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.     

Point Mutations of Nicotinic Receptor α1 Subunit Reveal New Molecular Features of G153S Slow-Channel Myasthenia

Slow-channel congenital myasthenic syndromes (SCCMSs) are rare genetic diseases caused by mutations in muscle nicotinic acetylcholine receptor (nAChR) subunits. Most of the known SCCMS-associated mutations localize at the transmembrane region near the ion pore. Only two SCCMS point mutations are at the extracellular domains near the acetylcholine binding site, α1(G153S) being one of them. In this work, a combination of molecular dynamics, targeted mutagenesis, fluorescent Ca²⁺ imaging and patch-clamp electrophysiology has been applied to G153S mutant muscle nAChR to investigate the role of hydrogen bonds formed by Ser 153 with C-loop residues near the acetylcholine-binding site. Introduction of L199T mutation to the C-loop in the vicinity of Ser 153 changed hydrogen bonds distribution, decreased acetylcholine potency (EC₅₀ 2607 vs. 146 nM) of the double mutant and decay kinetics of acetylcholine-evoked cytoplasmic Ca²⁺ rise (τ 14.2 ± 0.3 vs. 34.0 ± 0.4 s). These results shed light on molecular mechanisms of nAChR activation-desensitization and on the involvement of such mechanisms in channelopathy genesis.     

Doxorubicin Encapsulation in Carbon Nanotubes Having Haeckelite or Stone–Wales Defects as Drug Carriers: A Molecular Dynamics Approach

Doxorubicin (DOX), a recognized anticancer drug, forms stable associations with carbon nanotubes (CNTs). CNTs when properly functionalized have the ability to anchor directly in cancerous tumors where the release of the drug occurs thanks to the tumor slightly acidic pH. Herein, we study the armchair and zigzag CNTs with Stone–Wales (SW) defects to rank their ability to encapsulate DOX by determining the DOX-CNT binding free energies using the MM/PBSA and MM/GBSA methods implemented in AMBER16. We investigate also the chiral CNTs with haeckelite defects. Each haeckelite defect consists of a pair of square and octagonal rings. The armchair and zigzag CNT with SW defects and chiral nanotubes with haeckelite defects predict DOX-CNT interactions that depend on the length of the nanotube, the number of present defects and nitrogen doping. Chiral nanotubes having two haeckelite defects reveal a clear dependence on the nitrogen content with DOX-CNT interaction forces decreasing in the order 0N > 4N > 8N. These results contribute to a further understanding of drug-nanotube interactions and to the design of new drug delivery systems based on CNTs.     

医药洁净室的计算流体动力学模拟及实测对比

采用计算流体动力学(CFD)模拟,研究3个医药洁净室的气流流型及颗粒物浓度.采用标准k-ε双方程模型,通过模拟颗粒物在洁净室的分布,分析合理的污染物散发位置及散发比例.对比参考发尘量下的结果与实测数据的差异,根据实测数据确定污染散发量,通过试验不同的单位容积发尘量,计算对应的洁净度,得到与实测数据吻合最好的单位容积发尘量.在单位容积发尘量为1 000pc·(m3·min)-1计算条件下,各房间的模拟结果与实测数据数值比较吻合,且经CFD预测的3个房间的洁净度变化趋势与实测一致.     

用带时序子模块的系统动力学模型预测Brent原油价格

提出在系统动力学模型中加入时序自回归AR(p)子模块，并且自动确定每个AR(p)子模块的阶数p。带时序子模块的系统动力学模型既体现了因素问的横向因果关系，又体现了每个因素的纵向关系。建立欧佩克(OPEC)石油产量、世界GDP、煤炭产量与价格、天然气、需求量、供求差额、消费系数、非欧佩克石油产量、非欧佩克供求差额，石油库存和OPEC组织的期望油价共十一个因素影响下的Brent原油价格预测模型，模型的预测结果表明：在系统动力学模型中加入时序自回归AR(p)子模块的方法是可行的、有效的，并且能提高模型的预测精度。     

带电胶体系统固液相变的分子动力学研究

在修正Yukawa相互作用的基础上，采用常温分子动力学方法数值研究了带电胶体系统的大离子屏蔽效应和多分散性效应对其固液边界的影响．研究结果发现，在屏蔽长度较大时，固液相变曲线出现了明显偏差．初步定性认为这种相边界偏差现象来自于系统多体效应的增强．另外，数值研究了固液相变时键接取向序参数的变化．     

THE QUALITATIVE CONTENT OF RENEWABLE RESOURCE MODELS

This paper analyzes the extent to which standard dynamic renewable resource models possess refutable implications. Both the steady state comparative static and local comparative dynamic properties of the standard model are studied. A unified framework is developed which enables one to analyze the qualitative properties of any standard renewable resource model. This is achieved by explicitly linking the local stability, steady state comparative static, and local comparative dynamic properties of the model.     

非完整系统Chetaev动力学和vakonomic动力学的等价条件

就一般非完整约束系统，从约束方程满足的变分恒等式出发，利用增广位形流形上的向量场定义三类非自由变分，即非完整变分：vakonomic变分、Hlder变分、Suslov变分，并讨论它们之间的关系以及它们成为自由变分的充要条件.利用非完整变分以及相应的积分变分原理建立两类动力学方程：vakonomic方程和Routh方程或Chaplygin方程.通过vakonomic方程分别与Routh方程和Chaplygin方程比较，得到它们具有共同解的两类充分必要条件.这些条件并不是约束的可积性条件. 关键词： 非完整约束 非完整变分 Chetaev条件 vakonomic动力学     

Investigations of Solid State Dynamics at the NRSSR Beamline at PETRA II. An Overview

The present status of the new nuclear resonance beamline PETRA 1 at HASYLAB, DESY, Hamburg is described. Besides an overview of the experimental setup some examples of recent experiments are given. Those cover the main applications, i.e., inelastic scattering from iron alloys and quasielastic scattering from glass-forming liquids. This revised version was published online in August 2006 with corrections to the Cover Date.     

Charge transport in a polypeptide chain

Charge transport is one important example of signal transduction in a protein which is responsible for action at a distance, and is a fundamental process in biochemical action. A model is presented in which electronic effects interact with motional processes to combine into a bifunctional model. This model is investigated with new detailed molecular dynamics calculations and successfully explains such action at a distance. Received 1st February 2002 / Received in final form 26 May 2002 Published online 13 September 2002