We studied the influence of cosolvents (urea and trimethylamine-N-oxide (TMAO)) on the distribution of the conformations (PII, αR in β) of the dipeptides and of the glutathione (GSH; γ-Glu-Cys-Gly). The impact of cosolvents on the conformations of the peptide backbone in the amide III region and value of 3J(HN, Hα) coupling constants of the dipeptides are negligible. We notice a large increase in the value of 3J(HN, Hα) coupling constant of Ala in Val dipeptides in nonpolar solvent tetrachlomethane in comparison with water solution of cosolvents. The population of the β conformation of the Ala in Gly dipeptides in the amide III region increase. Molecules of TMAO have an influence on the structure of water in the peptide hydration layer of GSH and thus stabilizing the conformation of GSH (indirect impact). The impact on the conformation of GSH was observed in the case of urea. The GSH represents one of the main sources of nonprotein sulfur for complexation Cd2+. The deprotonated carboxylic group COO- of Glu and the Cys thiol S- group stabilize the Cd2+•••GSH complex through interaction with positively charged Cd2+. Cd2+ binding to the side chain of the Cys at the neutral pH values is due to the proton transfer from the thiol SH group to the deprotonated carboxylic group COO- of Gly. The formation of the complex Cd2+•••GSH affect the conformation of the peptide backbone of GSH. In a solution of GSH with the increase in the fraction of Cd2+, the population of the β conformation decreased with an increase in the population of the PII. We also isolated chloroplastic form of the carbonic anhydrase from the leaves of T. caerulescens J. & C. Presl. With the »de novo« sequencing of carbonic anhydrase isolated from T. caerulescens treated with Cd or Zn and alignment of amino acid residues with representatives of different classes of carbonic anhydrase, we tested the possibility of changing metals (Zn with Cd) in the active site of the enzyme. The analysis revealed the complete conservation of the Zn ligand and other amino acid residues involved in substrate binding in the active site of the enzyme. The presence of Zn in the isolated carbonic anhydrase of T. caerulescens treated with Cd was additionally confirmed by laser ablation and inductively coupled plasma mass spectrometry.
D.09 Tutoring for postgraduate students
COBISS.SI-ID: 762743PhD thesis deals with the microscopic picture of hydrophobic interaction, which is crucial for understanding many phenomena in molecular biophysics. Results are based on atomistic Monte-Carlo simulations of water and generic model solutes using methods of classical statistical mechanics. The work demonstrates an application of a series of innovative methodological approaches as well as of theoretical innovations that significantly complement the existing physical picture of the hydrophobic effect. It is clearly shown that the consistent description of the hydrophobic effect is possible only upon the proper inclusion of many-body correlations between water molecules. The main results and conclusions of the doctoral thesis can be summarized in four parts: i) water molecules response to the increasing solute polarity, ii) the microscopic origin of the entropy loss upon hydrophobic hydration, iii) the role of many-body correlations at the interaction between two hydrophobic solutes, and iv) the concept of local thermodynamics as the most appropriate tool to describe local inhomogeneities in liquids
D.09 Tutoring for postgraduate students
COBISS.SI-ID: 2418788Development of novel antibacterial agents is one of the most important measures against increasing bacterial resistance. MurD ligase is an essential bacterial enzyme, which represents an attractive target for the development of new antibacterial agents. Our research was focused on the determination of the binding mode of novel MurD ligase inhibitors. 1H/13C HSQC experiments on the 13C methyl (Ile (δ1), Val and Leu) selectively labeled MurD were used to determine the ligand binding sites. Comparison of the chemical shift perturbation patterns induced by the binding of structurally different ligands was applied to assign crucial methyl signals in the active site. Conformational properties of the bound ligands were investigated using transferred NOE experiments. The ligand-protein contacts were studied by application of saturation transfer difference (STD) NMR. The binding mode was also studied by unrestrained molecular dynamics (MD) simulations in CHARMM program. Different degrees of ligand flexibility were observed, which affect the ligand-protein interactions. Developed methodology can be also used for binding studies for other muramyl ligases or receptors with similar size.
D.09 Tutoring for postgraduate students
COBISS.SI-ID: 5099802Our strategy for the development of novel antibacterial agents, which is based on the improvement of structure based drug design methodology, implementation of novel protein targets and development of multitarget inhibitors, was presented. An overview of results of our NMR based investigation of binding mode of various types of novel muramyl ligaze inhibitors was given. Our resent discovery of complex dynamic processes in ligand-enzyme complexes and their influence on ligand activity was highlighted.
B.04 Guest lecture
COBISS.SI-ID: 5059354Simona Golič Grdadolnik, Jože Grdadolnik and Franci Merzel are mentors of five graduate students
D.10 Educational activities