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.     

Semi-implicit complementary volume scheme for solving level set like equations in image processing and curve evolution

Summary. We introduce linear semi-implicit complementary volume numerical scheme for solving level set like nonlinear degenerate diffusion equations arising in image processing and curve evolution problems. We study discretization of image selective smoothing equation of mean curvature flow type given by Alvarez, Lions and Morel ([3]). Solution of the level set equation of Osher and Sethian ([26], \[30]) is also included in the study. We prove and estimates for the proposed scheme and give existence of its (generalized) solution in every discrete time-scale step. Efficiency of the scheme is given by its linearity and stability. Preconditioned iterative solvers are used for computing arising linear systems. We present computational results related to image processing and plane curve evolution. Received April 25, 2000 / Revised version received June 11, 2001 / Published online November 15, 2001     

Families of Line-Graphs and Their Quantization

Any directed graph G with N vertices and J edges has an associated line-graph L(G) where the J edges form the vertices of L(G). We show that the non-zero eigenvalues of the adjacency matrices are the same for all graphs of such a family L ⁿ (G). We give necessary and sufficient conditions for a line-graph to be quantisable and demonstrate that the spectra of associated quantum propagators follow the predictions of random matrices under very general conditions. Line-graphs may therefore serve as models to study the semiclassical limit (of large matrix size) of a quantum dynamics on graphs with fixed classical behaviour.     

Determination of the Lipophilicity of Xanthines by Reversed-Phase Liquid Chromatography

JPC – Journal of Planar Chromatography – Modern TLC -     

31P and 1h NMR as probes of domain alignment in a rigid crystalline surfactant mesophase

A viscous reverse hexagonal surfactant mesophase containing bis(2-ethylhexyl) sodium sulfosuccinate (AOT) and alpha-phosphatidylcholine (lecithin), with comparable volume fractions of isooctane and water, was characterized by Fourier transform (31)P and (1)H NMR spectroscopy. Shear alignment was reflected through both (31)P NMR and (1)H NMR spectra. A complicated (31)P spectrum was observed as a result of superposition of chemical shifts according to the distribution of crystalline domains prior to shear. The initially disordered samples with polydomain structures become macroscopically aligned after Couette shear. (31)P NMR chemical shift anisotropy characteristics are used to elucidate orientation of the hexagonal phase. Interestingly, (1)H NMR spectra exhibit spectral changes upon shear alignment closely corresponding with that of (31)P NMR spectra. These observations complement the findings of mesophase alignment obtained using SANS and imply that (31)P and (1)H NMR spectroscopy can be used as probes to define microstructure and monitor orientation changes in this binary surfactant system. This is especially beneficial if these mesophases are used as templates for materials synthesis.     

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.     

On relatively short and long sides of convex pentagons

By the relative distance of pointsa andb of a convex bodyC we mean the ratio of the Euclidean distance ofa andb to the half of the Euclidean distance ofa, b C such thatab is a longest chord ofC parallel to the segmentab. We say that a sideab of a convexn-gon is relatively short (respectively: relatively long) if the relative distance ofa andb is at most (respectively: at least) the relative distance of two consecutive vertices of the regularn-gon. We show that every convexn-gon, wheren 5, has a relatively short side and a relatively long side, and that it is affine-regular if and only if all its sides are of equal relative lengths.Research supported in part by Komitet Bada Naukowych (Committee of Scientific Research), grant number 2 2005 92 03.     

On functions having Cauchy differences in some prescribed sets

Summary AssumeE is a real topological vector space,F is a real Banach space,K is a discrete subgroup ofF andC is a symmetric, convex and compact subset ofF such thatK (6C) = {0}. If a functionh:E F is continuous at at least one point andh(x + y) – h(x) – h(y) K + C for allx, y E, then there exists a continuous linear functiona:E F such thath(x) – a(x) K + C for everyx E.     

Electron impact mass spectra of some tertiary aliphatic nitro compounds. Nitrocarbonyl compounds and some analogues

The mass spectra of some tertiary aliphatic nitroaldehydes, nitroketones, nitroesters, nitronitriles and related nitrocarbonyl compounds are discussed and compared with those of some analogous nitro compounds lacking the carbonyl function. The M⁺˙ ? NO₂˙ and in several cases M⁺˙ ? HNO₂ fragmentation seem to be the most characteristic features of all tertiary aliphatic nitro compounds. In the presence of the primary nitro group, the loss of NHO₂ is always observed.     

An investigation of the reliability of the Galerkin-Petrov method

It is shown that the Galerkin-Petrov method if applied in a controlled way yields reliable results for excited states of the same symmetry classifications as the ground state. Computations are performed for the 2¹ S and 3¹ S states of He. The problem of optimizing nonlinear parameters of the basis functions by means of the GP method is discussed. A special optimization scheme is suggested and numerically illustrated for someS states of He.