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Projects / Programmes source: ARIS

Structural Biology

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Periods
January 1, 2009 - December 31, 2013
Research activity

Code Science Field Subfield
1.05.00  Natural sciences and mathematics  Biochemistry and molecular biology   

Code Science Field
P250  Natural sciences and mathematics  Condensed matter: structure, thermal and mechanical properties, crystallography, phase equilibria 
P310  Natural sciences and mathematics  Proteins, enzymology 
P351  Natural sciences and mathematics  Structure chemistry 
P370  Natural sciences and mathematics  Macromolecular chemistry 
B110  Biomedical sciences  Bioinformatics, medical informatics, biomathematics biometrics 
B120  Biomedical sciences  Molecular biophysics 
B500  Biomedical sciences  Immunology, serology, transplantation 
T360  Technological sciences  Biochemical technology 
T410  Technological sciences  Pharmaceuticals and related technologies 
T490  Technological sciences  Biotechnology 

Code Science Field
1.06  Natural Sciences  Biological sciences 
Keywords
structural biology, macromolecular crystallography, immunology,limited proteolysis, MHC class II, cathepsins, invariant chain, antigen presentation, endosomlal pathway, computational methods
Evaluation (rules)
source: COBISS
Evaluation of bibliographic research performance indicators according to ARIS methodology
Citations Citations for bibliographic records in COBIB.SI that are linked to records in citation databases
source: WoS source: Scopus source: COBISS
Researchers (15)
no. Code Name and surname Research area Role Period No. of publications
1.  22282  PhD Miha Andrejašič  Biochemistry and molecular biology  Researcher  2009  18 
2.  32145  PhD Leon Bedrač  Chemistry  Junior researcher  2009 - 2010  19 
3.  23477  PhD Mojca Beseničar  Biochemistry and molecular biology  Researcher  2009 - 2011  40 
4.  22470  PhD Katarina Črnigoj Kristan  Biochemistry and molecular biology  Researcher  2010 - 2011  35 
5.  15970  Andreja Doberšek  Biochemistry and molecular biology  Technical associate  2009 - 2013  25 
6.  06416  PhD Marko Dolinar  Biochemistry and molecular biology  Researcher  2009 - 2013  341 
7.  15639  PhD Gregor Gunčar  Biochemistry and molecular biology  Researcher  2009 - 2010  262 
8.  29526  MSc Blanka Hanzlowsky  Chemistry  Junior researcher  2009  0 
9.  22320  PhD Marko Mihelič  Biochemistry and molecular biology  Researcher  2009 - 2013  78 
10.  36346  PhD Sara Pintar  Biochemistry and molecular biology  Junior researcher  2013  20 
11.  19422  Polonca Pirš    Technical associate  2009 - 2013  0 
12.  25629  PhD Miha Renko  Biochemistry and molecular biology  Researcher  2009 - 2013  87 
13.  35125  PhD Abelardo Manuel Silva  Biochemistry and molecular biology  Researcher  2012 - 2013  2 
14.  04988  PhD Dušan Turk  Biochemistry and molecular biology  Head  2009 - 2013  621 
15.  26515  PhD Aleksandra Usenik  Biochemistry and molecular biology  Researcher  2011 - 2013  54 
Organisations (2)
no. Code Research organisation City Registration number No. of publications
1.  0103  University of Ljubljana, Faculty of Chemistry and Chemical Technology  Ljubljana  1626990  23,083 
2.  0106  Jožef Stefan Institute  Ljubljana  5051606000  90,682 
Significance for science
Dušan Turk is one of the most cited researchers in the area of life sciences working and living in Slovenia. In the world he is noticeable developer of computational methods of macromolecular crystallography )Turk, 2013) as indicated by talks at international conferences. In this period the group caught the technological edge also in the experimental part of structural biology and became internationally competitive (for example talk at the Keystone conference). This was made possible by substantial investments in equipment in the frame of the Centre of excellence CIPKEBIP project. D. Turk coordinated preparation of the project and later the conducted the project as Scientific director of the Centre. Publications in this period mostly continued research from the previous period. These were studies of mechanisms of regulation of proteolisys. Published works described srudies of cysteine proteases and their inhibitors. Our studies revealed the structure of clitocypins as a new family of protease inhibitors with the ß-trefoil fold and their mechanism of inhibition of cysteine proteases. This studies provided insight into into mechanism by which the inhibitors sharing the ß-trefoil fold inhibit also serine proteases and legumain family of cysteine proteases. There are papers published in JBC (Renko in sod. 2010; Sabotič in sod., 2012; Pohleven in sod., 2012) and review in Biological Chemistry in a dedicated issue (Renko et al., 2012). With the aid of knowhow and available infrastructure the Structural biology group elevates the level of research also other groups in the area )Brvare et al., 2012, Mirković et al., 2011). Important are also collaborations within the Department of Biochemistry and Molecular and Structural Biology with the group of Boris Turk.
Significance for the country
The development of structural biology as a field started 50 years ago, however, in Slovenia we followed with a 30 year delay. This group made a significant contribution to the field with the determination of the first protein crystal structures in the country. Knowledge in this field was gained by the PI of this program working on his PhD thesis with Nobel laureate Robert Huber at the Max­Planck Institute in Martinsried, Munich. The first crystal structures of cysteine cathepsins, their inhibitors stefins and cystatins, and the mechanism of their interactions were determined. With these achievements, the Slovenian researchers became recognized in their home country and internationally. They published a series of prominent publications with high citation rate including crystal structure of the complex cathepsin L­p41 Ii (EMBO J., 1999). They became a worldwide recognized group, thus contributing to the reputation of Slovenian science. Later, they also participated in the EU Framework Programmes. The obtained knowledge shows potential in the pharmaceutical industry and biotech SMEs. In the past it was an active cooperation with the pharmaceutical industry, which contributed significantly to the purchase of equipment. This research provided the basis of structural biology at the Jožef Stefan Institute, University of Ljubljana, University of Primorska, and the International Postgraduate School IJS. The research work resulted in doctoral dissertations, master's and bachelor's degrees. Former students and employees are currently employed in industry, other institutes, universities, administration (such as EU) or abroad. Lack of investment in the past has a serious impact on our research. Development in this area is linked to significant investment in research itself, as well as in infrastructure for protein production, crystallization and structure determination. The recent and pending investments in the equipment within the Centre of Excellence CIPKeBiP now brought the equipment and achievements to the competitive level of research (as demonstrated by in the invitation to present our work at Keystone Conference “High throughput Structural Biology” 2012, and one paper first in the field, 2013). However, the size of the team below the critical mass (4.7 FTE) and the reducing resources for covering of material costs of research (30% reduction in the last two years, the value of 1 FTE is about 65 000 EUR in 2013) are now a serious limitation to perform research at the international competitive level. Nevertheless, our achievements contributed to the development of structural biology in Slovenia and internationally.
Most important scientific results Annual report 2009, 2010, 2011, 2012, final report, complete report on dLib.si
Most important socioeconomically and culturally relevant results Annual report 2009, 2010, 2011, 2012, final report, complete report on dLib.si
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