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. Simulations showed that the unfolding of PMPC involved significant weakening of non-local interactions whereas fucosylation led FPMPC to preserve the non-local interactions, even in its denatured form. Even in simulations over 16 ns at 350 K, FPMPC remained relatively stable in a less denatured conformation. However, the conformation of PMPC transformed to a fully unfolded state within 5 ns in the simulation at 350 K. This difference was due to the formation of fucose-mediated hydrogen bonds and non-local contacts by the attached fucose residue of FPMPC. In the case of FPMPC, fucosyl residue was involved in maintaining a rigid beta-sheet cluster through interaction with the hydrogen bond network. These high-temperature unfolding MD simulations provide a theoretical basis for a previous experimental work in which FPMPC showed stable unfolding thermodynamics compared to unfucosylated PMPC, suggesting that single fucosylation induces conformational stabilization of PMPC by tertiary contacts.

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. The measured peak potential separation (DeltaE(p)) was 110 mV. More favorable complexation between succinyl-beta-CD and quercetin may enhance relative selectivity to quercetin of the (succinyl-beta-CD + MWNT)/GCE in quercetin-rutin mixture as compared to the beta-CD-modified GCE.

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.

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. Mono-Suc-beta-CD effectively separated (+/-)-catechin, and additional substituted CDs (di- and tri-Suc-beta-CD) were capable of chiral separation at a broad pH range. The optimum running conditions were found to be 100 mM borate buffer (pH 9.8) containing 5 mM mono-Suc-beta-CD with no methanol organic modifier.

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. These defects suggest that PtdIns[4,5]P2 participates in multiple trafficking and/or sorting events during endocytosis. Coexpression of the PtdIns[4,5]P2 synthesizing enzyme, PIP5KI gamma, was able to rescue these endocytic defects. Furthermore, decreased levels of PtdIns[4,5]P2 caused delays in rapid and slow membrane recycling pathways as well as a severe backup of endocytosed membrane. Taken together, our results demonstrate that PtdIns[4,5]P2 availability regulates multiple steps in the endocytic cycle in non-neuronal 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. All beta-(1-->2)-glycosidic linkages of OPGR adopted stable conformations, and the dihedral angles fluctuated in this energy region with some flexibility. However, despite the inherent flexibility of the alpha-(1-->6) linkage, the dihedral angles have no transition and are more rigid than that in a linear glucan. CYS13, which consists of only beta-(1-->2) linkages, is somewhat less flexible than other glycans, and one of its linkages adopts a higher energy conformation. In addition, the root-mean-square fluctuation of this linkage is lower than that of other linkages. Furthermore, the potential energy of glucans increases in the order of LINEAR, OPGR, and CYS13. These results provide evidence of the existence of conformational constraints in the cyclic glucan. The alpha-(1-->6)-glycosidic linkage can relieve this constraint more efficiently than the beta-(1-->2) linkage. The conformation of OPGR can reconcile the tendency for individual glycosidic bonds to adopt energetically favorable conformations with the requirement for closure of the macrocyclic ring by losing the inherent flexibility of the alpha-(1-->6)-glycosidic linkage.

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.

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. Excellent agreement was found between experimental data and corresponding values predicted by molecular modeling. Most glycosidic linkages were concentrated in the lowest energy region of phi-psi energy map, and the values of radius of gyration (R(G)) and the nuclear Overhauser effect (NOE) distance data derived from our simulations were finely consistent with the reported experimental values. This result will also give novel insights for the molecular complexation mechanism of Cys-A with various guest chemicals.