白杨素-6-磺酸钠及其Zn(Ⅱ)、Ca(Ⅱ)配位化合物与NDA作用的研究

采用紫外、荧光、粘度法研究了白杨素-6-磺酸钠、白杨素-6磺酸双核锌及白杨素-6-磺酸四核钙与小牛胸腺DNA的结合常数分别是KNa=1.52×104L.mol-1、KZn=3.56×104L.mol-1和KCa=1.54×104L.mol-1。实验结果表明,白杨素-6-磺酸双核锌和白杨素-6-磺酸四核钙;白杨素-6-磺酸钠与DNA间的作用方主要为静电结合。     

A structural and energetics analysis of the binding of a series of N-acetylneuraminic-acid-based inhibitors to influenza virus sialidase

Summary A molecular dynamics/energy-minimisation protocol has been used to analyse the structural and energetic effects of functional group substitution on the binding of a series of C4-modified 2-deoxy-2,3-didehydro-N-acetylneuraminic acid inhibitors to influenza virus sialidase. Based on the crystal structure of sialidase, a conformational searching protocol, incorporating multiple randomisation steps in a molecular dynamics simulation was used to generate a range of minimum-energy structures. The calculations were useful for predicting the number, location, and orientation of structural water molecules within protein-ligand complexes. Relative binding energies were calculated for the series of complexes using several empirical molecular modelling approaches. Energies were computed using molecular-mechanics-derived interactions as the sum of pairwise atomic nonbonded energies, and in a more rigorous manner including solvation effects as the change in total electrostatic energy of complexation, using a continuum-electrostatics (CE) approach. The CE approach exhibited the superior correlation with observed affinities. Both methods showed definite trends in observed and calculated binding affinities; in both cases inhibitors with a positively charged C4 substituent formed the tightest binding to the enzyme, as observed experimentally.This paper is based on a presentation given at the 14th Molecular Graphics and Modelling Society Conference, held in Cairns, Australia, August 27–September 1, 1995.Presently on a visiting postdoctoral fellowship in the Department of Biomolecular Structure, Glaxo Research & Development Ltd, Greenford, Middlesex UB6 OHE, U.K.     

Sequence‐based prediction of protein–peptide binding sites using support vector machine

Protein–peptide interactions are essential for all cellular processes including DNA repair, replication, gene‐expression, and metabolism. As most protein – peptide interactions are uncharacterized, it is cost effective to investigate them computationally as the first step. All existing approaches for predicting protein – peptide binding sites, however, are based on protein structures despite the fact that the structures for most proteins are not yet solved. This article proposes the first machine‐learning method called SPRINT to make Sequence‐based prediction of Protein – peptide Residue‐level Interactions. SPRINT yields a robust and consistent performance for 10‐fold cross validations and independent test. The most important feature is evolution‐generated sequence profiles. For the test set (1056 binding and non‐binding residues), it yields a Matthews’ Correlation Coefficient of 0.326 with a sensitivity of 64% and a specificity of 68%. This sequence‐based technique shows comparable or more accurate than structure‐based methods for peptide‐binding site prediction. SPRINT is available as an online server at: http://sparks-lab.org/ . © 2016 Wiley Periodicals, Inc.     

官能团修饰对MOF-5的气体分子吸附影响

采用紧束缚近似计算方法,研究了金属有机骨架(MOF-5)和不同官能团(―NO2,―NH2,―CH3,―OZn)修饰后的MOF-5不同吸附位点的CO2等温室气体和部分工业废气吸附性能以及对不同气体的选择性吸附能力.结果表明,对于未修饰的MOF-5,位点I和II是主要的吸附位点,最大吸附能可达-0.25eV.官能团修饰提高了MOF-5对CO2的吸附能力,其与官能团活性和局部位型密切相关.其中―NO2修饰使各位点的CO2吸附能力都有一定提高.同时,―NO2修饰后MOF-5对空气环境(O2,N2,H2O,CO2),工业废气环境(CO2,CO,NO,NO2,SO2,SO3)中不同气体有明显的选择性吸附能力.     

Evaluation of docking/scoring approaches: A comparative study based on MMP3 inhibitors

An increasing number of docking/scoring programs are available that use different sampling and scoring algorithms. A reliable scoring function is the crucial element of such approaches. Comparative studies are needed to evaluate their current capabilities. DOCK4 with force field and PMF scoring as well as FlexX were used to evaluate the predictive power of these docking/scoring approaches to identify the correct binding mode of 61 MMP-3 inhibitors in a crystal structure of stromelysin and also to rank them according to their different binding affinities. It was found that DOCK4/PMF scoring performs significantly better than FlexX and DOCK4/FF in both ranking ligands and predicting their binding modes. Most notably, DOCK4/PMF was the only scoring/docking approach that found a significant correlation between binding affinity and predicted score of the docked inhibitors. However, comparing only those cases where the correct binding mode was identified (scoring highest among sampled poses), FlexX showed the best `fine tuning' (lowest rmsd) in predicted binding modes. The results suggest that not so much the sampling procedure but rather the scoring function is the crucial element of a docking program.     

Can Helical Peptides Unwind One Turn at a Time? ‐ Controlled Conformational Transitions in α,β2,3‐Hybrid Peptides

Unfolding of helical trans‐β^2,3‐hybrid peptides with (α–β)_nα composition, when executed by increasing solvent polarity or temperature, proceeded in a systematic manner with the turns unwinding sequentially; C‐terminal region of these peptides were first to unwind and the process propagated towards N terminus with more and more β residues equilibrating from the gauche to the anti rotameric state across C_α?C_β. This is evidenced by clear change in their C_βH signal splitting, ³J_CαH–CβH values, and sequential disappearance of i,i+2 NOEs.     

Cu2+ Effects on Beta-Amyloid Oligomerisation Monitored by the Fluorescence of Intrinsic Tyrosine

A non-invasive intrinsic fluorescence sensing of the early stages of Alzheimer's beta amyloid peptide aggregation in the presence of copper ions is reported. By using time-resolved fluorescence techniques the formation of beta amyloid-copper complexes and the accelerated peptide aggregation are demonstrated. The shifts in the emission spectral peaks indicate that the peptides exhibit different aggregation pathways than in the absence of copper.     

Effects of ultrasonic–microwave combination treatment on the physicochemical,structure and gel properties of myofibrillar protein in Penaeus vannamei (Litopenaeus vannamei) surimi

The objective of this study was to evaluate the effects of single ultrasound (360 W, 20 min), single microwave (10 W/g, 120 s) and ultrasonic–microwave combination treatment on shrimp surimi gel properties. The structure and physicochemical properties of myofibrillar protein (MP) were also determined. Low-field nuclear magnetic resonance showed that the fluidity of water molecules and the moisture content decreased, the stability and water holding capacity (WHC) increased after single ultrasound, single microwave and ultrasonic–microwave combination treatment. Compared with the traditional water bath treatment, ultrasound and microwave treatment reduced the total sulfhydryl content and promoted the formation of intermolecular disulfide bonds and hydrophobic interactions, which improved the compactness of the network structure of shrimp surimi gel. Moreover, Fourier transform infrared spectroscopy and sodium dodecyl sulfate–polyacrylamide gel electrophoresis analysis revealed that these treatments not only inhibited the degradation of MP, but also decreased the α-helix content and increased the β-sheet content. The three treatments also significantly reduced the particle size and decreased the solubility of MP. Overall, the effect of ultrasonic–microwave combination treatment was superior to that of either single treatment.     

高蛋白食物—螺旋藻

螺旋藻为原核生物。其所含蛋白质的质量和数量均为植物世界之冠;尚含各种维生素和生长因子;细胞壁易被人体消化;风味可口;无毒性。