Structural mining: self-consistent design on flexible protein-peptide docking and transferable binding affinity potential

A flexible protein-peptide docking method has been designed to consider not only ligand flexibility but also the flexibility of the protein. The method is based on a Monte Carlo annealing process. Simulations with a distance root-mean-square (dRMS) virtual energy function revealed that the flexibility of protein side chains was as important as ligand flexibility for successful protein-peptide docking. On the basis of mean field theory, a transferable potential was designed to evaluate distance-dependent protein-ligand interactions and atomic solvation energies. The potential parameters were developed using a self-consistent process based on only 10 known complex structures. The effectiveness of each intermediate potential was judged on the basis of a Z score, approximating the gap between the energy of the native complex and the average energy of a decoy set. The Z score was determined using experimentally determined native structures and decoys generated by docking with the intermediate potentials. Using 6600 generated decoys and the Z score optimization criterion proposed in this work, the developed potential yielded an acceptable correlation of R(2) = 0.77, with binding free energies determined for known MHC I complexes (Class I Major Histocompatibility protein HLA-A(*)0201) which were not present in the training set. Test docking on 25 complexes further revealed a significant correlation between energy and dRMS, important for identifying native-like conformations. The near-native structures always belonged to one of the conformational classes with lower predicted binding energy. The lowest energy docked conformations are generally associated with near-native conformations, less than 3.0 Angstrom dRMS (and in many cases less than 1.0 Angstrom) from the experimentally determined structures.     

Characterization of the Fe(III)‐binding Site in Sepia Eumelanin by Resonance Raman Confocal Microspectroscopy¶

The resonance Raman spectrum of Sepia eumelanin is discussed by analogy to model compounds containing catechol (CAT)‐like structural units. These data are then compared with the analogous data on Fe(III)‐enriched Sepia eumelanin. In contrast to the natural eumelanin, the Fe(III)‐enriched samples exhibit absorption features in the visible and near‐IR spectral regions, which are attributed to ligand‐to‐metal charge‐transfer (LMCT) bands. Resonance Raman spectra collected by exciting these LMCT bands reveal bands at 580 and 1470 cm^?1; the intensity of these features increases wioth increasing Fe(III) content. The 580 and 1470 cm^?1 bands are assigned to Fe‐OR stretching and ring deformation modes, respectively. These data further substantiate that the Fe(III)‐ melanin‐binding site in melanin is composed of CAT‐like structural units.     

Preparation of TiO2 Sol Using TiCl4 as a Precursor

A titanium dioxide sol with narrow particle size distribution was synthesized using TiCl₄ as the starting material. The sol was prepared by a process where HCl was added to a gel of hydrated titanium oxide to dissolve it. The resulting aqueous titanic acid solution was heated to form titanium dioxide sol. The effects of preparation parameters were investigated. TiCl₄ was slowly added to distilled water at 5°C. Aqueous solution of sodium hydroxide was added to adjust the pH of the system to 8–12. After aging for a period of time, the peptized sol was filtered and sufficiently washed. The filtered cake was repulped in water. Hydrochloric acid was slowly added to the solution with stirring. After condensation reaction and crystallization, a transparent sol with suspended TiO₂ was formed. XRD results show that the crystalline phase was anatase. The suspended TiO₂ particles were rhombus primary particles with the major axis ca. 20 nm and the minor axis ca. 5 nm. The TiO₂ particles prepared at pH 8 had the largest surface area of 141 cm³/g and it was microporous. The compositions of the solution which yielded the smallest suspended TiO₂ particles were TiO₂:HCl (35% HCl) = 1:1 (molar ratio), concentration of TiO₂ = 10%. Hydroxypropyl cellulose with viscosity of 150–400 cps was added as a dispersant. The sol was excellent in dispersibility and long-term stability. Transparent thin films could be obtained through dip-coating glass substrate in the sol. The dip-coating on glass can be less than three times to have one monolayer TiO₂. The transparent TiO₂ thin film had strong hydrophilicity after being illuminated by UV light.     

两亲性丙烯酸酯共聚物的聚合研究

利用过氧化苯甲酰为引发剂探讨了甲基丙烯酸β－羟乙酯和丙烯酸长链烷基酯的自由基共聚合。重点讨论了合成条件如溶剂、沉淀剂、引发剂用量、单体配比、反应时间等对共聚反应的影响以及各种聚合条件对该共聚物的组成、结构和性能的影响。并用ＩＲ，ＧＰＣ，＾１３ＣＮＭＲ等手段对共聚物进行了表征。     

Binding of wogonin to human serum albumin: a common binding site of wogonin in subdomain IIA

The binding of wogonin to human serum albumin (HSA) has been studied by spectroscopic method including circular dichroism (CD), infrared spectra (IR) and fluorescence spectra. The fluorescence properties of HSA were examined in presence of wogonin and the fluorescence intensity of HSA was significantly decreased in the presence of wogonin. The binding parameters of wogonin were studied from the fluorescence decreasing of HSA by the fluoremetric titrations. The Stern-Volmer plots indicated that the binding of wogonin to HSA at 296, 303, 310 K is characterized by one binding site with the binding constant K(S-V) at 1.872 x 10(5), 1.561 x 10(5), 1.392 x 10(5), respectively, which are good agreement with the results from the Scatchard plots. The binding process was exothermic, enthalpy driven and spontaneous, as indicated by the thermodynamic analyses, and the major part of the binding energy is hydrophobic interaction, which were consistent with the result of molecule modelling study, and there are also a numbers of hydrogen bonds between wogonin and HSA. Furthermore, the displacement experiments indicate that wogonin can bind to the subdomain IIA, that is, the site I of HSA, which is also good agreement with the result of molecule modelling study.     

Short range photoinduced electron transfer in proteins: QM-MM simulations of tryptophan and flavin fluorescence quenching in proteins

Hybrid quantum mechanical-molecular mechanics (dynamics) were performed on flavin reductase (Fre) and flavodoxin reductase (Fdr), both from Escherichia coli. Each was complexed with riboflavin (Rbf) or flavin mononucleotide (FMN). During 50 ps trajectories, the relative energies of the fluorescing state (S₁) of the isoalloxazine ring and the lowest charge transfer state (CT) were assessed to aid prediction of fluorescence lifetimes that are shortened due to quenching by electron transfer from tyrosine. The simulations for the four cases display a wide range in CT–S₁ energy gap caused by the presence of phosphate, other charged and polar residues, water, and by intermolecular separation between donor and acceptor. This suggests that the Gibbs energy change (ΔG₀) and reorganization energy (λ) for the electron transfer may differ in different flavoproteins.     

Effect of the Secondary Reduction on the Enantioselectivity and Function of Additives in the Chiral Oxazaborolidine‐Catalyzed Asymmetric Borane Reduction of Ketones

The secondary reduction in the direct and oxazaborolidine‐catalyzed asymmetric borane reduction of ketones was investigated by the use of GC/MS tracing titration and control experiments. The results indicate that the secondary reduction affects the enantioselectivity only in noncoordinated solvents at low temperature and not under the usual catalytic reduction conditions because the intermediate alkoxyborane is unstable and quickly converts to borane and dialkoxyborane. The function of an alcohol additive in the asymmetric borane reduction of ketones is to consume excess borane in the reduction system thus inhibiting noncatalytic reduction, which leads to increased enantioselectivity in the catalytic reduction.     

DNA electrochemistry through the base pairs not the sugar-phosphate backbone

Using intercalated, covalently bound daunomycin as a redox probe, ground state charge transport in DNA films with a perturbation in base pair stacking was examined in comparison with breaks in the sugar-phosphate backbone. While the introduction of one or even two nicks in the sugar-phosphate backbone yields no detectable effect on electron transfer, a CA mismatch significantly attenuates the electron transfer yield. These results confirm that the base pair stack is the pathway for DNA-mediated charge transfer, not the sugar-phosphate backbone.     

SnO2TiO2 复合半导体纳米薄膜的研究进展

本文概述了SnO₂TiO₂ 复合半导体纳米薄膜的发展历史和研究现状,对比分析了“混合”、“核壳”和“叠层”3 种复合薄膜的结构和性能特点,着重论述了叠层结构的SnO₂ /TiO₂复合薄膜的光电化学和光催化特性。结合作者的研究工作,探讨了SnO₂ /TiO₂双层复合薄膜上下层厚度对其光催化活性的影响,指出复合薄膜光催化活性的提高可归因于电子从TiO₂ 向SnO₂ 的迁移。最后对SnO₂ /TiO₂复合薄膜的局限性和发展潜势做一简要分析,强调了该复合薄膜本身的应用特点。     

A new strategy for the synthesis of α,β-diaroylpropionates promoted by samarium metal in DMF

When promoted by samarium in DMF, aroyl chlorides react readily with acrylates to afford α,β-diaroylpropionates in good to excellent yields without pretreating or activating the metallic samarium.