Molecular docking and 3D-QSAR study of pyranmycin derivatives against 16S rRNA A site

To understand pharmacophore properties of pyranmycin derivatives and to design novel inhibitors of 16S rRNA A site, comparative molecular field analysis (CoMFA) approach was applied to analyze three-dimensional quantitative structure-activity relationship (3D-QSAR) of 17 compounds. AutoDock 3.0.5 program was employed to locate the orientations and conformations of the inhibitors interacting with 16S rRNA A site. The interaction mode was demonstrated in the aspects of inhibitor conformation, hydrogen bonding and electrostatic interaction. Similar binding conformations of these inhibitors and good correlations between the calculated binding free energies and experimental biological activities suggest that the binding conformations of these inhibitors derived from docking procedure were reasonable. Robust and predictive 3D-QSAR model was obtained by CoMFA with q(2) values of 0.723 and 0.993 for cross-validated and noncross-validated, respectively. The 3D-QSAR model built here will provide clear guidelines for novel inhibitors design based on the Pyranmycin derivatives against 16S rRNA A site. (c) 2005 Elsevier B.V. All rights reserved.

Consensus scoring for enriching near-native structures from protein-protein docking decoys

The identification of near native protein-protein complexes among a set of decoys remains highly challenging. A stategy for improving the success rate of near native detection is to enrich near native docking decoys in a small number of top ranked decoys. Recently, we found that a combination of three scoring functions (energy, conservation, and interface propensity) can predict the location of binding interface regions with reasonable accuracy. Here, these three scoring functions are modified and combined into a consensus scoring function called ENDES for enriching near native docking decoys. We found that all individual scores result in enrichment for the majority of 28 targets in ZDOCK2.3 decoy set and the 22 targets in Benchmark 2.0. Among the three scores, the interface propensity score yields the highest enrichment in both sets of protein complexes. When these scores are combined into the ENDES consensus score, a significant increase in enrichment of near-native structures is found. For example, when 2000 dock decoys are reduced to 200 decoys by ENDES, the fraction of near-native structures in docking decoys increases by a factor of about six in average. ENDES was implemented into a computer program that is available for download at http://sparks.informatics.iupui.edu.

Refining near-native protein-protein docking decoys by local resampling and energy minimization

How to refine a near-native structure to make it closer to its native conformation is an unsolved problem in protein-structure and protein-protein complex-structure prediction. In this article, we first test several scoring functions for selecting locally resampled near-native protein-protein docking conformations and then propose a computationally efficient protocol for structure refinement via local resampling and energy minimization. The proposed method employs a statistical energy function based on a Distance-scaled Ideal-gas REference state (DFIRE) as an initial filter and an empirical energy function EMPIRE (EMpirical Protein-InteRaction Energy) for optimization and re-ranking. Significant improvement of final top-1 ranked structures over initial near-native structures is observed in the ZDOCK 2.3 decoy set for Benchmark 1.0 (74% whose global rmsd reduced by 0.5 angstrom or more and only 7% increased by 0.5 angstrom or more). Less significant improvement is observed for Benchmark 2.0 (38% versus 33%). Possible reasons are discussed.

Docking and molecular dynamics study on the inhibitory activity of coumarins on aldose reductase

In order to explore the inhibitory mechanism of coumarins toward aldose reductase (ALR2), AutoDock and Gromacs software were used for docking and molecular dynamics studies on 14 coumarins (CM) and ALR2 protease. The docking results indicate that residues TYR48, HIS110, and TRP111 construct the active pocket of ALR2 and, besides van der Waals and hydrophobic interaction, CM mainly interact with ALR2 by forming hydrogen bonds to cause inhibitory behavior. Except for CM1, all the other coumarins take the lactone part as acceptor to build up the hydrogen bond network with active-pocket residues. Unlike CM3, which has two comparable binding modes with ALR2, most coumarins only have one dominant orientation in their binding sites. The molecular dynamics calculation, based on the docking results, implies that the orientations of CM in the active pocket show different stabilities. Orientation of CM1 and CM3a take an unstable binding mode with ALR2; their conformations and RMSDs relative to ALR2 change a lot with the dynamic process. While the remaining CM are always hydrogen-bonded with residues TYR48 and HIS110 through the carbonyl O atom of the lactone group during the whole process, they retain the original binding mode and gradually reach dynamic equilibrium.

Docking and molecular dynamics studies toward the binding of new natural phenolic marine inhibitors and aldose reductase

Phenolic marine natural product is a kind of new potential aldose reductase inhibitors (ARIs). In order to investigate the binding mode and inhibition mechanism, molecular docking and dynamics studies were performed to explore the interactions of six phenolic inhibitors with human aldose reductase (hALR2). Considering physiological environment, all the neutral and other two ionized states of each phenolic inhibitor were adopted in the simulation. The calculations indicate that all the inhibitors are able to form stable hydrogen bonds with the hALR2 active pocket which is mainly constructed by residues TYR48, HIS110 and TRP111, and they impose the inhibition effect by occupying the active space. In all inhibitors, only La and its two ionized derivatives La_ion1 and La_ion2, in which neither of the ortho-hydrogens of 3-hydroxyl is substituted by Br, bind with hALR2 active residues using the terminal 3-hydroxyl. While, all the other inhibitors, at least one of whose ortho-sites of 3- and 6-hydroxyls are substituted by Br substituent which take much electron-withdrawing effect and steric hindrance, bind with hALR2 through the lactone group. This means that the Br substituent can effectively regulate the binding modes of phenolic inhibitors. Although the lactone bound inhibitors have relatively high RMSD values, our dynamics study shows that both binding modes are of high stability. For each inhibitor molecule, the ionization does not change its original binding mode, but it does gradually increase the binding free energy, which reveals that besides hydrogen bonds, the electrostatic effect is also important to the inhibitor–hALR2 interaction.

Structural and functional characterization of the human CCR5 receptor in complex with HIV gp120 envelope glycoprotein and CD4 receptor by molecular modeling studies

The entry of human immunodeficiency virus (HIV) into cells depends on a sequential interaction of the gp120 envelope glycoprotein with the cellular receptors CD4 and members of the chemokine receptor family. The CC chemokine receptor CCR5 is such a receptor for several chemokines and a major coreceptor for the entry of R5 HIV type-1 (HIV-1) into cells. Although many studies focus on the interaction of CCR5 with HIV-1, the corresponding interaction sites in CCR5 and gp120 have not been matched. Here we used an approach combining protein structure modeling, docking and molecular dynamics simulation to build a series of structural models of the CCR5 in complexes with gp120 and CD4. Interactions such as hydrogen bonds, salt bridges and van der Waals contacts between CCR5 and gp120 were investigated. Three snapshots of CCR5-gp120-CD4 models revealed that the initial interactions of CCR5 with gp120 are involved in the negatively charged N-terminus (Nt) region of CCR5 and positively charged bridging sheet region of gp120. Further interactions occurred between extracellular loop2 (ECL2) of CCR5 and the base of V3 loop regions of gp120. These interactions may induce the conformational changes in gp120 and lead to the final entry of HIV into the cell. These results not only strongly support the two-step gp120-CCR5 binding mechanism, but also rationalize extensive biological data about the role of CCR5 in HIV-1 gp120 binding and entry, and may guide efforts to design novel inhibitors.

Quantifying intrinsic specificity: A potential complement to affinity in drug screening

We report here the investigation of a novel description of specificity in protein-ligand binding based on energy landscape theory. We define a new term, intrinsic specificity ratio (ISR), which describes the level of discrimination in binding free energies of the native basin for a protein-ligand complex from the weaker binding states of the same ligand. We discuss the relationship between the intrinsic specificity we defined here and the conventional definition of specificity. In a docking study of molecules with the enzyme COX-2, we demonstrate a statistical correspondence between ISR value and geometrical shapes of the small molecules binding to COX-2. We further observe that the known selective (nonselective) inhibitors of COX-2 have higher (lower) ISR values. We suggest that intrinsic specificity ratio may be a useful new criterion and a complement to affinity in drug screening and in searching for potential drug lead compounds.

In-situ microscopic FTIR spectroelectrochemistry of ascorbic acid in poly(ethylene glycol)/LiClO4 electrolyte paste and in the presence of dispersed cobalt hexacyanoferrate microcrystalline powder

In-situ microscopic FTIR spectroelectrochemical technique(MFTIRs) was applied to studying the electrochemical oxidation of ascorbic acid(AA) in poly(ethylene glycol)(PEG) paste at a 100 mu m diameter Pt disk electrode. Using this technique, the catalytic ability of cobalt hexacyanoferrate(CoHCF) microcrystalline toward AA oxidation was also studied, it was found that the dispersed CoHCF powder in the PEG paste can generate well-shaped thin-layer cyclic voltammetric waves with the peak height proportional to the scan rate, corresponding to the Fe centered redox reactions. This oxidation step catalyzed the AA oxidation. Also, this pasted CoHCF powder generated well-resolved in-situ MFTIRs spectra, by which a chemical interaction between C = C bond of AA ring and CoHCF lattice was revealed. A corresponding surface docking mechanism for the catalytic reaction has been proposed.

SNAP-23蛋白在鲈鱼巨噬细胞白细胞介素1β分泌过程中的功能

SNARE蛋白家族是所有真核细胞胞吐及分泌作用中的关键因子，由其介导的运输囊泡膜与靶膜的锚靠、融合为胞内蛋白的运出提供了一条重要途径。体外试验表明，Syntaxin6-Syntaxin7-Vti1b，SNAP-23-Syntaxin4等SNARE核心蛋白之间精确的相互作用是哺乳动物巨噬细胞肿瘤坏死因子α (TNF-α)运输和分泌的必备条件，在机体非特异性免疫应答反应过程中起重要作用。 本研究受上述启示，旨在揭示SNARE蛋白在海洋鱼类免疫细胞内重要细胞因子白细胞介素1β (IL-1β)的分泌过程中的作用。参照Percoll密度梯度离心技术，从鲈鱼头肾组织分离纯化巨噬细胞进行稳定培养；利用RT-PCR方法克隆出鲈鱼t-SNARE蛋白SNAP-23和Syntaxin3的部分cDNA序列，再结合先前克隆的VAMP2和已知的鲈鱼IL-1β，TNF-α和IL-8的基因序列，设计特异性引物。利用Real-time PCR技术在mRNA水平上精确测定鲈鱼巨噬细胞中上述6种基因在革兰氏阴性菌脂多糖(LPS)分子刺激下的表达变化，发现SNAP-23基因与三种细胞因子基因的表达正相关；通过免疫印迹检测SNAP-23蛋白表达变化，利用酶联免疫吸附试验(ELISA)检测IL-1β的分泌水平，在蛋白水平上验证了SNAP-23表达与IL-1β分泌的正相关性；利用5`RACE和3`RACE技术克隆出鲈鱼SNAP-23全长基因，结合定点突变策略和靶向PCR克隆手段，构建鲈鱼SNAP-23野生型融合质粒pEGFP-SNAP-23wt，Cys缺失突变融合质粒pEGFP-SNAP-23ΔCys和模拟E型肉毒神经毒素(BoNT/E)切割突变融合质粒pEGFP-SNAP-23ΔBoNT/E，以及鲈鱼IL-1β野生型融合表达质粒IL-1β-pEGFP和IL-1β-pEYFP。所有融合蛋白均在鲈鱼巨噬细胞内成功表达，结合ELISA实验结果发现，SNAP-23野生型的表达对IL-1β的分泌有促进作用，而Cys缺失突变体的表达则抑制IL-1β向胞外分泌。首次证实了鱼类巨噬细胞内SNAP-23蛋白在IL-1β分泌过程中的重要作用。此外通过与GFP共表达，定位了IL-1β分子在巨噬细胞内的分布，发现新合成的IL-1β分子很可能像TNFα一样经“内质网－胞质－伪足－胞外” 的分泌路径运出胞外。

基于有限状态机的空间对接仿真平台控制系统设计

给出了一种基于分层式有限状态机的五自由度空间对接仿真平台控制系统设计方法,对状态机进行了扩展定义.增加了一个定义于状态上的变量属性集合,使其有利于系统的代码实现.结合控制系统采用的10 ms定时中断机制,将状态机层次划分到了可以分析每个10 ms硬件中断程序所需实现的控制功能状态及其转移、继承关系的程度,可以更清晰地设计出中断程序所需要的构成结构.系统的实际应用结果证明了上述方法的有效性.

基于有限状态机与Petri网的系统分析与设计

从系统组成、功能需求和体系结构方面介绍了航天器空间对接仿真系统的实时多任务控制系统,基于有限状态机和Petri网方法对其进行了单任务级和多任务级的分析建模,并以此为基础完成系统的详细设计,其中应用分叉和资源共享模型实现了系统的同步和互斥问题。实际应用中应用工程化和模块化的方法完成系统设计,系统运行性能良好。试验证明这种分析设计方法合理可行。

基于二维位置敏感探测器的空间对接过程研究

为了准确地捕捉机器人空间对接的传感器信息,从对接机构的设计入手,研究了空间对接中传感器的选择、改制和基于传感器信息的空间对接问题.考虑到安装空间的限制和处理的信息量太多,提出了利用二维位置敏感探测器(PSD)配合红外发光器阵列的方法完成机器人的空间对接.通过对位置敏感探测器工作原理的分析和对传感器特性的试验,提出了在PSD光敏面上增加光学装置的方法以扩大它的探测范围和精度,同时大大减小了它对光信号的依赖程度.把该方法应用于可重构模块化探测机器人系统中,提出了基于传感器信息的轨迹规划方法,对子机器人空间对接过程的仿真试验验证了轨迹规划和空间对接的可行性.

可重构星球探测机器人的空间对接研究

提出了以改装后的位置敏感传感器来引导机器人完成自动对接的方法,分析了具体工作原理。对可重构星球探测机器人在运动模式下完成对接的两种姿态进行了比较,分别用一般方法和改进后的规划方法计算出了对接工作空间,比较结果说明,机器人在运动模式下三角边着地有利于完成自动对接。对工作模式机器人在工作空间内的运动进行了静力学分析,分析结果表明,机器人在工作空间内可以自由运动。用VC和OpenGL搭建的平台对空间对接进行了仿真试验,试验结果验证了对接工作空间计算的正确性和完成空间自动对接的可能性。

空间对接机构缓冲系统及其运动学建模

以异体同构周边式对接机构差动式缓冲系统为对象 ,将缓冲机构分解成 6个独立分支 ,通过设立局部坐标系 ,建立缓冲系统运动学正、逆解模型。该建模方法可以消除各分支之间的耦合关系 ,使建模得以简化。算例说明这种缓冲系统运动学模型是正确有效的。

基于Stewart平台六维力传感器的分区静态标定方法

基于Stewart平台的六维力传感器具有结构紧凑、刚度大、量程宽等特点,它在工业机器人、空间站对接等领域具有广泛的应用前景。好的标定方法是正确使用传感器的基础。由于基于Stewart平台的六维力传感器是一个复杂的非线性系统,所以采用常规的线性标定方法必将带来较大的标定误差从而影响其使用性能。标定的实质是,由测量值空间到理论值空间的映射函数的确定过程。由函数逼近理论可知,当只在已知点集上给出函数值时,可用多项式或分段多项式等较简单函数逼近待定函数。基于上述思想,本文将整个测量空间划分为若干连续的子测量空间,再对每个子空间进行线性标定,从而提高了整个测量系统的标定精度。实验分析结果表明了该标定方法有效。