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.     

An Improved Composite Multiscale Fuzzy Entropy for Feature Extraction of MI-EEG

Motor Imagery Electroencephalography (MI-EEG) has shown good prospects in neurorehabilitation, and the entropy-based nonlinear dynamic methods have been successfully applied to feature extraction of MI-EEG. Especially based on Multiscale Fuzzy Entropy (MFE), the fuzzy entropies of the τ coarse-grained sequences in τ scale are calculated and averaged to develop the Composite MFE (CMFE) with more feature information. However, the coarse-grained process fails to match the nonstationary characteristic of MI-EEG by a mean filtering algorithm. In this paper, CMFE is improved by assigning the different weight factors to the different sample points in the coarse-grained process, i.e., using the weighted mean filters instead of the original mean filters, which is conductive to signal filtering and feature extraction, and the resulting personalized Weighted CMFE (WCMFE) is more suitable to represent the nonstationary MI-EEG for different subjects. All the WCMFEs of multi-channel MI-EEG are fused in serial to construct the feature vector, which is evaluated by a back-propagation neural network. Based on a public dataset, extensive experiments are conducted, yielding a relatively higher classification accuracy by WCMFE, and the statistical significance is examined by two-sample t-test. The results suggest that WCMFE is superior to the other entropy-based and traditional feature extraction methods.     

Anticancer SAR establishment and novel accruing signal transduction model of drug action using biscoumarin scaffold

In this paper, we have established methylenebis (4-hydroxy-2H-chromen-2-one) as a promising anticancer scaffold with kinesin spindle protein (KSP) inhibitory activity under malignant condition. A series of biscoumarin derivatives (MN1 to MN30) with different substituent were synthesized, and their anticancer activity was explored. Six biscoumarin derivatives that were found active were further selected to formulate organic nanoparticles (ONPs). Anticancer activity of both the forms (viz conventional and ONPs) was compared. MN30 was found most potent whereby MN10 showed good anticancer activity in both, i.e., conventional and ONP form; the structural activity relationship (SAR) study has been established. Computational investigation revealed biscoumarin scaffold as a suitable pharmacophore to bind against KSP protein. Molecular dynamics simulation studies revealed protein-ligand stability and dynamic behavior of biscoumarin-KSP complex. Finally, accruing signal transduction model was formulated to explain the observed MTT trend of conventional and ONP form. The model seems useful towards solving population specific varied results of chemotherapeutic agents. According to the model, MN10 and MN30 derivatives have good pharmacodynamics inertia and therefore, both the molecules were able to provide dose-dependent cytotoxic results.     

Thermodynamic study of transthyretin association (wild‐type and senile forms) with heparan sulfate proteoglycan: pH effect and implication of the reactive histidine residue

The tetramer destabilization of transthyretin into monomers and its fibrillation are phenomena leading to amyloid deposition. Heparan sulfate proteoglycan (HSPG) has been found in all amyloid deposits. A chromatographic approach was developed to compare binding parameters between wild‐type transthyretin (wtTTR) and an amyloidogenic transthyretin (sTTR). Results showed a greater affinity of sTTR for HSPG at pH 7.4 compared with wtTTR owing to the monomeric form of sTTR. Analysis of the thermodynamic parameters showed that van der Waals interactions were involved at the complex interface for both transthyretin forms. For sTTR, results from the plot representing the number of protons exchanged vs pH showed that the binding mechanism was pH‐dependent with a critical value at a pH 6.5. This observation was due to the protonation of a histidine residue as an imidazolium cation, which was not accessible when TTR was in its tetrameric structure. At pH >6.5, dehydration at the binding interface and several contacts between nonpolar groups of sTTR and HSPG were also coupled to binding for an optimal hydrogen‐bond network. At pH <6.5, the protonation of the His residue from sTTR monomer when pH decreased broke the hydrogen‐bond network, leading to its destabilization and thus producing slight conformational changes in the sTTR monomer structure. Copyright © 2014 John Wiley & Sons, Ltd.     

Synthesis and characterization of molybdenum incorporated mesoporous aluminophosphate

A synthesis of molybdenum incorporated mesoporous aluminophosphate with long-chain n-alkylamine as template material had been prepared under non-aqueous condition. These materials were extensively characterized by using X-ray diffraction (XRD), nitrogen sorption isotherms, nuclear magnetic resonance of ²⁷Al and ³¹P (NMR), inductive coupled plasma (ICP), electron spin resonance (ESR), Fourier transform infrared (FTIR) and thermogravimetric-differential thermal analysis (TG-DTA). Morphology of the materials had been observed by using transmission electron microscope (TEM) that revealed the mesoporous materials possessed wormhole-like structures. Alkaline solvent extraction using n-butylamine/ethanol had been efficiently removed the n-alkylamine from the mesoporous samples which yielded BET surface areas around 550-730 m²/g. BJH analysis showed a narrow pore size distribution which increased with increasing of the carbon chain length of alkylamine (template). Valence state and coordination of the molybdenum in the obtained samples were investigated by using ESR and FTIR where it was found that Mo⁴⁺ and Mo⁶⁺ molybdenum species existed in the molybdenum incorporated mesoporous aluminophosphate in tetrahedral coordination.     

与HBV X蛋白相互作用的细胞蛋白的筛选及其鉴定

参考GenBank核苷酸序列库中的HBV的核苷酸序列设计合成了一对对应于HBx基因的引物，从原发性肝癌(hepatocellular carcinoma，HCC)患者的血清中提取HBV基因组DNA作为模板，扩增HBx编码区并测定了核苷酸序列．将该编码区克隆到酵母双杂交系统的诱饵蛋白表达载体pGBKT7中，转入酵母细胞AH109，进行表型鉴定．然后通过Mating实验从已制备好用于酵母双杂交系统的肝cDNA表达文库中筛选与HBx相互作用的细胞蛋白，并用体外免疫共沉淀实验进一步验证．研究表明，分离得到的与HBx基因编码的蛋白相互作用的4种新的细胞蛋白，分别是醛缩酶B、C8α亚基、一种丝氨酸蛋白酶Hepsin和一种未知蛋白．     

Structure and properties of the mesophase of syndiotactic polystyrene. II. Effect of stepwise extraction on the preparation of the mesophase

In this study, a novel stepwise extraction method has been examined. The guest molecules housed between the helices of the clathrate δ form of syndiotactic polystyrene can be removed completely with this method. A systematic study of the preparation of a solvent‐free mesophase (emptied clathrate) membrane, its helical and residual solvent contents, and its structural transformations has been performed. In this first attempt, an enhancement in the TTGG helical content has been observed in the extracted membrane, and a conceptual mechanism is proposed. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 269–273, 2003     

Structure and properties of the mesophase of syndiotactic polystyrene—III. Selective sorption of the mesophase of syndiotactic polystyrene

Syndiotactic polystyrene (sPS) has various crystalline forms such as α, β, γ, and δ forms, and a mesophase depending on the preparation method. In this study, we focused on the mesophase with the molecular cavity of sPS, which is obtained by step‐wise extraction of the guest molecules from the sPS δ form. To prepare the mesophase containing different shapes and sizes of the cavity, two kinds of the sPS δ form membrane cast from either toluene or chloroform solution were first prepared and then the guest molecules were removed by a step‐wise extraction method using acetone and methanol. We could succeed in the preparation of two kinds of mesophase with different shapes and sizes of the molecular cavity. Either toluene or chloroform vapor sorption to the sPS mesophase membranes was examined at 25 °C. Sorption analysis indicates that the mesophase with large molecular cavities can mainly sorb large molecules; on the other hand, the mesophase with small cavities can sorb only the small molecules, and is unable to sorb a large amount of large molecule because the cavity was too small to sorb the large molecules. Therefore, the sPS mesophase membrane has sorption selectivity based on the size of the molecular cavity. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 238–245, 2004     

Self-Interactions of Strands and Sheets

Physical strands or sheets that can be modelled as curves or surfaces embedded in three dimensions are ubiquitous in nature, and are of fundamental importance in mathematics, physics, biology, and engineering. Often the physical interpretation dictates that self-avoidance should be enforced in the continuum model, i.e., finite energy configurations should not self-intersect. Current continuum models with self-avoidance frequently employ pairwise repulsive potentials, which are of necessity singular. Moreover the potentials do not have an intrinsic length scale appropriate for modelling the finite thickness of the physical systems. Here we develop a framework for modelling self-avoiding strands and sheets which avoids singularities, and which provides a way to introduce a thickness length scale. In our approach pairwise interaction potentials are replaced by many-body potentials involving three or more points, and the radii of certain associated circles or spheres. Self-interaction energies based on these many-body potentials can be used to describe the statistical mechanics of self-interacting strands and sheets of finite thickness.     

含三正辛胺微胶囊对六价铬的富集

本文将对六价铬有效的萃取剂ＴＯＡ（三正辛胺）微胶囊化，制成填充柱型的酸性体系六价铬的富集分离装置。实验结果表明，微胶囊填充柱中每毫升ＴＯＡ对六价铬的最大萃取容量为１５８．０ｇ／ｍＬ，为纯ＴＯＡ液相萃取的４．９倍。微胶囊经碱／水洗涤后，可再生使用。