicaDifferent mechanisms of intra and intercellular communication are responsible for correct functioning of cells, tissues, and indirectly for the whole organism. Any disturbances in mentioned mechanisms influence on the organism with some serious health consequences. Knowledge about these mechanisms is required to better understand the pathogenesis of diseases that result from damage or disturbance to inter-and intracellular communication. Additionally, the identification of the potential new drug targets is possible.

The research work was focused on:
• Research into the mechanisms by intracellular signaling organelles,
• Research of lysosomes, vesicles, secretory/endolysomal routes, and the connection between their injury and initiation of apoptosis or autophagy,
• Research into signaling of protein kinases in disturbed insulin secretion in diabetes,
• Research into signaling pathway in terms of search and identification of new targets for small molecule,
• Synthesis of small molecules of potential biosubstances or their precursors,
• Super-resolution optical microscopy to study subcellular organelles in living cells.

Adaptation mechanisms of extremofille to environment

Principal investigator: Prof. Dr. Nina Gunde Cimerman

The research work was focused in investigation of scproteins involved in adaptation to high salinity in the halophilic fungi. Additionally we tried to determine their potential use in addressing environmental and industrial problems. We were particularly interested in the nature of interactions between proteins involved in signal transmission along the HOG signaling pathway. For this purpose, we performed a structural characterization of the most important proteins of halo tolerance.

The new knowledge was comparable with the currently known information about the yeast Saccharomyces cerevisiae, which was sensitive to elevated salt concentration. Comparing of the two systems allowenabled the interpretation of the mechanisms of halo tolerance. The role of individual proteins were further confirmed by functional complementation of S. cerevisiae.

Protein Bank: Production and storage of proteins and their complexes

Principal investigator: Prof. Dr. Dušan Turk

crystal• System for continuous production of proteins was developed and it is in permanent use. System includes some relevant protein targets, their analysis, cloning, expression, purification, and basic bio-physical characterization.
• All DNA constructs and isolated proteins are stored in a central storage system.
• We developed a database for recording and storage protocols for expression and isolation of proteins (and other experimental data), which are always available to partners in a CO CIPKEBIP and the wider environment.

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Past Projects (2010-2023)

Research project: Structural insight into the mechanism of Clostridium difficile surface formation

ARIS Code: J1-1709
Coordinator: Prof. Dr. Dušan Turk, CIPKeBiP
Duration: 2019-2022
CIPKEBIP Research project J1-1709

Research project: Inhibition of Staphylococcus aureus cell wall remodeling

ARIS Code: J1-8152
Coordinator: Prof. Dr. Dušan Turk, Jožef Stefan Institute
Duration: 2017-2020
Research project J1-8152

Research project: Role of legumain in infection and inflammation

ARIS Code: J7-9435
Coordinator: Prof. Dr. Marko Fonović, Jožef Stefan Institute
Duration: 2018-2021
Research project J7-9435

Research project: Structural insight into iodine metabolism

ARIS Code: J1-7479 (F)
Coordinator: Prof. Dr. Dušan Turk, CIPKeBiP
Duration: 2016-2018
Research project J1-7479

Research project: The development of enzyme formulation for disinfecting prion-contaminated areas

ARIS Code: L7-8277
Coordinator: Prof. Dr. Nataša Poklar Ulrih, Biotechnical Faculty, University of Ljubljana
Duration: 2017-2019
Research project L7-8277

Research project: Role of cysteine cathepsins in inflammation-associated diseases

ARIS Code: J1-6739
Coordinator: Prof. DDr. Boris Turk, Jožef Stefan Institute
Duration: 2014-2017
Research project J1-6739

Research project: Proteomic and aptamer-based approaches for study of host-pathogen interactions in staphylococcal and clostridial infections

ARIS Code: J3-5500
Coordinator: Prof. Dr. Maja Rupnik, CIPKeBiP
Duration: 2013-2016
Research project J3-5500

Research project: Role of cysteine proteases in the process of cancerogenesis

ARIS Code: J1-5449
Coordinator: Dr. Marko Fonović, Jožef Stefan Institute
Duration: 2013-2016
Research project J1-5449

Research project: Prevention of growth of pathogenic fungi in dishwashers

ARIS Code: L4-5533
Coordinator: Prof. Dr. Nina Gunde-Cimerman, Biotechnical Faculty, University of Ljubljana
Duration: 2013-2016
Research project L4-5533

Research project: Exosome-associated Nef released from HIV infected cells contributes importantly to the development of neuro AIDS

ARIS Code: J3-5499
Coordinator: Dr. Boris Matija Peterlin, Medical Faculty, University of Ljubljana
Duration: 2013-2016
Research project J3-5499

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Bilateral project with Russia: Processing of antigens and immune response

Slovenian coordinator Prof. Dr. Dušan Turk, CIPKeBiP, Ljubljana;
Russian coordinator Dr. Sergey V. Lapin, St Petersburg Pavlov State Medical University, St. Petersburg.
Duration: 2012-2013

Research project: Oligomers of amyloidogenic proteins from a to z: biophysical properties, structure, function and mutual interactions

ARIS Code: J7―4050
Coordinator: Dr. Eva Žerovnik, Jožef Stefan Institute
Duration: 1.7.2011―30.6.2014

Research project: Involvement of the Lysosomal Cysteine Peptidase Inhibitors in Progression and Metastasis of Mammary Cancer

Code: J3―4267
Coordinator: Dr. Olga Vasiljeva, Jožef Stefan Institute
Duration: 1.7.2011―30.6.2014

Research project: Role and relevance of empirical geometric parameters in crystal structure determination of macromolecules for prediction of ligand binding

Code: J1―4213
Coordinator: Prof. Dr. Dušan Turk, Jožef Stefan Institute
Duration: 1.7.2011―30.6.2014  

Research project: The role of cysteine cathepsins in cellular signalling

Code: J1―4121
Coordinator: Prof. DDr. Boris Turk, Jožef Stefan Institute
Duration: 1.7.2011―30.6.2014

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