Biomedical subjects

Drazen Vikić-Topić

Publications and source records attributed to Drazen Vikić-Topić.

4 recordsLinked to original sources

PubMed2006

On representation of proteins by star-like graphs.

To arrive at graphical representations of proteins one is confronted with number of arbitrary decisions how to assign the 20 natural amino acids to equivalent or non-equivalent sites of underlying geometrical objects used for construction of their graphical representation. Here we consider representation of proteins based on generalized star graphs, which are graphs with one vertex of maximal degree in the center to which are attached other vertices of either degree one or two. The matrix representation of proteins based on star-like graphs has an important advantage in that, while its pictorial representation depends on selected assignment of amino acids to various branches of star graph, its properties do not depend on the adopted assignment of vertices to amino acids. Hence, the derived graph invariants, devoid of artifacts associated with graphical representations of biosequences, will better reflect upon the inherent properties of protein structure. We describe several graph invariants, mostly extracted from distance matrices of star-like graphs, which can serve as protein descriptors. The approach is illustrated on strand A of the human insulin.

Amino Acids↗

PubMed2006

Lipid-protein interactions in human plasma LDL evidenced by magnetic resonance.

Low density lipoprotein (LDL) particles exhibit extremely complex three-dimensional structural organization which is still not understood at the molecular level. The aim of this study was to provide the experimental evidence of a direct non-covalent interaction of the protein part with the lipid matrix. The approach was based on the combination of (1)H NMR (600 MHz) spectroscopy with thiol-specific spin labeling of the protein (apoB). It is shown that the spectral peaks assigned to the methyl head groups of phosphatidylcholine and sphingomyelin in the (1)H spectra of LDL exhibit line broadening when otherwise free thiol groups of apoB are covalently modified by methanethiosulfonate spin label. The effect is similar in the presence of water soluble paramagnetic compound. These results indicate that fragments of apoB, which are part of the receptor binding region, are directly in contact with the solvated phospholipid head groups of the lipid matrix.

Apolipoproteins B↗

PubMed2004

Spectroscopic studies of methylglyoxal in water and dimethylsulfoxide.

Methylglyoxal is a highly reactive dicarbonyl compound, which reacts in vivo with biological macromolecules and thereby affects their structure and function. These changes are associated with complications during aging, diabetes and Alzheimer's disease as well as with growth inhibition in different tumors. Many enzymes are involved in the metabolism of methylglyoxal, but its true physiological role in metabolism and chemical properties are still obscure. In this study it was shown that methylglyoxal, during the freeze-drying of aqueous solutions, polymerizes into small polymeric structures which are stable in organic media such as dimethylsulfoxide. When re-exposed to water, the polymers are immediately transformed into the monomeric mono- and dihydrate forms of methylglyoxal. By NMR and UV spectroscopy, it was shown that solvent, temperature, and the amount of available water strongly influence the equilibrium of the different forms of methylglyoxal and thereby change its reactivity. 1H and 13C NMR spectroscopy were used to determine the structures of the different monomeric and oligomeric structures of methylglyoxal.

Carbon Isotopes↗

PubMedDate not supplied

Periodic cages.

Various cages are constructed by using three types of caps: f-cap (derived from spherical fullerenes by deleting zones of various size), kf-cap (obtainable by cutting off the polar ring, of size k), and t-cap ("tubercule"-cap). Building ways are presented, some of them being possible isomerization routes in the real chemistry of fullerenes. Periodic cages with ((5,7)3) covering are modeled, and their constitutive typing enumeration is given. Spectral data revealed some electronic periodicity in fullerene clusters. Semiempirical and strain energy calculations complete their characterization.

Journal Article↗