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.     

Comprehensive two‐dimensional gas chromatography coupled with static headspace sampling to analyze volatile compounds: Application to almonds

The hyphenation of static headspace sampling with comprehensive 2D GC equipped with a modulator based on capillary flow technology and a flame ionization detector was used to separate and identify 43 representative target volatile compounds (light hydrocarbons, carbonyls, pyrazines, alcohols, furans, and benzenes) frequently detected in the roasting process of nuts. Five column combinations with differing degrees of orthogonality (one conventional and four inverted phase sets) were tested in order to obtain the best conditions for analyzing these volatile compounds. Optimization of the working conditions for each of the different column combinations was performed by means of a central composite design. The best results in terms of separation and differentiation among the different chemical groups were achieved with a combination of inverted phase columns (first dimension: highly polar, INNOWax; second dimension: mid‐polar, ZB‐35). Additionally, a reference template was developed to provide an effective and rapid analysis of the target compounds. Finally, the proposed method was successfully employed to identify volatile compounds in raw and roasted almond samples from the Spanish cultivar Largueta.     

基于改进免疫遗传算法的近红外光谱变量选择方法

该文在免疫遗传算法（IGA）的基础上,提出一种改进免疫遗传算法（iIGA）用于近红外光谱波长变量的选择。该算法舍去了原算法中固定抗体相似度阈值的思想,取而代之的是抗体相似度阈值自适应,同时引入精英保留策略和贪心算法思想,使得算法朝着正确的方向进行局部性探优。将该算法在玉米的淀粉和蛋白质含量数据集上进行实验测试,建立偏最小二乘（PLS）分析模型,并与IGA、遗传算法（GA）以及全谱方法进行了对比。结果表明,在玉米淀粉含量的预测上,iIGA相较于原IGA算法,预测集均方根误差（RMSEP）从0.312 0降至0.298 0,预测集预测精度提升4.5%;在玉米蛋白质含量的预测上,RMSEP从0.124 4降至0.110 3,预测集预测精度提升11.3%。分别对预测淀粉和蛋白质模型的RMSEP值进行显著性检验,F值分别为165.22和182.05,P值分别为9.5 × 10－23和4.5 × 10－24,P值均小于0.05,因此,iIGA能显著提升模型预测精度。     

A method for C(alpha) direct-detection in protonless NMR

Attempts are made to efficiently decouple (13)C nuclei without significant loss of coherence during the application of the decoupling package. Such attempts are based on the S(3)E spin-state selection method. A newly developed double S(3)E (DS(3)E) is particularly efficient for C(alpha) detection for proteins as large as 480 kDa.     

毛细管电泳法高效筛选8-氧代鸟嘌呤DNA糖基化酶的核酸适配体

8-氧代鸟嘌呤DNA糖基化酶(OGG1)是人体中重要的功能蛋白,在修复DNA氧化性损伤过程中起关键作用。氧化应激等引起的氧化损伤易导致炎症反应的发生,对OGG1的抑制可以一定程度上起到缓解作用;对癌细胞OGG1的抑制有望作为癌症治疗的新方法。目前的研究多集中于小分子对OGG1功能的影响和调控,而OGG1的适配体筛选尚未见报道。作为功能配体,适配体具有合成简单、高亲和力及高特异性等优点。该文筛选了OGG1的核酸适配体,结合毛细管电泳高效快速的优点建立了两种基于毛细管电泳-指数富集进化(CE-SELEX)技术的筛选方法:同步竞争法和多轮筛选法。同步竞争法利用单链结合蛋白(SSB)与核酸库中单链核酸的强结合能力,与目标蛋白OGG1组成竞争体系,并通过增加SSB浓度来增加竞争筛选压力,以去除与OGG1弱结合的核酸序列,一步筛选即可获得与OGG1强结合的核酸序列。多轮筛选法在相同孵育条件和电泳条件下,经3轮筛选获得OGG1的核酸适配体。比较两种筛选方法的筛选结果,筛选结果中频次最高的3条候选核酸适配体序列一致,其解离常数(K_D)值在1.71~2.64 μmol/L之间。分子对接分析结果表明候选适配体1(Apt 1)可能与OGG1中具有修复氧化性损伤功能的活性口袋结合。通过对两种筛选方法的对比,证明同步竞争法更加快速高效,对其他蛋白核酸适配体筛选方法的选择具有一定的指导意义。得到的适配体有望用于OGG1功能调控,以抑制其修复功能。     

基于次梯度选取的非光滑优化强次可行方向法

本文结合次梯度选取技术及割平面法和强次可行方向法的思想,提出了一个求解目标函数非光滑约束优化问题的强次可行方向算法.通过设计一个新的寻找搜索方向子问题和构造新型线搜索,算法不仅能接受不可行的初始点,而且能保持迭代点的强次可行性,同时避免在可行域外目标函数值的不适度增加.算法具备全局收敛性,且初步的数值试验表明算法是稳定有效的.     

Weak temperature gradient effect on the stability of the circular Couette flow

We have investigated the influence of a weak radial temperature gradient in a wide gap and large aspect ratio Couette-Taylor system. The inner cylinder is rotating and can be heated or cooled, the outer cylinder is at rest and immersed in a large thermal bath. We found that a radial temperature gradient destabilizes the Couette flow leading to a pattern of traveling helicoidal vortices occurring only near the bottom of the system. The size of the pattern increases as the rotation frequency of the cylinder is increased. We have characterized the spatiotemporal properties of the pattern and we have shown that it behaves as a wall mode found in the simulation of the complex Ginzburg-Landau equation with homogeneous boundary conditions.     

Transitions in a genotype selection model driven by coloured noises

This paper investigates a genotype selection model subjected to both a multiplicative coloured noise and an additive coloured noise with different correlation time τ1 and τ2 by means of the numerical technique. By directly simulating the Langevin Equation, the following results are obtained. （1） The multiplicative coloured noise dominates, however, the effect of the additive coloured noise is not neglected in the practical gene selection process. The selection rate μ decides that the selection is propitious to gene A haploid or gene B haploid. （2） The additive coloured noise intensity and the correlation time τ2 play opposite roles. It is noted that α and τ2 can not separate the single peak, while can make the peak disappear and ~-2 can make the peak be sharp. （3） The multiplicative coloured noise intensity D and the correlation time τ1 can induce phase transition, at the same time they play opposite roles and the reentrance phenomenon appears. In this case, it is easy to select one type haploid from the group with increasing D and decreasing τ1.     

A Strong Limit Theorem on Random Selection

In this paper, the idea of random selection in the theorem on gambling system is extended to Markov chains, by using the notion likelihood ratio and an analytic technique. A strong limit theorem on the relative frequency of ordered couple under random selection is established.AMS Subject Classification (2001) primary 60F15 Secondary 60J10