Dipeptides are amino acids blocked with an acetyl and an N-methyl group. The amino acids in dipeptides have structural properties similar to amino acid residues in proteins; this is why structures of dipeptides are important for understanding structures of proteins. We have determined the dipeptide structures of 19 basic amino acids in a water solution. Using spectroscopic methods, we have demonstrated the presence of three conformations of dipeptides in water: the PII, β, and the αR. The proportion of the αR conformation in all dipeptides is surprisingly low (( 10%).
B.04 Guest lecture
COBISS.SI-ID: 4501018The capabilities and limitations of NMR methods for the investigation of ligand-receptor interactions were presented. Two of our case-studies of NMR-assisted discovery of novel inhibitors of attractive antibacterial targets were used to explain the application of ligand-based and protein-based NMR methods. Special attention was given to the advantage of NMR spectroscopy in the studies of dynamic processes in molecular complexes. The influence of conformational dynamics on the stability of ligand-receptor interactions and on the inhibitory activities of novel ligands was presented.
B.04 Guest lecture
COBISS.SI-ID: 4174618The capabilities and limitations of NMR methods for the investigation of ligand-protein interactions were presented. Our case-studies of NMR-assisted discovery of novel inhibitors of attractive antimicrobial targets were used to explain the application of ligand-based and protein-based NMR methods. Special attention was given to the advantage of NMR spectroscopy for the studies of dynamic processes in molecular complexes. The influence of conformational dynamics on the stability of ligand-receptor interactions and on the inhibitory activities of novel ligands was presented.
B.04 Guest lecture
COBISS.SI-ID: 4815130We 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: 762743Simona Golič Grdadolnik and Jože Grdadaolnik are mentors of four graduate students
D.10 Educational activities