基于接触数引导的迭代多组独立分子动力学模拟实现配体-蛋白质结合与解离过程

配体的结合与解离过程在蛋白质实现其生物学功能方面非常关键,因此对这些高度动态过程的研究变得非常重要. 尽管已有实验方法可以确定蛋白质-配体复合物的三维结构,但一般仅可获得静态图片. 随着计算机算力的快速提高以及算法的优化,分子动力学模拟在探索配体的结合与解离过程方面具有诸多优势. 然而,当系统变得足够大时,分子动力学模拟的时间和空间尺度成为了巨大的挑战. 本工作提出了一种研究配体-蛋白质结合与解离的增强采样工具,它基于配体和蛋白质之间形成的接触数来引导迭代多组独立分子动力学模拟. 在腺苷酸激酶的模拟结果中,观测到配体的结合和解离过程,而使用传统分子动力学模拟在同一时间尺度下则无法实现这一过程.     

Beam-based calibrations of the BPM offset at C-ADS Injector Ⅱ

Beam-based BPM offset calibration was carried out for Injector II at the C-ADS demonstration facility at the Institute of Modern Physics(IMP), Chinese Academy of Science(CAS). By using the steering coils integrated in the quadrupoles, the beam orbit can be effectively adjusted and BPM positions recorded at the Medium Energy Beam Transport of the Injector II Linac. The studies were done with a 2 m A, 2.1 Me V proton beam in pulsed mode.During the studies, the "null comparison method" was applied for the calibration. This method is less sensitive to errors compared with the traditional transmission matrix method. In addition, the quadrupole magnet's center can also be calibrated with this method.     

Sonochemical synthesis and characterization of new one-dimensional manganese(II) coordination polymer nanostructures

A new Mn(II) coordination polymer, [Mn (L₁)₂(NCS)₂]_n (1) [L₁ = 3,4-bis(4-pyridyl)-5-(2-pyridyl)-1,2,4-triazole] was synthesized by the reaction of ligand L₁ and mixtures of manganese(II) acetate and potassium thiocyanate using the heat gradient method. Compound 1 has been characterized by IR spectroscopy, elemental analyses and X-ray crystallography. The crystal structure of compound 1 was determined by single-crystal X-ray diffraction and shows a new interesting one-dimensional coordination polymer. Nanostructures of compound 1 have been synthesized by sonochemical method. The products were characterized by X-ray powder diffraction, scanning electron microscopy (SEM), and IR spectroscopy. The thermal stability of nano particles of compound 1 was studied by thermal gravimetric and differential thermal analyses.     

Correcting reaction rates measured by saturation-transfer magnetic resonance spectroscopy

Off-resonance or spillover irradiation and incomplete saturation can introduce significant errors in the estimates of chemical rate constants measured by saturation-transfer magnetic resonance spectroscopy (MRS). Existing methods of correction are effective only over a limited parameter range. Here, a general approach of numerically solving the Bloch-McConnell equations to calculate exchange rates, relaxation times and concentrations for the saturation-transfer experiment is investigated, but found to require more measurements and higher signal-to-noise ratios than in vivo studies can practically afford. As an alternative, correction formulae for the reaction rate are provided which account for the expected parameter ranges and limited measurements available in vivo. The correction term is a quadratic function of experimental measurements. In computer simulations, the new formulae showed negligible bias and reduced the maximum error in the rate constants by about 3-fold compared to traditional formulae, and the error scatter by about 4-fold, over a wide range of parameters for conventional saturation transfer employing progressive saturation, and for the four-angle saturation-transfer method applied to the creatine kinase (CK) reaction in the human heart at 1.5 T. In normal in vivo spectra affected by spillover, the correction increases the mean calculated forward CK reaction rate by 6-16% over traditional and prior correction formulae.     

Multifunctional human serum albumin in the surface‐enhanced Raman spectroscopy of porphyrin: demetalation promoter,molecular spacer and stabilizer

Human serum albumin (HSA), a model protein, was introduced to the surface‐enhanced Raman spectroscopy (SERS) of cationic porphyrin 5,10,15,20‐tetrakis(1‐methyl‐4‐pyridyl)‐21H,23H‐porphine (H₂TMPyP4). HSA was found to have a great influence not only on Ag nanoparticle aggregation state but also on the interaction between Ag nanoparticle and H₂TMPyP4 molecules. In the (H₂TMPyP4‐Ag colloid)/HSA system, addition of H₂TMPyP4 to Ag colloid led to a quick Ag colloid aggregation, and subsequent HSA addition could stabilize this system. The SERS spectrum was dominated by a combination of Ag(II)TMPyP4 and free base H₂TMPyP4. More interestingly, a photoinduced demetalation of Ag(II)TMPyP4 to free base H₂TMPyP4 was observed in the (H₂TMPyP4‐Ag colloid)/HSA system. This demetalation process was partially reversible when the laser was turned off or the laser power was reduced. In this case, HSA acts as both a stabilizer and a demetalation promoter. In the (HSA‐H₂TMPyP4)/Ag colloid system, when H₂TMPyP4 was premixed with HSA prior to the Ag colloid addition, no obvious Ag colloid aggregation appeared, and the SERS spectrum was just characteristic of free base H₂TMPyP4. In this case, HSA is proposed to function as both a stabilizer and a molecular spacer. Copyright © 2010 John Wiley & Sons, Ltd.     

Magneto-optical single dot spectroscopy of GaSb/GaAs type II quantum dots

We have investigated magneto-optical properties of GaSb/GaAs self-assemble type II quantum dots by single dot spectroscopy in magnetic field. We have observed clear Zeeman splitting and diamagnetic shift of GaSb/GaAs quantum dots. The diamagnetic coefficient ranges from 5 to 30 μeV/T². The large coefficient and their large distribution are attributed to the size inhomogeneity and electron localization outside the dot. The g-factor of GaSb/GaAs quantum dots is slightly larger than that of similar type I InGaAs/GaAs quantum dots. In addition, we find almost linear relationship between the diamagnetic coefficient and the g-factor. The linear increase of g-factor with diamagnetic coefficient is due to an increase of spin-orbit interaction with dot size.     

Vibrational Spectrum of a Platinum Complex of Piroxicam

The infrared and Raman spectra of a platinum complex of the antiinflammatory drug piroxicam (Pir) and dimethylsulfoxide (DMSO) of composition [PtCl₂Pir(DMSO)] were recorded and briefly discussed on the basis of its structural characteristics. The metal-to-ligand vibrations are analyzed in detail.     

X-ray diffuse scattering from incommensurable structures

X-Ray diffuse scattering from a series of examples where the reason for the existence of incommensurable features is fairly well understood, is described. They include in particular non stoichiometric compounds such as [DIPS Φ₄(l₃)0.76] and such as intercalated graphite RbC₂₄. and quasi one dimensional conductors. A particular emphasis is given on various 1 - D conductors and to the relation of the incommensurability to the characteristics of the electron conduction bands.     

Effect of multi-frequency power ultrasound (MFPU) treatment on enzyme hydrolysis of casein

Effect of multi-frequency power ultrasound (MFPU) pretreatments on the degree of hydrolysis (DH) and mechanism of casein during alcalase enzymolysis was investigated. Results showed that MFPU pretreatment in tri-frequency 20/40/60 kHz mode significantly (p < 0.05) improved the DH value of casein. Variation of intrinsic fluorescence spectrum indicated the unfolding and degradation of casein occurred after MFPU pretreatment. Fourier transform infrared spectra showed that α-helix and β-sheet content of MFPU pretreated casein decreased, while β-turn and random coil content increased. Surface topography and nanostructures of caseins were found modified after MFPU pretreatments by the analysis of scanning electron microscopy (SEM) and atomic force microscopy (AFM). The SEM analysis also indicated that the enzymolysis residues of casein pretreated by MFPU were smaller than untreated samples. In conclusion, the MFPU can be used as an efficient pretreatment method to promote the enzymolysis of casein.     

钛铁试剂-铜配合物荧光光谱法测定半胱氨酸

采用荧光光谱法和紫外-可见吸收光谱法研究了pH 8.0的B-R缓冲溶液中L-半胱氨酸与钛铁试剂-铜配合物的作用过程。研究发现,半胱氨酸的加入导致钛铁试剂-铜配合物在350 nm处的荧光显著增强,并且在一定浓度范围内体系荧光强度的增大与半胱氨酸浓度呈良好的线性相关性。据此建立了