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Projects / Programmes source: ARIS

Folding and dynamics of biomolecular systems

Periods
Research activity

Code Science Field Subfield
1.04.01  Natural sciences and mathematics  Chemistry  Phyisical chemistry 

Code Science Field
P400  Natural sciences and mathematics  Physical chemistry 

Code Science Field
1.04  Natural Sciences  Chemical sciences 
Keywords
biomolecular systems, structure, dynamics, protein folding, atomistic simulations, vibrational spectroscopy, NMR spectroscopy, hydration, hydrophobicity, intrinsically disordered proteins, ligand binding, hydrogen bonding, membrane proteins, aggregation, statistical thermodynamics
Evaluation (rules)
source: COBISS
Points
2,436.68
A''
76.42
A'
1,453.6
A1/2
1,828.28
CI10
4,731
CImax
163
h10
36
A1
8.72
A3
1.14
Data for the last 5 years (citations for the last 10 years) on July 24, 2024; A3 for period 2018-2022
Data for ARIS tenders ( 04.04.2019 – Programme tender , archive )
Database Linked records Citations Pure citations Average pure citations
WoS  287  7,275  6,046  21.07 
Scopus  299  7,837  6,546  21.89 
Researchers (11)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  57590  Mohamed Elwy Abdelhamed Abdelmonaem  Computer intensive methods and applications  Junior researcher  2023 - 2024  12 
2.  08329  PhD Simona Golič Grdadolnik  Chemistry  Researcher  2019 - 2024  323 
3.  08523  PhD Jože Grdadolnik  Chemistry  Researcher  2019 - 2024  258 
4.  57986  Anže Hubman  Computer intensive methods and applications  Junior researcher  2023 - 2024  14 
5.  13627  PhD Franci Merzel  Computer intensive methods and applications  Head  2019 - 2024  219 
6.  34527  PhD Urban Novak  Chemistry  Researcher  2019 - 2024  35 
7.  50459  Iza Ogris  Chemistry  Junior researcher  2019 - 2024  42 
8.  50851  PhD Francesca Paoletti  Chemistry  Researcher  2019 - 2022  41 
9.  54913  Neli Sedej  Computer intensive methods and applications  Technical associate  2020 - 2024 
10.  39115  PhD Marko Sever  Chemistry  Junior researcher  2019 - 2021  12 
11.  28608  PhD Barbara Zupančič  Computer intensive methods and applications  Researcher  2019 - 2024  180 
Organisations (1)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0104  National Institute of Chemistry  Ljubljana  5051592000  21,319 
Abstract
Gaining a predictive understanding of the behavior of complex biological systems based on physical and chemical principles is one of the greatest scientific challenges in life-sciences. The characterization of the structure and internal dynamics of biomolecules such as proteins is essential to understanding the mechanisms of their biological functions. Our research focuses on structure and dynamical processes in biomolecular systems and on the question of how these processes are driven by inter- and intra-molecular interactions. Specifically, we will pursue five specific aims: (1) to investigate the impact of hydrophobic/hydrophilic hydration on protein folding and association; (2) to evaluate the relevance of dynamical aspect of ligand binding to proteins; (3) to identify the role of intrinsically disordered protein regions; (4) to investigate the coupling of water and ion transport in membrane proteins with protein dynamics; (5) to investigate the local environment effect on proteins propensity to aggregate. Understanding how observable biomolecular processes, carried out over wide ranging temporal and spatial scales, arise from molecular scale events represents an outstanding challenge. Therefore, we propose a combined use of experimental and theoretical approaches mainly including vibrational spectroscopy, NMR spectroscopy and advanced computer simulation techniques based on classical force-field and ab-initio molecular dynamics and Monte-Carlo methods. While vibrational and NMR spectroscopies provide best-suited data relevant for the structure and internal dynamics of molecules, a major goal of applying theoretical models is to provide insight into the complexities arising from the non-linearity and hierarchical nature of biomolecular systems. In order to obtain optimal synergy between different approaches we develop our own computational methods that enable direct comparison between the experiments and computer simulations.
Significance for science
The growing understanding of topics addressed within this research program, which are all related to function of living organisms at the molecular level, increasingly drives advances in modern medicine. Moreover, revealing the physical and chemical mechanisms exploited in biological systems guides the development of new technologies. It became apparent that we could efficiently influence and control biological processes only by acting on macromolecular structures and dynamics. Powerful tools are being developed to apply this knowledge in biotechnology or in drug design pharmacology. The use of the rational design is based on the information of the conformational analysis of bioactive peptides. Thus, if we know the conformational properties of the peptides and the way they target their binding site then we can develop new ones with better pharmacological properties.   The results within this research program will provide mainly fundamental knowledge on the basic phenomena in biomolecular systems: hydrophobic/hydration effect, protein ligand binding, intrinsically disordered proteins, water transport in membrane proteins and the conformational preferences of peptides (oligomers). All these topics are essential in our life. Many diseases (i.e. Alzheimer, MSC...) are related to these phenomena and understanding of ligand binding is essential for rational drug design.   Our research is bridging between fundamental physics, chemistry and biology, we study biomolecular processes over a broad resolution range, from quantum chemistry to chemical kinetics, from atomistic descriptions of physical processes and chemical reactions to thermodynamics. To tackle the problems within the research program we are constantly developing novel approaches and methodologies that become available to research community.   As a team we have all the necessary expertize to apply excellent theoretical and experimental work. The researchers involved in the program are expert in the work-packages to undertake and the complementarity of the proposed work is well established. It is clear that only multidisciplinary approach described in the program provides the best way to approach the aimed scientific targets.
Significance for the country
Although it is difficult to anticipate immediate and direct socioeconomic or cultural relevance of research results these will certainly aid in the long run to tackle or understand the molecular basis of biological phenomena and diseases. The understanding of molecular phenomena like protein aggregation and misfolding is important to understand the molecular basis of diseases and the knowledge of the tridimensional structure of proteins is required for a successful rational drug design. It is therefore of paramount importance to get more knowledge and enrich our understanding on these aspects.   We are predominantly trying to publish our results in high-impact international journals in order to increase the visibility and reputation of our group and country. The results of our previous research have been published also in the renowned scientific journals with high impact factors (Proc. Natl. Acad. Sci. USA, J. Am. Chem. Soc., Phys. Rev. Lett.) and presented in invited talks at the international conference. That shows the high quality of our research and its capacity to promote Slovenian science worldwide.   We also maintain collaborations and good personal relations with eminent foreign researchers.   We actively participate in training PhD students. We are taking steps in attracting also undergraduate students to participate actively in our research thus obtaining pool of highly motivated students for the PhD positions eventually available in our group. The members of the team are lecturers at University of Ljubljana, University of Nova Gorica, University of Maribor, and Faculty of Technologies and Systems, Novo mesto. They are disseminating the advances in biophysical experimental techniques and molecular modeling, as well as, their application in current research topics to students of natural sciences. Our results will be valuable for pharmaceutical companies and will further extend the collaboration of National Institute of Chemistry and Faculty of Pharmacy with Slovenian pharmaceutical industry, Lek and Krka Pharmaceuticals. The members of the group have successfully performed many projects for these two companies in the past. The young researchers, who will be associated in the research program will gain new skills and knowledge for the establishment of spin-off companies.
Most important scientific results Interim report
Most important socioeconomically and culturally relevant results Interim report
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