Insights into the Allosteric Effect of SENP1 Q597A Mutation on the Hydrolytic Reaction of SUMO1 via an Integrated Computational Study

Small ubiquitin-related modifier (SUMO)-specific protease 1 (SENP1) is a cysteine protease that catalyzes the cleavage of the C-terminus of SUMO1 for the processing of SUMO precursors and deSUMOylation of target proteins. SENP1 is considered to be a promising target for the treatment of hepatocellular carcinoma (HCC) and prostate cancer. SENP1 Gln597 is located at the unstructured loop connecting the helices α4 to α5. The Q597A mutation of SENP1 allosterically disrupts the hydrolytic reaction of SUMO1 through an unknown mechanism. Here, extensive multiple replicates of microsecond molecular dynamics (MD) simulations, coupled with principal component analysis, dynamic cross-correlation analysis, community network analysis, and binding free energy calculations, were performed to elucidate the detailed mechanism. Our MD simulations showed that the Q597A mutation induced marked dynamic conformational changes in SENP1, especially in the unstructured loop connecting the helices α4 to α5 which the mutation site occupies. Moreover, the Q597A mutation caused conformational changes to catalytic Cys603 and His533 at the active site, which might impair the catalytic activity of SENP1 in processing SUMO1. Moreover, binding free energy calculations revealed that the Q597A mutation had a minor effect on the binding affinity of SUMO1 to SENP1. Together, these results may broaden our understanding of the allosteric modulation of the SENP1−SUMO1 complex.     

Electronic structure of strongly correlated systems: recent developments in multiconfiguration pair-density functional theory and multiconfiguration nonclassical-energy functional theory

Strong electron correlation plays an important role in transition-metal and heavy-metal chemistry, magnetic molecules, bond breaking, biradicals, excited states, and many functional materials, but it provides a significant challenge for modern electronic structure theory. The treatment of strongly correlated systems usually requires a multireference method to adequately describe spin densities and near-degeneracy correlation. However, quantitative computation of dynamic correlation with multireference wave functions is often difficult or impractical. Multiconfiguration pair-density functional theory (MC-PDFT) provides a way to blend multiconfiguration wave function theory and density functional theory to quantitatively treat both near-degeneracy correlation and dynamic correlation in strongly correlated systems; it is more affordable than multireference perturbation theory, multireference configuration interaction, or multireference coupled cluster theory and more accurate for many properties than Kohn–Sham density functional theory. This perspective article provides a brief introduction to strongly correlated systems and previously reviewed progress on MC-PDFT followed by a discussion of several recent developments and applications of MC-PDFT and related methods, including localized-active-space MC-PDFT, generalized active-space MC-PDFT, density-matrix-renormalization-group MC-PDFT, hybrid MC-PDFT, multistate MC-PDFT, spin–orbit coupling, analytic gradients, and dipole moments. We also review the more recently introduced multiconfiguration nonclassical-energy functional theory (MC-NEFT), which is like MC-PDFT but allows for other ingredients in the nonclassical-energy functional. We discuss two new kinds of MC-NEFT methods, namely multiconfiguration density coherence functional theory and machine-learned functionals.

This feature article overviews recent work on active spaces, matrix product reference states, treatment of quasidegeneracy, hybrid theory, density-coherence functionals, machine-learned functionals, spin–orbit coupling, gradients, and dipole moments.     

复数星图与单路的多染色拉姆齐数

对给定的简单图$H_1,H_2,\ldots,H_c$, 我们将使完全图$K_n$的任意边分解$\{G_i\}^c_{i=1}$都存在至少一个$G_i$有子图同构于$H_i$的最小正整数$n$称为多染色拉姆齐数 $R(H_1,H_2,\ldots,$ $H_c)$. 对正整数$m,n_1,n_2,\ldots,n_c$, 令$\Sigma=\sum_{i=1}^{c}(n_i-1)$. 在文献中,我们已经获得了$R(K_{1,n_1},\ldots,K_{1,n_c},P_m)$ 的一些界和精确值.Wang推测若$\Sigma\not\equiv 0\pmod{m-1}$且$\Sigma+1\ge (m-3)^2$, 则有$R(K_{1,n_1},\ldots, K_{1,n_c}, P_m)=\Sigma+m-1.$ 本文中, 我们给出了一个新的下界并给出$R(K_{1,n_1},\ldots,K_{1,n_c},P_m)$在$m\leq\Sigma$, $\Sigma\equiv k\pmod{m-1}$且$2\leq k \leq m-2$情况下的部分精确值. 这些结果部分证实了Wang的猜想.     

Anisotropic Superconducting Properties of Kagome Metal CsV_3Sb_5

We systematically measure the superconducting(SC) and mixed state properties of high-quality CsV_3 Sb_5 single crystals with T_c～3.5 K.We find that the upper critical field H_(c2)(T) exhibits a large anisotropic ratio of H_(c2)~(ab)/H_(c2)~c～9 at zero temperature and fitting its temperature dependence requires a minimum two-band effective model.Moreover,the ratio of the lower critical field,H_(c1)~(ab)/H_(c1)~c,is also found to be larger than 1,which indicates that the in-plane energy dispersion is strongly renormalized near Fermi energy.Both H_(c1)(T) and SC diamagnetic signal are found to change little initially below T_c～3.5 K and then to increase abruptly upon cooling to a characteristic temperature of ～2.8 K.Furthermore,we identify a two-fold anisotropy of in-plane angular-dependent magnetoresistance in the mixed state.Interestingly,we find that,below the same characteristic T～2.8 K,the orientation of this two-fold anisotropy displays a peculiar twist by an angle of 60° characteristic of the Kagome geometry.Our results suggest an intriguing superconducting state emerging in the complex environment of Kagome lattice,which,at least,is partially driven by electron-electron correlation.     

Surfactant-Assisted Assembly of Dipeptide Forming a Broom-like Structure

Understanding the influence of surfactants on the assembly of peptides has a considerable practical motivation. In this paper, we systematically study the anionic surfactant-assisted assembly of diphenylalanine (FF). FF forms broom-like structures in a concentration of sodium cholate (NaC) around the CMC, and assembles into linear and unidirectional rods in the presence of low and high surfactant concentrations. FF’s improved hydrogen bonding and controlled assembly rates are appropriate for other anionic surfactants. At this stage, the use of FF as the simplest protein consequence can be helpful in the investigation of further protein–surfactant interactions.     

Single-Stage Extraction and Separation of Co2+ from Ni2+ Using Ionic Liquid of [C4H9NH3][Cyanex 272]

The purpose of this study was to optimize the extraction conditions for separating Co²⁺ from Ni²⁺ using N-butylamine phosphinate ionic liquid of [C₄H₉NH₃][Cyanex 272]. A Box–Behnken design of response surface methodology was used to analyze the effects of the initial pH, extraction time, and extraction temperature on the separation factor of Co²⁺ from sulfuric acid solution containing Ni²⁺. The concentrations of Co²⁺ and Ni²⁺ in an aqueous solution were determined using inductively coupled plasma-optical emission spectrometry. The optimized extraction conditions were as follows: an initial pH of 3.7, an extraction time of 55.8 min, and an extraction temperature of 330.4 K. The separation factor of Co²⁺ from Ni²⁺ under optimized extraction conditions was 66.1, which was very close to the predicted value of 67.2, and the error was 1.7%. The equation for single-stage extraction with high reliability can be used for optimizing the multi-stage extraction process of Co²⁺ from Ni²⁺. The stoichiometry of chemical reaction for ion-exchange extraction was also investigated using the slope method.     

西南地区金荞麦(Fagopyrum dibotrys(D.Don)Hara)居群遗传多样性研究

采用等位酶电泳技术研究了云南省和四川省西南共 5个县境内金荞麦 (Fagopyrumdibotrys(D .Don)Hara) 5个天然居群的遗传多样性 .金荞麦居群内维持有较高的遗传多样性 ,多态位点比率为 5 6 .7% ,预期杂合度和观察杂合度分别为 0 .2 2 1和 0 .36 3.并对金荞麦与栽培荞麦之间遗传变异作了比较 .     

衣康酸生产菌株土曲霉QD-1发酵工艺的研究

筛选得到衣康酸生产菌株土曲霉QD 1,对其适宜的发酵工艺条件进行了研究。确定了最佳种龄、接种量和发酵最适初始pH。通过正交试验确定了最适发酵培养基组成,并对发酵过程中衣康酸生成 、菌体生长和糖的消耗规律进行了分析。     

一种改进的最大熵方法在船舶辐射噪声盲分离中的应用

对于船舶辐射噪声信号的盲信号分离(BSS)问题，由于常用的最小互信息(MMI)方法需要估计输出信号的高阶累积量，这对于非高斯、非平稳的船舶辐射噪声来说信号估计的精度将会降低．为此，本文验证了最大熵(ME)方法在处理此类复杂信号时能作为最佳对比函数的条件，并在此基础上用高斯混合模型来估计信号的概率分布，提高了信号概率密度估计的精度；同时在算法的迭代过程中使用自然梯度下降法代替随机梯度下降法，提高了算法的收敛速度．通过对船舶辐射噪声信号的盲分离实验，证明了此分离算法是有效的．     

基于独立成分分析的强背景噪声去噪方法

由于许多传统的去噪方法在强背景噪声情况下提取声音信号的能力变弱甚至失效，提出应用独立成分分析(ICA)方法对声音信号进行特征提取，并证明了这种ICA变换能增强语音和音乐信号的超高斯性．在此基础上，应用ICA基函数作为滤波器，通过阈值化的去噪方法对含有强高斯背景噪声的声音信号进行去噪仿真实验．结果表明，本方法明显优于传统的均值滤波和小波去噪方法，为强背景噪声下弱信号的检测提供了新的途径．