Biomedical subjects

S Kralj

Publications and source records attributed to S Kralj.

At least 19 recordsLinked to original sources

PubMed2002

Molecular dynamics study of the isotropic-nematic quench.

Effects of cylindrical and spherical confinement on the kinetics of the isotropic-nematic quench is studied numerically. The nematic liquid crystal structure was modeled by a modified induced-dipole--induced-dipole interaction. Molecules were allowed to wander around points of a hexagonal lattice. Brownian molecular dynamics was used in order to access macroscopic time scales. In the bulk we distinguish between the early, domain, and late stage regime. The early regime is characterized by the exponential growth of the nematic uniaxial order parameter. In the domain regime domains are clearly visible and the average nematic domain size xi(d) obeys the dynamical scaling law xi(d)-t(gamma). The late stage evolution is dominated by dynamics of individual defects. In a confined system the qualitative change of the scaling behavior appears when xi(d) becomes comparable to a typical linear dimension R of the confinement. In the confining regime (xi(d)>or=R) the scaling coefficient gamma depends on the details of the confinement and also the final equilibrium nematic structure. The domain growth is well described with the Kibble-Zurek mechanism.

Journal Article↗

PubMed2002

Molecular characterization of a novel glucosyltransferase from Lactobacillus reuteri strain 121 synthesizing a unique, highly branched glucan with alpha-(1-->4) and alpha-(1-->6) glucosidic bonds.

Lactobacillus reuteri strain 121 produces a unique, highly branched, soluble glucan in which the majority of the linkages are of the alpha-(1-->4) glucosidic type. The glucan also contains alpha-(1-->6)-linked glucosyl units and 4,6-disubstituted alpha-glucosyl units at the branching points. Using degenerate primers, based on the amino acid sequences of conserved regions from known glucosyltransferase (gtf) genes from lactic acid bacteria, the L. reuteri strain 121 glucosyltransferase gene (gtfA) was isolated. The gtfA open reading frame (ORF) was 5,343 bp, and it encodes a protein of 1,781 amino acids with a deduced M(r) of 198,637. The deduced amino acid sequence of GTFA revealed clear similarities with other glucosyltransferases. GTFA has a relatively large variable N-terminal domain (702 amino acids) with five unique repeats and a relatively short C-terminal domain (267 amino acids). The gtfA gene was expressed in Escherichia coli, yielding an active GTFA enzyme. With respect to binding type and size distribution, the recombinant GTFA enzyme and the L. reuteri strain 121 culture supernatants synthesized identical glucan polymers. Furthermore, the deduced amino acid sequence of the gtfA ORF and the N-terminal amino acid sequence of the glucosyltransferase isolated from culture supernatants of L. reuteri strain 121 were the same. GTFA is thus responsible for the synthesis of the unique glucan polymer in L. reuteri strain 121. This is the first report on the molecular characterization of a glucosyltransferase from a Lactobacillus strain.

Amino Acid Sequence↗

PubMed2001

Hydrophobic amino acid residues in the acceptor binding site are main determinants for reaction mechanism and specificity of cyclodextrin-glycosyltransferase.

Cyclodextrin-glycosyltransferases (CGTases) (EC ) preferably catalyze transglycosylation reactions with glucosyl residues as acceptor, whereas the homologous alpha-amylases catalyze hydrolysis reactions using water as acceptor. This difference in reaction specificity is most likely caused by the acceptor binding site. To investigate this in detail we altered the acceptor site residues Lys-232, Phe-183, Phe-259, and Glu-264 of Bacillus circulans strain 251 CGTase using site-directed mutagenesis. Lys-232 is of general importance for catalysis, which appears to result mainly from stabilization of the conformation of the loop containing the catalytic nucleophile Asp-229 and His-233, a residue that has been implied in transition state stabilization. Glu-264 contributes to the disproportionation reaction only, where it is involved in initial binding of the (maltose) acceptor. Phe-183 and Phe-259 play important and distinct roles in the transglycosylation reactions catalyzed by CGTase. Mutation of Phe-183 affects especially the cyclization and coupling reactions, whereas Phe-259 is most important for the cyclization and disproportionation reactions. Moreover, the hydrophobisity of Phe-183 and Phe-259 limits the hydrolyzing activity of the enzyme. Hydrolysis can be enhanced by making these residues more polar, which concomitantly results in a lower transglycosylation activity. A double mutant was constructed that yielded an enzyme preferring hydrolysis over cyclization (15:1), whereas the wild type favors cyclization over hydrolysis (90:1).

Amino Acids↗

PubMed2001

Surface depinning of smectic-A edge dislocations.

Using a Landau-de Gennes approach, we model the formation of an edge dislocation in a smectic-A cell initially in the bookshelf structure. The driving force is the mismatch between the layer thickness in a bulk smectic-A liquid crystal and that imposed by confining plates. The core structure of the dislocation is calculated taking into account spatial variations of the smectic translational order parameter. We numerically determine the critical condition for the surface-driven formation and depinning of the dislocation. By exploiting this phenomenon, we show how the value of the positional anchoring strength at the surface can be determined.

Journal Article↗

PubMed2000

Influence of surface treatment on the smectic ordering within porous glass

The influence of the surface treatment on the Sm-A-N phase transition of the 8CB (octylcyanobiphenyl) liquid crystal confined to controlled pore glass (CPG) matrices is studied. The characteristic linear size of voids in the chosen CPG matrix is 0.2 &mgr;m. The voids' surface was either nontreated or silane treated enforcing tangential or homeotropic anchoring, respectively. In both cases the x-ray measurements reveal a qualitative change of the temperature dependence of the smectic order-parameter correlation length in comparison to the bulk sample. In addition, the apparent smectic pretransitional ordering is observed for the silane-treated sample. A theoretical description based on the Landau-de Gennes type approach is developed to explain the experimental data. The surface positional anchoring strength of the silane-treated sample is estimated to be of the order of 10(-4) J/m(2) and at least 100 times weaker for the nontreated case.

Journal Article↗

PubMed1999

Biaxial torus around nematic point defects.

We study the biaxial structure of both line and point defects in a nematic liquid crystal confined within a capillary tube whose lateral boundary enforces homeotropic anchoring. According to Landau-de Gennes theory the local order in the material is described by a second-order tensor Q, which encompasses both uniaxial and biaxial states. Our study is both analytical and numerical. We show that the core of a line defect with topological charge M=1 is uniaxial in the axial direction. At the lateral boundary, the uniaxial ordering along the radial direction is reached in two qualitatively different ways, depending on the sign of the order parameter on the axis. The point defects with charge M=+/-1 exhibit a uniaxial ring in the plane orthogonal to the cylinder axis. This ring is in turn surrounded by a torus on which the degree of biaxiality attains its maximum. The typical lengths that characterize the structure of these defects depend both on the cylinder radius and the biaxial correlation length. It seems that the core of the point defect does not depend on the far nematic director field in the bulk limit.

Journal Article↗

PubMed1996