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.     

Statistics of polymer capture by a nanopore: A Brownian dynamics simulation study

We investigate the statistics of polymer capture by a nanopore using Brownian dynamics simulations. It is found that when the velocity flux is greater than a critical velocity flux, the capture picture is a random selection process, otherwise it tends to a statistical process governed by energetic considerations. In addition, the chain ends capture probability decreases as the chain length increases and satisfies a power-law scaling of P0(N)~N-0.8.     

Recent trends in capillary and micro-chip electrophoretic instrumentation for field-analysis

Technical advances in the development of field-deployable capillary and microchip electrophoretic instruments and reports of their deployment between 2013 and 2017 were reviewed. Strategies and considerations in the design of the injection, separation and detection hardware, chemistry and associated infrastructure were discussed from an in-field perspective, with portability, robustness and automation/“ease of use” featuring as key requirements. Integration of functionality is important for adequate in-field performance. Progress was made towards the use of multiple channel devices for increased throughput and/or resolving power, mixing devices for on-line/in-line sample derivatization, battery operation and temperature control. The strengths and weaknesses of the various approaches described in the literature are discussed from the perspective of in-field operation. An overview of the applications of the field electrophoretic instruments is provided, including environmental science and planetary investigation.     

Total Variation and Multisymplectic Structure for CNLS System

The relation between the total variation of classical field theory and the multisymplectic structure is shown. Then the multisymplectic structure and the corresponding multisymplectic conservation of the coupled nonlinear Schrodinger system are obtained directly from the variational principle.     

〈111〉晶向冲击加载下单晶铜中纳米孔洞增长的早期动力学行为

利用分子动力学方法模拟计算了单晶铜中纳米孔洞在沿〈111〉晶向冲击加载下增长的早期过程.测量发现不同加载强度下等效孔洞半径随时间近似成线性变化.观测到单孔洞增长的两种位错生长机理：加载强度较低时，只在沿着冲击加载方向的孔洞顶点附近区域有位错的成核和运动；而随着加载强度超过一定阈值，在沿冲击加载和其垂直方向的孔洞顶点区域都观察到位错的成核和运动.在前一种机理作用下，孔洞只沿加载方向增长；在后一种机理作用下，孔洞同时沿加载和垂直于加载方向增长.分析孔洞表面原子的位移历史，发现沿加载及与其垂直方向的孔洞顶点沿径向的速度基本恒定，由此提出了一个孔洞生长模型，可以解释孔洞增长的线性生长规律. 关键词： 纳米孔洞 分子动力学 冲击加载 位错     

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.