Projects / Programmes source: ARIS

Folding and Dynamics of Biomolecular Systems

Research activity

Code Science Field Subfield
1.04.00  Natural sciences and mathematics  Chemistry   

Code Science Field
P351  Natural sciences and mathematics  Structure chemistry 
P370  Natural sciences and mathematics  Macromolecular chemistry 
P400  Natural sciences and mathematics  Physical chemistry 
P410  Natural sciences and mathematics  Theoretical chemistry, quantum chemistry 
P310  Natural sciences and mathematics  Proteins, enzymology 
P340  Natural sciences and mathematics  Lipids, steroids, membranes 
Evaluation (rules)
source: COBISS
Researchers (4)
no. Code Name and surname Research area Role Period No. of publicationsNo. of publications
1.  09899  PhD Franc Avbelj  Chemistry  Head  2001 - 2003  72 
2.  08329  PhD Simona Golič Grdadolnik  Chemistry  Researcher  2001 - 2003  323 
3.  08523  PhD Jože Grdadolnik  Chemistry  Researcher  2001 - 2003  258 
4.  06033  Silva Zagorc    Researcher  2001 - 2003 
Organisations (1)
no. Code Research organisation City Registration number No. of publicationsNo. of publications
1.  0104  National Institute of Chemistry  Ljubljana  5051592000  21,271 
Activity of biomolecular systems is intrinsically connected to dynamical processes such as: protein and RNA folding, allosteric changes on receptors, and interactions of various biomolecules with membranes. The dynamics of biomolecular systems is in our laboratory studied by theoretical and experimental methods. The research is focussed on solving the protein folding problem, characterization of physical properties of biologically relevant molecules in solution, and interactions of biomolecules with membranes. The mechanism by which a globular protein folds from denatured state to native conformation is one of the unsolved key problems in protein chemistry. Recently, we have shown that the conformational preferences of amino acid residues is determined by the screening of main chain electrostatic interactions. This electrostatic screening model of conformational preferences is implemented in the algorithm for predicting the three-dimensional structure of one domain proteins. Understanding the dynamics of biopolymer - membrane systems, is crucial for drug design and gene therapy. The mechanism of the biological activity of the antibiotic vancomycin is explored by NMR, vibrational spectroscopy, and molecular modeling. Detailed knowledge of the structure, dynamics and binding interactions will allow the rational design of novel biologically active substances based on vancomycin, which should be important for clinical treatment of life-threatening Gram-positive bacterial infections. The interaction of vancomycin with the membrane, which was discovered in our laboratory, supports the hypothesis that membrane association is important for biological activity by reducing the binding event into a two-dimensional diffusion process. The dynamics of molecular systems DNA - membrane is analyzed with infrared spectroscopy to explore the possibilities for transferring genes into living cells. The description of interaction between DNA and cationic amphiphiles on a molecular level using spectroscopic techniques will assist the understanding of many other important processes involving predominantly electrostatic interaction between charged guest molecule and cell membranes. Infrared spectroscopy is also used to study hydration of proteins, urea and DNA. Stopped and quenched flow methods will be utilized to study the mechanism of the protein folding process in near future. The prospect of predicting the three-dimensional structure of RNA is also examined.
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