On the induced‐fit mechanism of substrate‐enzyme binding structures of nylon‐oligomer hydrolase

We present a detailed computational investigation of the induced‐fit motion in a nylon‐oligomer hydrolase (NylB) upon substrate binding. To this aim, we resort on the recently introduced parallel cascade selection molecular dynamics approach, allowing for an accelerated access to the set of conformational changes from an open‐ to a closed‐state structure to form the enzyme‐substrate complex in a specific induce‐fit mechanism. The structural investigation is quantitatively complemented by free energy analyses within the umbrella sampling algorithm accompanied by weighted histogram analysis. We find that the stabilization free energy is about 1.4 kcal/mol, whereas the highest free energy barrier to be overcome is about 2.3 kcal/mol. Conversely, the energetic contribution for the substrate binding is about 20 kcal/mol, as estimated from Generalized Born/Surface Area. This means that the open‐close induced‐fit motion could occur frequently once the substrate binds to the open state of NylB. © 2014 Wiley Periodicals, Inc.     

配合参数对单晶炉驱动系统的影响分析

光伏产业的发展使得对硅材料的需求日益增加,同时硅单晶生产行业竞争也日趋激烈。作为生产硅单晶的重要装备,单晶炉的稳定性和可靠性关系到硅单晶生产效率的提升和成本的下降,因此其驱动系统的设计和优化成为装备制造的关键环节。本文以NVT-HG2000-V1型硅单晶生长炉的驱动系统为研究对象,用SolidWorks三维建模实现虚拟装配,采用ADAMS建立其动力学仿真模型,并对驱动系统的运动过程进行仿真模拟。采用控制变量法定量分析了铜套与升降轴的配合间隙及丝杠参数对驱动力和驱动力矩的影响规律,进而在提高硅单晶生长炉装备稳定性和可靠性方面给出合理的技术建议。结果表明,铜套与升降轴的配合间隙达到0.071 mm后能有效降低驱动系统运行所需驱动力矩,丝杠倾斜度、螺纹螺距与螺纹间摩擦系数的增大均会导致驱动系统运行所需力矩大幅增加。     

Bcl-2蛋白结合底物时的诱导契合及高效抑制剂的柔性对接研究

Bcl-2蛋白是目前抗肿瘤药物研究很具前景的新靶点. Bcl-2蛋白与底物作用的活性腔生理情况下是蛋白与蛋白作用接触面大而平坦, 与底物结合时发生明显的诱导契合. 通过分析和比较Bcl-2蛋白和其高同源的Bcl-x_L蛋白的自由状态及与底物复合时的9个相关三维结构模型, 明确了蛋白及活性腔的骨架结构特征, 活性腔内的重要位点和关键残基, 及它们结合底物时发生的诱导契合. 基于以上认识, 采用柔性对接的方法得到了高亲和力的小分子抑制剂与Bcl-2蛋白的合理结合模式, 为以后设计合成新型高效Bcl-2蛋白抑制剂打下了坚实基础.     

An empirical fit to estimated neutron emission cross sections from proton induced reactions

Neutron emission cross section for various elements from⁹Be to²⁰⁹Bi have been calculated using the hybrid model code ALICE-91 for proton induced reactions in the energy range 25 MeV to 105 Me V. An empirical expression relating neutron emission cross section to target mass number and incident proton energy has been obtained. The simple expression reduces the computation time significantly. The trend in the variation of neutron emission cross sections with respect to the target mass number and incident proton energy has been discussed within the framework of the model used.     

A new strategy for the design of water-soluble synthetic receptors: specific recognition of DNA intercalators and diamines

Water-soluble zinc bisporphyrin receptors 1 and 2 having two Lewis acidic sites (zinc) in the hydrophobic environment consisting of alkyl chains and a bisporphyrin framework, and covered with hydrophilic exterior (twelve or eighteen carboxyl groups) were prepared. The receptors show high affinity for diamines and DNA intercalators in water where the binding constants K(a) are of the order of 10(7) and 10(8) M(-1), respectively. Diamines and DNA intercalators are bound to the receptor through different mechanisms. Diamines are bound through hydrophobic interactions and zinc-nitrogen interactions, while DNA intercalators are bound through hydrophobic interactions and charge-transfer interactions. Flexible alkyl chains can make van der Waals contact with guests and create a hydrophobic environment around the bound guest by an induced-fit-type mechanism. For the binding of DNA intercalators, the following features are noteworthy: 1). Binding constants are similar between the zinc porphyrins and zinc-free porphyrins; 2). the binding constant is larger for the guest having the lower LUMO; this indicates the important contribution of charge-transfer interactions to binding; 3). the hydrophobic and cationic nature of DNA intercalators is substantially important, and 4). higher ionic strength reduced the binding affinities; this shows a moderate contribution of electrostatic interactions. The conformational instability of the receptors also contributes to the tight binding: hydrophobic and electrostatic interactions cannot both be favorable at the same time in the guest-free receptor. Enthalpy-entropy compensation observed for the binding of diamines and DNA intercalators is characterized by a relatively small slope (alpha=0.74) and a large intercept (beta=7.75 kcal mol(-1)) in the DeltaH degrees versus TDeltaS degrees plot; this shows that a conformational change of receptors and a significant desolvation occur upon binding. The receptor can competitively bind to propidium iodide to deprive DNA of the intercalated propidium iodide. These features of water-soluble receptors consisting of a rigid framework and flexible side chains with a large solvent-accessible area are in contrast to highly preorganized rigid receptors, and they can provide useful guidelines for rational design of induced-fit artificial receptors in water.     

Local Power Properties of Kernel Based Goodness of Fit Tests

If (X_i, i ) is a strictly stationary process with marginal density function f, we are interested in testing the hypothesis H₀: {f=f₀}, where f₀ is given. We consider different test statistics based on integrated quadratic forms measuring the proximity between f_n, a kernel estimator of f, and f₀, or between f_n and its expected value computed under H₀. We study the asymptotic local power properties of the testing procedures under local alternatives. This study generalizes to the multidimensional case in a context of dependence the corresponding one made by P. J. Bickel and M. Rosenblatt in 1973 (Ann. Statist.1, 1071–1095).     

Electroweak precision data and gravitino dark matter

Electroweak precision measurements can provide indirect information about the possible scale of supersymmetry already at the present level of accuracy. We review present day sensitivities of precision data in mSUGRA-type models with the gravitino as the lightest supersymmetric particle (LSP). The χ ² fit is based on M _W , sin² θ _eff, (g−2) _μ , BR(b → sγ) and the lightest MSSM Higgs boson mass, M _h . We find indications for relatively light soft supersymmetry-breaking masses, offering good prospects for the LHC and the ILC, and in some cases also for the Tevatron.      

抽取信号的χ2分布拟合方法

BESⅡ上测量ψ(2S)辐射衰变时, 鉴于本底道的污染非常严重, 提出了一种抽取信号事例数的χ²拟合方法. 大量的蒙特卡罗模拟表明, 信号道与各个本底道的χ²分布形状各不相同. 这些特点提供了从数据的χ²分布中抽出信号道事例数的χ²拟合方法. 从蒙特卡罗模拟的结果来看, χ²拟合方法的误差小于2%.     

Insights into docking and scoring neuronal α4β2 nicotinic receptor agonists using molecular dynamics simulations and QM/MM calculations

A combined quantum mechanical (QM)‐polarized docking and molecular dynamics approach to study the binding mode and to predict the binding affinity of ligands acting at the α4β2‐nAChR is presented. The results obtained in this study indicate that the quantum mechanical/molecular mechanics docking protocol well describes the charge‐driven interactions occurring in the binding of nicotinic agonists, and it is able to represent the polarization effects on the ligand exerted by the surrounding atoms of the receptor at the binding site. This makes it possible to properly score agonists of α4β2‐nAChR and to reproduce the experimental binding affinity data with good accuracy, within a mean error of 2.2 kcal/mol. Moreover, applying the QM‐polarized docking to an ensemble of nAChR conformations obtained from MD simulations enabled us to accurately capture nAChR‐ligand induced‐fit effects. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

A viable method for goodness-of-fit test in maximum likelihood fit

A test statistic is proposed to perform the goodness-of-fit test in the unbinned maximum likelihood fit. Without using a detailed expression of the efficiency function, the test statistic is found to be strongly correlated with the maximum likelihood function if the efficiency function varies smoothly. We point out that the correlation coefficient can be estimated by the Monte Carlo technique. With the established method, two examples are given to illustrate the performance of the test statistic.