Structural stabilization of a rigid beta-sheet cluster of fucosylated proteinase inhibitor PMPC (Pars intercerebralis major peptide C) against thermal denaturation: An unfolding molecular dynamics simulation study.

Unfolding behavior of glycosylated- and unglycosylated proteinase inhibitor Pars intercerebralis major peptide C (PMPC) at 350 K were traced with molecular dynamics simulations using the CHARMM program. The fucosylated PMPC (FPMPC) possesses a nearly identical protein structure with PMPC, differing only by the presence of a single fucose residue linked to Thr9 in the PMPC. Attachment of a monomeric fucose residue to the Thr9 in PMPC resulted in a change of the denaturing process of FPMPC.

Electrochemical selectivity enhancement by using monosuccinyl beta-cyclodextrin as a dopant for multi-wall carbon nanotube-modified glassy carbon electrode in simultaneous determination of quercetin and rutin.

Monosuccinyl beta-cyclodextrin (succinyl-beta-CD) was synthesized and the selectivity to quercetin and rutin of the succinyl-beta-CD-modified, multi-wall carbon nanotube (MWNT)-coated, glassy carbon electrode [(succinyl-beta-CD + MWNT)/GCE] was investigated. (1)H NMR and MALDI-MS data confirmed molecular structure of the synthesized succinyl-beta-CD. As a dopant in carboxylated MWNT-modified electrode, succinyl-beta-CD clearly separated the peak potential (E(p)) of quercetin from that of rutin.

Chiral separation of catechin by capillary electrophoresis using mono-, di-, tri-succinyl-beta-cyclodextrin as chiral selectors.

The chiral separation of (+/-)-catechin was investigated by capillary electrophoresis using characterized succinyl-beta-cyclodextrins (Suc-beta-CDs) with one to three degree of substitution values. The effects of nature and concentration of Suc-beta-CDs and running buffer pH on the migration time and resolution of (+/-)-catechin are discussed. All three kinds of Suc-beta-CDs show a clear baseline separation of (+/-)-catechin in capillary electrophoresis.

Systematic probing of an atomic charge set of sialic acid disaccharides for the rational molecular modeling of avian influenza virus based on molecular dynamics simulations.

A systematic searching approach for an atomic charge set through molecular dynamics simulations is introduced to calculate a reasonable sialic acid carbohydrate conformation with respect to the experimentally observed structures. The present molecular dynamics simulation study demonstrated that B3LYP/6-31G is the most suitable basis set for the sialic acid disaccharides, attaining good agreement with experimental data.

Regulation of transferrin recycling kinetics by PtdIns[4,5]P2 availability.

Phosphatidylinositol 4,5-bisphosphate (PtdIns[4,5]P2) is a phosphoinositide involved in a variety of cellular functions, including signal transduction, organelle trafficking, and actin dynamics. Although the role of PtdIns[4,5]P2 in endocytosis is well established, the precise trafficking steps relying on normal PtdIns[4,5]P2 balance in the endosomal pathway have not yet been elucidated. Here we show that decrease in intracellular PtdIns[4,5]P2 levels achieved by the overexpression of the 5-phosphatase domain of synaptojanin 1 or by siRNA knock-down of PIP5Ks expression lead to severe defects in the internalization of transferrin as well as in the recycling of internalized transferrin back to the cell surface in COS-7 cells.

Molecular dynamics simulations of a cyclic-beta-(1-->2) glucan containing an alpha-(1-->6) linkage as a 'molecular alleviator' for the macrocyclic conformational strain.

The conformational preferences of a cyclic osmoregulated periplasmic glucan of Ralstonia solanacearum (OPGR), which is composed of 13 glucose units and linked entirely via beta-(1-->2) linkages excluding one alpha-(1-->6) linkage, were characterized by molecular dynamics simulations. Of the three force fields modified for carbohydrates that were applied to select a suitable one for the cyclic glucan, the carbohydrate solution force field (CSFF) was found to most accurately simulate the cyclic molecule. To determine the conformational characteristics of OPGR, we investigated the glycosidic dihedral angle distribution, fluctuation, and the potential energy of the glucan and constructed hypothetical cyclic (CYS13) and linear (LINEAR) glucans.

Molecular dynamics simulation of cyclosophoroheptadecaose (Cys-A).

The conformational preferences of cyclosophoroheptadecaose (Cys-A), which is a member of a class of cyclic (1 --> 2)-beta-D-glucan, were characterized by molecular dynamics simulations. Simulated annealing and constant temperature molecular dynamics simulations were performed on the Cys-A. The simulations produced various types of compact and asymmetrical conformations of Cys-A.

Monte Carlo docking simulations of cyclomaltoheptaose and dimethyl cyclomaltoheptaose with paclitaxel.

The molecular basis for the remarkable enhancement of the solubility of paclitaxel by O-dimethylcyclomaltoheptaose (DM-beta-CD) over cyclomaltoheptaose (beta-cyclodextrin, beta-CD) was investigated with Monte Carlo docking-minimization simulation. As possible guests of inclusion complexation for the host cyclic oligosaccharides, two functional moieties of the suggested solution structure of paclitaxel were used where one is the C-3'N benzoyl moiety (B-ring) and the other is a hydrophobic (HP) cluster site among the C-3' phenyl (C-ring), C-2 benzoate (A-ring), and C-4 acetoxy moieties. The energetic preference of inclusion complexation of DM-beta-CD over beta-CD was analyzed on the basis of more efficient partitioning process of DM-beta-CD into the hydrophobic cluster site of the paclitaxel.