Ligand-protein docking using a quantum stochastic tunneling optimization method

A novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand-protein complexes using the PLP score to represent the ligand-protein potential energy surface and ScreenScore to score the ligand-protein binding energies. When taking the top energy-ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened.     

高效液相色谱蛋白质手性固定相

本文综述了近年文献中已报道的各种高效液相色谱蛋白质（酶）手性固定相及其在手性拆分中的应用，并阐述了蛋白质作为手性选择剂拆分机理的研究进展。     

高效毛细管电泳前沿分析法研究酸性药物那格列奈与人血浆白蛋白的结合

用高效毛细管电泳前沿分析法研究了酸性药物那格列奈与人血浆白蛋白的结合常数、结合位点和结合率。使用未涂层的毛细管柱 (4 0cm× 5 0 μmi.d .;有效柱长 32cm) ,磷酸盐缓冲溶液 (pH 7.4 ,离子强度0 .17)为背景溶液 ,在紫外检测波长 2 14nm、运行电压 18kV和重力进样 10 0s的条件下 ,利用那格列奈谱峰的平台高度和游离药物浓度的良好线性关系 (r>0 .999,n =6 ) ,测定了那格列奈的游离药物浓度。固定药物浓度 (2 0 0 μmol L ,2 5 0 μmol L) ,考察不同的蛋白质浓度对结合的影响 ;固定蛋白质浓度 (10 0 μmol L) ,考察不同的药物浓度对结合的影响。实验数据采用非线性拟和程序进行处理 ,得到了那格列奈的蛋白质结合参数。高效毛细管电泳前沿分析法测定的数据重现性良好 (RSD <2 .5 % ,n =3) ,在药代动力学和药效学研究方面具有简便、准确的优点。     

高效前沿分析的发展及在药物-蛋白结合研究中的应用

介绍了高效前沿分析方法的原理、特点、种类，综述了它在药物与蛋白结合研究中的应用及国内外研究概况；通过与高效液相色谱／前沿分析比较，阐明了毛细管电泳／前沿分析在药物蛋白结合研究中的优势；分析了在药物与蛋白结合研究中所采用的各种研究方法，通过与这些研究方法的比较，阐明了高效前沿分析的优越性及其广阔的应用前景，同时提出了在高效前沿分析方法中有待完善和注意的问题。     

水/有机两相体系中催化氧化反应的研究进展

论述了水／有机两相体系中催化氧化反应的一些最新进展。由于采用水溶性催化剂，使得水／有机两相体系中的催化反应具有催化剂与产物容易分离的优点。阐述了水溶性催化剂在催化氧化反应中的应用，列举了一些典型的水溶性配体、水溶性催化剂以及催化氧化反应实例。参考文献21篇。     

富硒灵芝中一种新含硒蛋白的纯化、性质及其自由基清除活性研究

通过硫酸铵沉淀、离子交换层析和分子排阻层析等方法, 从富硒灵芝中获得了一种新的含硒蛋白, 命名为Se-GL-P, 并研究了此蛋白的性质、抗氧化活性与其硒含量间的关系. 结果表明, 此蛋白的分子量为36600, 分子中约含有19.8%的糖链, N端的氨基酸残基序列为DINGGGATLPQKLYLTPDVL, 属于DING蛋白家族. 硒含量为4.87 mg/g, 具有较高的羟自由基和超氧自由基清除活性. 研究发现, Se-GL-P的抗氧化活性的提高与其中硒含量的提高相关.     

Optimization of on-chip elongation for fabricating double-stranded DNA microarrays

The sequence-specific recognitions between DNA and proteins are playing important roles in many biological functions. The double-stranded DNA microarrays (dsDNA microarrays) can be used to study the sequence-specific recognitions between DNAs and proteins in highly parallel way. In this paper, two different elongation processes in forming dsDNA from the immobilized oligonucleotides have been compared in order to optimize the fabrication of dsDNA microarrays: (1) elongation from the hairpins formed by the self-hybridized oligonucleatides spotted on a glass; (2) elongation from the complementary primers hybridized on the spotted oligonucleatides. The results suggested that the dsDNA probes density produced by the hybridized-primer extension was about four times lower than those by the self-hybridized hairpins. Meanwhile, in order to reduce the cost of dsDNA microarrays, we have replaced the Klenow DNA polymerase with Taq DNA polymerase, and optimized the reaction conditions of on-chip elongation. Our experiements showed that the elongation temperature of 50 °C and the Mg²⁺ concentration of 2.5 mM are the optimized conditions in elongation with Taq DNA polymerase. A dsDNA microarray has been successfully constructed with the above method to detect NF-kB protein.     

NMR spectroscopy techniques for screening and identifying ligand binding to protein receptors

Binding events of ligands to receptors are the key for an understanding of biological processes. Gaining insight into protein-protein and protein-ligand interactions in solution has recently become possible on an atomic level by new NMR spectroscopic techniques. These experiments identify binding events either by looking at the resonance signals of the ligand or the protein. Ideally, both techniques together deliver a complete picture of ligand binding to a receptor. The approaches discussed in this review allow screening of compound libraries as well as a detailed identification of the groups involved in the binding events. Also, characterization of the binding strength and kinetics is possible, competitive binding as well as allosteric effects can be identified, and it has even been possible to identify ligand binding to intact viruses and membrane-bound proteins.     

Genomic variation and point mutations analysis of Indian COVID-19 patient samples submitted in GISAID database

Corona virus disease 2019 (COVID-19) endemic has havoc on the world; the causative virus of the pandemic is SARS CoV-2. Pharmaceutical companies and academic institutes are in continuous efforts to identify anti-viral therapy or vaccines, but the most significant challenge faced is the highly evolving genome of SARS CoV-2, which is imparting evolutionary selective benefits to the virus. To understand the viral mutations, we have retrieved nine hundred and thirty-four samples from different states of India via the GISAID database and analyzed the frequency of all types of point mutation in all structural, non-structural proteins, and accessory factors of SARS CoV-2. Spike glycol protein, nsp3, nsp6, nsp12, N and NS3 were the most evolving proteins. High frequency point mutations were Q496P (nsp2), A380V (nsp4), A994D (nsp3), L37F (nsp6), P323L & A97V (nsp12), Q57H (ns3), D614G (S), P13L (N), R203K (N), G204R (N) and S194L (N).     

SPECIFIC PROTEIN OCCURRENCE RELATED WITH PHOTOPERIODIC FLOWER INDUCTION IN THE COTYLEDONS OF Pharbitis nil CV. VIOLET

In our experiment, three groups of seedlings of SDP Pharbitis nil cv. violet were sepa-rately treated with three different photoperiods (1,16 h dark period--SD; 2, continuous illumi-nation--CL; 3, 16 h dark treatment with 10 min white light in the middle of the dark period--NB). By analysing proteins in the cotyledons from three groups with 2-D PAGE, we found nodifference in protein pattern between the three groups at 0 or 8 h after photoperiodic treatments.At 24 h after the treatments, a specific protein(MW:19 kD; pI: 4.5)appeared only in the cotyledonsof the seedlings which endured SD. This protein disappeared at 72 h after SD. ActinomycinD could inhibit flowering and the specific protein occurrence when applied to cotyledonsprior to SD, but it had no inhibition effect on flowering as well as the specific proteinoccurrence when applied to cotyledons after SD. Chloroamphenicol, a protein synthesisinhibitor, inhibited flowering when applied to cotyledons prior to or immediately after SD,but it did not i