Comparative structural and energetic analysis of WW domain-peptide interactions

WW domains are small globular protein interaction modules found in a wide spectrum of proteins. They recognize their target proteins by binding specifically to short linear peptide motifs that are often proline-rich. To infer the determinants of the ligand binding propensities of WW domains, we analyzed 42 WW domains. We built models of the 3D structures of the WW domains and their peptide complexes by comparative modeling supplemented with experimental data from peptide library screens. The models provide new insights into the orientation and position of the peptide in structures of WW domain-peptide complexes that have not yet been determined experimentally. From a protein interaction property similarity analysis (PIPSA) of the WW domain structures, we show that electrostatic potential is a distinguishing feature of WW domains and we propose a structure-based classification of WW domains that expands the existent ligand-based classification scheme. Application of the comparative molecular field analysis (CoMFA), GRID/GOLPE and comparative binding energy (COMBINE) analysis methods permitted the derivation of quantitative structure-activity relationships (QSARs) that aid in identifying the specificity-determining residues within WW domains and their ligand-recognition motifs. Using these QSARs, a new group-specific sequence feature of WW domains that target arginine-containing peptides was identified. Finally, the QSAR models were applied to the design of a peptide to bind with greater affinity than the known binding peptide sequences of the yRSP5-1 WW domain. The prediction was verified experimentally, providing validation of the QSAR models and demonstrating the possibility of rationally improving peptide affinity for WW domains. The QSAR models may also be applied to the prediction of the specificity of WW domains with uncharacterized ligand-binding properties.     

人基质金属蛋白酶-2的表达、纯化和性质鉴定

PCR方法扩增人基质金属蛋白酶 2 (MMP 2 )不含信号肽的表达序列 ,酶切和测序鉴定正确后 ,构建酵母重组表达质粒pPIC9 MMP 2 ,电击法转化毕赤酵母 (Pichiapastoris)细胞得到阳性克隆 ,甲醇诱导获得含大量基质金属蛋白酶 2的培养上清 ,经SephacrylS 2 0 0纯化后 ,纯度达到电泳纯。明胶酶谱和SDS PAGE分析说明重组MMP 2能够降解明胶和IV型胶原 ,表明重组蛋白具有与天然MMP 2相似的底物特异性。糖基化分析和SDS PAGE表明 ,表达产物的分子量约为 5 0kD ,重组MMP 2的C 末段可能发生了降解。     

Identification,purification and partial characterization of tissue inhibitor of matrix metalloproteinase-2 in bovine pulmonary artery smooth muscle

Bovine pulmonary artery smooth muscle possesses the tissue inhibitor of matrix metalloproteinase-2 (TIMP-2) as revealed by Western immunoblot study of its cytosol fraction with bovine polyclonal TIMP-2 antibody. This potent polypeptide inhibitor of matrix metalloproteinases (MMPs) was purified to homogeneity from cytosol fraction of bovine pulmonary artery smooth muscle. This inhibitor was purified by ammonium sulfate precipitation followed by gelatin sepharose and lentil lectin sepharose affinity chromatography and continuous elution electrophoresis by Prep Cell Model 491 (Bio-Rad, USA). SDS-PAGE revealed that the inhibitor has an apparent molecular mass of 21 kDa and was confirmed as TIMP-2 by (i) Western immunoblot assay using bovine polyclonal TIMP-2 antibody; and also by (ii) amino terminal amino acid sequence analysis of the purified inhibitor is found to be identical with TIMP-2 obtained from other sources. The purified 21 kDa inhibitor was found to be active against matrix metalloproteinase-2 (MMP-2, 72 kDa gelatinase) and matrix metalloproteinase-9 (MMP-9, 92 kDa gelatinase), the ambient MMPs in the pulmonary artery smooth muscle. The inhibitor was also found to be sensitive to the activated 72 kDa gelatinase-TIMP-2 complex and also active human interstitial collagenase. By contrast, it was found to be insensitive to the serine proteases: trypsin and plasmin. The inhibitor was heat and acid resistant and it had the sensitivity to trypsin degradation and reduction-alkylation. Treatment of the inhibitor with hydrogen peroxide, superoxide generating system (hypoxanthine plus xanthine oxidase) and peroxynitrite inactivated the inhibitor.     

MMP-2结合肽-蜂毒素杂合基因的表达纯化及活性测定

为开发抗癌导向多肽药物,用从噬菌体十二肽库中筛选的与MMP-2具有高度亲和性的十二肽与蜂毒素连接,采用基因工程方法在大肠杆菌中进行了高效表达;并分别通过亲和层析、肠激酶酶切、凝胶层析获得高纯度的多肽(相对分子质量45000),经体外抑瘤作用测定该融合蛋白具有明显抑制肿瘤细胞的生长。该研究对肿瘤的导向治疗和临床应用提供了一定的帮助。     

葛根素对糖尿病大鼠肾组织MMP-2的表达及活性的影响

为探讨葛根素对糖尿病大鼠肾组织基质金属蛋白酶2(MMP-2)及活性表达的影响,采用单侧肾切除大鼠ip链脲佐菌素诱发糖尿病模型的方法,每日ip葛根素注射液,共16周。采用原位杂交法检测肾小球MMP-2、TIMP-2mRNA表达,流式细胞术和免疫组织化学检测肾皮质MMP-2、TIMP-2及Ⅳ型胶原表达;酶谱分析检测肾皮质MMP-2活性变化。结果发现糖尿病组较对照组肾小球MMP-2mRNA及蛋白表达降低而TIMP-2mRNA及蛋白表达升高,Ⅳ型胶原表达亦增加,MMP-2活性降低,肾功能恶化;葛根素用药组较糖尿病组MMP-2mRNA及蛋白表达升高而TIMP-1、Ⅳ型胶原表达减少,MMP-2活性部分恢复,肾功能改善。表明葛根素可能部分是通过调节肾小球MMP-2蛋白表达及活性的改变从而减轻肾小球细胞外基质沉积,保护糖尿病大鼠的肾功能和形态。     

Stereoselective effect of phenprocoumon enantiomers on the binding of benzodiazepines to human serum albumin.

The effect of phenprocoumon enantiomers on the stereoselective binding of 3-substituted 1,4-benzodiazepines to human serum albumin (HSA) was studied by chromatography on HSA-Sepharose column. (S)-Phenprocoumon exerts stereoselective allosteric interaction on the binding of benzodiazepines. The structural requirements of enhanced stereoselectivities are similar to those found previously with (S)-warfarin.     

MMP-2 inhibition reduces renal macrophage infiltration with increased fibrosis in UUO

We examined the role of matrix metalloproteinase-2 (MMP-2) in renal fibrosis and its effect on interstitial macrophage infiltration in a mouse model of unilateral ureteral obstruction (UUO). TISAM, a selective inhibitor of MMP-2, was administered during early stage (day -2 to 4; protocol A) and late stage (day 7 to 13; protocol B) after UUO. Treatment with TISAM accelerated fibrosis both at day 5 (A) and at day 14 (B). The degree of macrophage infiltration was decreased by the treatment with TISAM at day 14, but not at day 5. In vitro macrophage migration assay showed a greater migration to renal tissue of control UUO kidney (day 14) than to TISAM-treated kidney, which was suppressed by preincubating macrophages with RGDS, a fibronectin degradation peptide. These results suggest that MMP-2 acts to accelerate macrophage infiltration in the late stage of UUO, possibly by degrading extracellular matrix components.     

Control of insulin receptor affinity by a Ca2+-sensitive binding site

Calcium (Ca²⁺) increased insulin-receptor binding in both membrane and solubilised receptor preparations. Ca²⁺ increased both receptor affinity and initial rate of association of [¹²⁵I]insulin to the receptor preparations. Ca²⁺ had no effect on insulin receptor number in either receptor preparation. The effect of Ca²⁺ on affinity could be mimicked by ions with similar ionic radii and properties (e.g., Ba²⁺, Mg²⁺ and Sr²⁺). EDTA and oleic acid reduced insulin binding and receptor affinity and these effects were reversed by the addition of Ca²⁺. These studies suggest that Ca²⁺ and Ca²⁺-like ions may bind to a site on or near the receptor and may be responsible for a conformational change with a consequent increase in receptor affinity.     

The discovery of reverse tricyclic pyridone JAK2 inhibitors. Part 2: Lead optimization

This communication discusses the discovery of novel reverse tricyclic pyridones as inhibitors of Janus kinase 2 (JAK2). By using a kinase cross screening approach coupled with molecular modeling, a unique inhibitor–water interaction was discovered to impart excellent broad kinase selectivity. Improvements in intrinsic potency were achieved by utilizing a rapid library approach, while targeted structural changes to lower lipophilicity led to improved rat pharmacokinetics. This multi-pronged approach led to the identification of 31, which demonstrated encouraging rat pharmacokinetics, in vivo potency, and excellent off-target kinase selectivity.