1H, 15N, 13C resonance assignments of the reduced and active form of human Protein Tyrosine Phosphatase, PRL-1

Phosphatase of regenerating liver-1 (PRL-1) is a novel target for potentially treating cancer metastases. Although its specific biochemical role in these processes has yet to be delineated, considerable evidence suggests the phosphatase activity of PRL-1 is required for promoting cancer and metastasis. PRL-1 belongs to the protein tyrosine phosphatase (PTPase) family and functions using the CX₅R consensus active site motif. Like other PTPases, PRL-1 is inhibited by oxidation at its active site Cys, however, disulfide bond formation occurs unusually readily in wild-type PRL-1. Chemical shift assignments are available for oxidized wild type, but numerous, substantial changes are observed in the spectra upon reduction. Because the reduced form is active, we sought to identify a stable mutant that would resist oxidation and be useful for facilitating drug screening and development using NMR-based assays. We present here NMR assignments for a full-length, reduced and active form of PRL-1, PRL-1-C170S-C171S, that is well suited for this purpose.     

High‐throughput protein refolding screening method using zeolite

We established a 96‐well‐plate‐based refolding screening system using zeolite. In this system, protein denatured and solubilized with 6 M guanidine hydrochloride is adsorbed onto zeolite placed in a 96‐well plate. The refolding conditions can be tested by incubating the samples with refolding buffers under various conditions of pH, salts, and additives. In this study, we chose green fluorescent protein as the model protein. Green fluorescent protein was expressed as inclusion bodies, and we tested the effects of four pH conditions and six additives on its refolding. The results demonstrate that green fluorescent protein was more efficiently refolded with zeolite than with the conventional dilution method. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009     

基于流式细胞术分选的高效表达外源基因细胞的筛选

目的：以增强型绿色荧光蛋白（EGFP）作为报告基因,用流式细胞术筛选高表达EGFP的细胞,从而获得外源基因高效表达细胞株。方法：构建在EGFPC端编码区融合新霉素（neomycin）抗性基因的融合基因EGFP-Neomycin,将其插入pcDNA3.1（＋）载体,构建EGFP-Neomycin融合基因表达载体pcDNAEN,转染CHO-K1细胞,G418加压筛选和倒置荧光显微镜观察证实所表达的EGFP-Neomycin融合蛋白具有新霉素抗性和激发EGFP荧光双功能;将编码组织型纤溶酶原激活剂（tPA）的cDNA插入pcDNAEN中CMV启动子下游,构建表达tPA的表达载体pcDNAEN/tPA。结果：流式细胞术分析和tPA纤维蛋白溶解活性测定表明,pcDNAEN/tPA转染CHO-K1细胞的EGFP相对荧光强度（RFT）的自然对数值与tPA表达水平呈明显的直线相关关系,相关系数为0.983;比较部分未经流式细胞仪分选的pcDNAEN/tPA转染阳性细胞克隆和RFT分布在100～1000的pcDNAEN/tPA转染阳性细胞克隆的tPA表达水平,经流式细胞术分选获得的细胞克隆的tPA平均表达水平和最高表达水平分别是未经分选获得的细胞克隆的3.9倍和4.1倍。结论：构建的EGFP-Neomycin融合基因具有双功能,建立了利用流式细胞术筛选外源基因高效表达物细胞株的方法。     

Docking, virtual high throughput screening and in silico fragment-based drug design

The drug discovery process has been profoundly changed recently by the adoption of computational methods helping the design of new drug candidates more rapidly and at lower costs. In silico drug design consists of a collection of tools helping to make rational decisions at the different steps of the drug discovery process, such as the identification of a biomolecular target of therapeutical interest, the selection or the design of new lead compounds and their modification to obtain better affinities, as well as pharmacokinetic and pharmacodynamic properties. Among the different tools available, a particular emphasis is placed in this review on molecular docking, virtual high-throughput screening and fragment-based ligand design.     

黑曲霉生产菊粉酶工艺条件的研究

从徐州市沛县河口镇秦庄村牛蒡种植基地取得的土壤样本中,筛选出产菊粉酶的菌株,对从土壤中分离到的40株产菊粉酶的各类微生物进行酶活的测定。通过透明圈法初筛及摇瓶复筛,获得产菊粉酶能力较高的霉菌菌株3株,为C122803、D081506和D081513,这3株菌株的酶活分别达到：C122803：1.411 U/ml;D081506 ：1.895U/ml;D081513 ：1.792U/ml。其中D081506的酶活最高,为1.895U/ml;对D081506号黑曲霉产菊粉酶的发酵条件进行了研究,确定了优化的发酵条件为：牛蒡汁2%,酵母膏1.6%,(NH4)2SO41.6%,NaCl 0.5%,K2HPO4 0.5%,pH 5.0,在27℃、140 r/min条件下,摇瓶培养24h, D081506酶活力为2.958U/ml,酶活力提高56.09%。     

Developing a pre-entry weed risk assessment system for use in Japan

We evaluated the applicability of the Australian Weed Risk Assessment (AWRA) system in Japan. Native weeds (n = 117) and introduced plants (n = 142), whose weed status was classified by 20 plant experts, were assessed using a slightly modified version of the AWRA system designed to fit Japanese conditions. A receiver operating characteristic (ROC) curve for the system, when classifying two-thirds of the 259 taxa as weeds or non-weeds, was plotted and the area under the ROC curve was calculated. The area was 0.88 and significantly greater than 0.5. Thus, the validity of the system to classify plants was proven. The best cut-off level for the WRA score using Youden’s index was 10. When taxa whose AWRA scores were greater than 10 were regarded as weeds, the sensitivity and specificity were 0.88 and 0.78, respectively. These values were verified with the remaining one-third of the taxa. From these findings, the modified AWRA system was considered to be effective for use in Japan. However, further studies are required to set the best cut-off level in terms of maximising the benefits gained from using the system. A second screening test associated with the cut-off level also needs to be developed.     

Binding interaction of quercetin-3-beta-galactoside and its synthetic derivatives with SARS-CoV 3CL(pro): structure-activity relationship studies reveal salient pharmacophore features

The 3C-like protease (3CL^pro) of severe acute respiratory syndrome-associated coronavirus (SARS-CoV) is one of the most promising targets for discovery of drugs against SARS, because of its critical role in the viral life cycle. In this study, a natural compound called quercetin-3-β-galactoside was identified as an inhibitor of the protease by molecular docking, SPR/FRET-based bioassays, and mutagenesis studies. Both molecular modeling and Q189A mutation revealed that Gln189 plays a key role in the binding. Furthermore, experimental evidence showed that the secondary structure and enzymatic activity of SARS-CoV 3CL^pro were not affected by the Q189A mutation. With the help of molecular modeling, eight new derivatives of the natural product were designed and synthesized. Bioassay results reveal salient features of the structure–activity relationship of the new compounds: (1) removal of the 7-hydroxy group of the quercetin moiety decreases the bioactivity of the derivatives; (2) acetoxylation of the sugar moiety abolishes inhibitor action; (3) introduction of a large sugar substituent on 7-hydroxy of quercetin can be tolerated; (4) replacement of the galactose moiety with other sugars does not affect inhibitor potency. This study not only reveals a new class of compounds as potential drug leads against the SARS virus, but also provides a solid understanding of the mechanism of inhibition against the target enzyme.     

乳酸乳球菌Nisin抗性基因nisI的克隆及作为筛选标记的研究

摘要：【目的】为了优化LJ1菌株的培养条件使之产生高活性的胞外褐藻胶裂解酶。【方法】通过富集培养技术从海带筛选到一株褐藻胶裂解酶产生菌LJ1, 依据表型特征、脂肪酸组成分析及16S rRNA基因序列分析对该菌株进行鉴定。通过单因子和正交试验对LJ1 菌株产胞外褐藻胶裂解酶的培养条件进行了优化。【结果】LJ1菌株属于假交替单胞菌属（Pseudoalteromonas）。该菌株产酶的最佳培养基组成为：褐藻胶3 g/L、(NH4)2SO4 3 g/L、NaCl 20 g/L、KH2PO4 0.1 g/L、CaCl2 0.1 g/L;最佳培养条件为：250 mL三角烧瓶中装液量25 mL、接种量3%、摇瓶转速150 r/min、pH7.5、培养温度为28℃、培养时间为24 h。LJ1菌株所产褐藻胶裂解酶的最适温度为40℃,最适pH7.6,最适NaCl浓度为0.3 mol/L。1 mol/L金属离子Mg2+对酶活力有明显的促进作用,而Co2+ 和Zn2+对酶活力有较强的抑制作用。【结论】LJ1菌株是Pseudoalteromonas 新的胞外褐藻胶裂解酶产生菌,在最佳培养条件下,该菌株的酶活力提高了66%。     

Absolute binding free energy calculations: On the accuracy of computational scoring of protein–ligand interactions

Calculating the absolute binding free energies is a challenging task. Reliable estimates of binding free energies should provide a guide for rational drug design. It should also provide us with deeper understanding of the correlation between protein structure and its function. Further applications may include identifying novel molecular scaffolds and optimizing lead compounds in computer‐aided drug design. Available options to evaluate the absolute binding free energies range from the rigorous but expensive free energy perturbation to the microscopic linear response approximation (LRA/β version) and related approaches including the linear interaction energy (LIE) to the more approximated and considerably faster scaled protein dipoles Langevin dipoles (PDLD/S‐LRA version) as well as the less rigorous molecular mechanics Poisson–Boltzmann/surface area (MM/PBSA) and generalized born/surface area (MM/GBSA) to the less accurate scoring functions. There is a need for an assessment of the performance of different approaches in terms of computer time and reliability. We present a comparative study of the LRA/β, the LIE, the PDLD/S‐LRA/β, and the more widely used MM/PBSA and assess their abilities to estimate the absolute binding energies. The LRA and LIE methods perform reasonably well but require specialized parameterization for the nonelectrostatic term. The PDLD/S‐LRA/β performs effectively without the need of reparameterization. Our assessment of the MM/PBSA is less optimistic. This approach appears to provide erroneous estimates of the absolute binding energies because of its incorrect entropies and the problematic treatment of electrostatic energies. Overall, the PDLD/S‐LRA/β appears to offer an appealing option for the final stages of massive screening approaches. Proteins 2010. © 2010 Wiley‐Liss, Inc.