Study of Endogen Substrates,Drug Substrates and Inhibitors Binding Conformations on MRP4 and Its Variants by Molecular Docking and Molecular Dynamics

Multidrug resistance protein-4 (MRP4) belongs to the ABC transporter superfamily and promotes the transport of xenobiotics including drugs. A non-synonymous single nucleotide polymorphisms (nsSNPs) in the ABCC4 gene can promote changes in the structure and function of MRP4. In this work, the interaction of certain endogen substrates, drug substrates, and inhibitors with wild type-MRP4 (WT-MRP4) and its variants G187W and Y556C were studied to determine differences in the intermolecular interactions and affinity related to SNPs using protein threading modeling, molecular docking, all-atom, coarse grained, and umbrella sampling molecular dynamics simulations (AA-MDS and CG-MDS, respectively). The results showed that the three MRP4 structures had significantly different conformations at given sites, leading to differences in the docking scores (DS) and binding sites of three different groups of molecules. Folic acid (FA) had the highest variation in DS on G187W concerning WT-MRP4. WT-MRP4, G187W, Y556C, and FA had different conformations through 25 ns AA-MD. Umbrella sampling simulations indicated that the Y556C-FA complex was the most stable one with or without ATP. In Y556C, the cyclic adenosine monophosphate (cAMP) and ceefourin-1 binding sites are located out of the entrance of the inner cavity, which suggests that both cAMP and ceefourin-1 may not be transported. The binding site for cAMP and ceefourin-1 is quite similar and the affinity (binding energy) of ceefourin-1 to WT-MRP4, G187W, and Y556C is greater than the affinity of cAMP, which may suggest that ceefourin-1 works as a competitive inhibitor. In conclusion, the nsSNPs G187W and Y556C lead to changes in protein conformation, which modifies the ligand binding site, DS, and binding energy.     

The use of solid-phase supported 1-N-piperazine-4-N-carboxaldehyde in Vilsmeier reactions

A Vilsmeier salt supported on solid phase was prepared using piperazine bound to Merrifield resin. Piperazine was selected because it contains two secondary amines: one of the amines is protected upon binding to the resin, and the second was formylated to give resin-1-N-piperazine-4-N-carboxaldehyde (9). Activation of the formamide with either bis(trichloromethyl)carbonate (BTC) or POCl(3) afforded the Vilsmeier salt 10. Several olefins were used to test the supported Vilsmeier reagent. The in-solution activation with BTC and POCl(3) of various secondary amides was also evaluated: dimethylformamide (1), N-methyformanilide (4), 4-formylmorpholine (5), and 1,4-dicarboxylpiperazine (6), which showed that amides with one additional heteroatom increase the yields in the Vilsmeier salt formation.     

NADH Electrooxidation Using Bis(1,10-phenanthroline-5,6-dione) (2,2'-bipyridine)ruthenium(II)-Exchanged Zirconium Phosphate Modified Carbon Paste Electrodes

We present a carbon paste electrode (CPE) modified using the electron mediator bis(1,10‐phenanthroline‐5,6‐dione)(2,2′‐bipyridine)ruthenium(II) ([Ru(phend)₂bpy]²⁺) exchanged into the inorganic layered material zirconium phosphate (ZrP). X‐Ray powder diffraction showed that the interlayer distance of ZrP increases upon [Ru(phend)₂bpy]²⁺ intercalation from 10.3 Å to 14.2 Å. The UV‐vis and IR spectroscopies results showed the characteristic peaks expected for [Ru(phend)₂bpy]²⁺. The UV‐vis spectrophotometric results indicate that the [Ru(phend)₂bpy]²⁺ concentration inside the ZrP layers increased as a function of the loading level. The exchanged [Ru(phend)₂bpy]²⁺ exhibited luminescence even at low concentration. Modified CPEs were constructed and analyzed using cyclic voltammetry. The intercalated mediator remained electroactive within the layers (E°′=–38.5 mV vs. Ag/AgCl, 3.5 M NaCl) and electrocatalysis of NADH oxidation was observed. The kinetics of the modified CPE shows a Michaelis–Menten behavior. This CPE was used for the oxidation of NADH in the presence of Bakers' yeast alcohol dehydrogenase. A calibration plot for ethanol is presented.     

Study of reactive ion etching of Si and SiO2 for CFxCl4−x gases

A parametric study of the etching of Si and SiO₂ by reactive ion etching (RIE) was carried out to gain a better understanding of the etching mechanisms. The following fluorocarbons (FCs) were used in order to study the effect of the F-to-Cl atom ratio in the parent molecule to the plasma and the etching properties: CF₄, CF₃Cl, CF₂Cl₂, and CFCl₃ (FC-14, FC-13, FC-12, and FC-11 respectively). The Si etch rate uniformity across the wafer as a function of the temperature of the wafer and the Si load, the optical emission as a function of the temperature of the load, the etch rate of SiO₂ as a function of the sheath voltage, and the mass spectra for each of the FCs were measured. The temperature of the wafer and that of the surrounding Si load strongly influence the etch rate of Si, the uniformity of etching, and the optical emission of F, Cl, and CF₂. The activation energy for the etching reaction of Si during CF₄ RIE was measured. The etch rate of Si depends more strongly on the gas composition than on the sheath voltage; it seems to be dominated by ion-assisted chemical etching. The etching of photoresist shifted from chemical etching to ion-assisted chemical etching as a function of the F-to-Cl ratio and the sheath voltage. The etch rate of SiO₂ depended more strongly on the sheath voltage than on the F-to-Cl ratio.     

Synthesis and optical nondestructive evaluation of GaN nanorods on silicon surfaces with gold catalyst

Nanometric gallium-nitride rods were grown on a silicon (1 1 1) substrate through a chemical vapor deposition process with gold particles as the catalyst. Randomly distributed gallium-nitride rods of 20–200 nm in diameter and of various densities and lengths were formed under different deposition conditions. Characterization analyses, such as scanning electron microscopy and optical reflection spectroscopy, have been carried out on samples containing gallium-nitride rods different in size, shape, length and density. While the scanning electron microscopy shows directly the images of the sample surfaces, the optical spectroscopy provides a nondestructive evaluation of the sample surfaces, especially helpful for checking the uniformity of the samples.