孕烷X受体配体结合结构域蛋白晶体的X线衍射结构解析

目的:利用X线衍射技术解析孕烷X受体(PXR)配体结合结构域(LBD)蛋白晶体的3维结构。方法:对PXR蛋白LBD(130~434氨基酸残基)序列进行密码子优化并化学合成后克隆至pRSFDuet-1表达载体,再将载体导入大肠杆菌BL21(DE3),对PXR-LBD蛋白进行原核表达与分离纯化;采用晶体筛选试剂盒筛选蛋白结晶条件,采用悬滴法获得目标蛋白的晶体;对获得的蛋白晶体进行X线晶体衍射检测,并收集相关数据建立PXR-LBD的三维结构。结果:获得了PXR-LBD的高质量晶体并利用X线衍射解析了该蛋白质晶体的结构数据,使用Phenix.refine软件和COOT软件等对结构进行修正,最终获得了高分辨率的3维结构数据。结论:完成了孕烷X受体配体结合结构域蛋白晶体的X线衍射结构解析,为研究和开发PXR相关药物奠定了基础。     

尿激酶催化结构域S356A突变体在毕氏酵母中的表达、纯化及结晶

采用定位突变和重叠延伸PCR方法扩增尿激酶催化结构域基因片段,将其克隆至表达栽体pPICZαA上,转化毕氏酵母X-33.重组蛋白通过阳离子琼脂糖柱纯化、凝胶层析柱检测,纯度达到99%以上,该重组的尿激酶催化结构域(C279A/N302Q/S356A)不具有丝氨酸蛋白酶活性.用气相扩散法获得蛋白晶体,其衍射分辨率迭1.77(A),结构解析发现在其复合物结构中有三个抑制剂分子苯甲醚.     

X射线衍射晶体法解析脱卤酶DehDIV-R结构的研究

R-2-卤代酸脱卤酶能立体选择性水解R-2-卤代酸。解析酶的单晶结构对提高酶的选择性和活性提供了直接的结构指导,是目前酶结构领域研究的前沿。以实验室前期得到的来自假单胞菌ZJU26的R-2-氯丙酸脱卤酶(Deh DIV-R)为研究对象,采用X射线衍射晶体法进行结构解析。采用pp SUMO载体融合表达Deh DIV-R蛋白,依次通过Ni-NTA亲和层析、透析酶切、二次NiNTA亲和层析以及凝胶过滤层析纯化得到单一条带,且均一性好的蛋白。接着对结晶条件进行初筛与优化,得到的最佳结晶条件为0.1mol/L HEPES p H 7,12%PEG 6 000,0.2mol/L Mg Cl2,8mmol/L CHAPS。晶体在上海同步辐射光源BL18U1线站上收集衍射数据,采用分子置换法成功解析获得了分辨率为2.35的Deh DIV-R的晶体结构。Ramachandran图表明98.02%的氨基酸位于最适区,证明了该结构的合理性。Deh DIV-R的纯化、结晶以及结构解析为进一步深入了解其结构和功能奠定了基础。     

利用6-磷酸-β-葡萄糖苷酶在低温条件下获得酶-底物复合物实际结构的方法

利用“酶晶体低温抑活底物固定”方法,在?20 ℃条件下,将6-磷酸-β-葡萄糖苷酶 (BglA) 晶体与底物对硝基苯-β-D-吡喃葡萄糖苷-6-磷酸 (pNPβG6P) 进行浸泡试验,通过X射线进行衍射数据收集并处理,获得了完整的底物电子密度图。研究结果表明,在不突变酶中关键基团使酶失活,以及不选用底物类似物替代原有底物的情况下,通过上述方法,可以获得酶与底物复合物的实际结构。该研究结果可为今后低温酶学及复合物中间态的进一步研究提供帮助。     

绿豆胰蛋白酶抑制剂—猪胰蛋白酶复合物的四方晶体结构

本文报道了绿豆胰蛋白酶抑制剂－猪胰蛋白酶复合物的四方晶体的结构２测定。晶体属于１４２２空间群,衍射分辨率为０．２５ｎｍ,共确定了绿豆抑制剂５６个残基的空间位置。与已报道的三方结构相比,其中的抑制剂分子的结构基本相同,并且抑制剂－酶三元复合物在四方晶体中也处于堆积无序状态,即复合物按两种取向进行堆积;Ｔａ;ＭａＭｂ;Ｔｂ和Ｔｂ：ＭｂＭａ：ａ。     

棉铃虫细胞色素P450 337B3(CYP337B3)的表达、纯化及结晶

【目的】以抗性棉铃虫Helicoverpa armigera体内发现的一种基因重组导致的嵌合型P450酶CYP337B3作为研究对象,通过基因克隆、体外重组表达、蛋白质结晶等技术手段,获得CYP337B3(△23)的晶体结构,为深入了解棉铃虫P450酶CYP337B3的结构与功能奠定基础。【方法】对CYP337B3编码基因进行了密码子优化,通过基因重组,将其转化至BL21(DE3)感受态细胞中进行原核表达尝试,通过亲和层析及RESOURCETM Q离子交换层析对CYP337B3(△23)进行体外纯化,利用气相悬滴结晶方法对CYP337B3(△23)进行结晶条件的筛选及X射线晶体衍射。【结果】通过密码子优化,实现了CYP337B3(△23)在大肠杆菌原核表达系统内的大量表达,经过体外纯化及十二烷基硫酸钠-聚丙烯酰胺凝胶电泳检测,CYP337B3(△23)蛋白纯度可达到95%左右,我们对CYP337B3(△23)进行了蛋白结晶条件的筛选,最终获得了CYP337B3(△23)的结晶条件和蛋白晶体。【结论】本文利用气相悬滴结晶方法获得了CYP337B3(△23)的蛋白晶体,为今后CYP337B3的三维结构解析、功能研究以及最终阐述该种新型的棉铃虫抗药机制奠定了良好的基础。     

辣椒疫霉PcCRN20-C蛋白的表达纯化及结晶 *

CRN(crinkling and necrosis-inducing protein)为疫霉菌在与寄主互作过程中分泌的一类特有胞质效应因子,干扰寄主细胞正常的生理代谢和功能。采用PCR法从辣椒疫霉LT1534菌株cDNA中克隆PcCRN20-C基因。该基因序列长783bp,编码261个氨基酸。构建重组表达载体,并转化大肠杆菌BL21(DE3)。在优化条件下诱导表达重组蛋白,利用Ni-NTA金属螯合层析、离子交换层析、分子筛层析和胰蛋白酶酶解技术获得高纯目的蛋白,SDS-PAGE分析表明,蛋白质分子量约为25kDa。采用座滴气相扩散法进行晶体制备和筛选,成功获得了蛋白质晶体,并通过X-射线衍射仪收集了晶体衍射花样。结合蛋白质晶体学方法,获得了有衍射的辣椒疫霉PcCRN20-C蛋白晶体,为进一步研究CRN蛋白的结构与病原菌致病机制提供参考资料。     

辣椒疫霉PcCRN20-C蛋白的表达纯化及结晶

CRN(crinkling and necrosis-inducing protein)为疫霉菌在与寄主互作过程中分泌的一类特有胞质效应因子,干扰寄主细胞正常的生理代谢和功能。采用PCR法从辣椒疫霉LT1534菌株c DNA中克隆PcCRN20-C基因。该基因序列长783bp,编码261个氨基酸。构建重组表达载体,并转化大肠杆菌BL21(DE3)。在优化条件下诱导表达重组蛋白,利用Ni-NTA金属螯合层析、离子交换层析、分子筛层析和胰蛋白酶酶解技术获得高纯目的蛋白,SDS-PAGE分析表明,蛋白质分子量约为25kDa。采用座滴气相扩散法进行晶体制备和筛选,成功获得了蛋白质晶体,并通过X-射线衍射仪收集了晶体衍射花样。结合蛋白质晶体学方法,获得了有衍射的辣椒疫霉PcCRN20-C蛋白晶体,为进一步研究CRN蛋白的结构与病原菌致病机制提供参考资料。     

FS36作为新型人源Hsp90抑制剂的发现（英文）

热休克蛋白90(Hsp90)通过对几百种蛋白质底物(客户蛋白质)进行合理的折叠、成熟其构象并且激活,在肿瘤细胞的生长和繁殖中发挥重要作用.因此,Hsp90成为非常有吸引力、有前途的抗肿瘤药物靶点,并且超过20种抑制剂已经进入临床实验阶段.我们在这里设计并合成了一个小分子抑制剂:FS36.收集了Hsp90~N-FS36复合物晶体结构的X射线衍射实验数据.高分辨率X射线晶体结构表明,FS36在ATP结合位点上与Hsp90~N相互作用,并且FS36可能替代核苷酸与Hsp90~N结合.FS36和Hsp90~N的复合物晶体结构和相互作用为后期设计和优化新型抗肿瘤药物奠定基础.     

绿豆胰蛋白酶抑制剂┐猪胰蛋白酶复合物的四方晶体结构

本文报道了绿豆胰蛋白酶抑制剂－猪胰蛋白酶（１∶２）复合物的四方晶体的结构测定。晶体属于Ｉ４２２空间群,衍射分辨率为０．２５ｎｍ,共确定了绿豆抑制剂５６个残基的空间位置。与已报道的三方晶体结构相比,其中的抑制剂分子的结构基本相同,并且抑制剂－酶三元复合物在四方晶体中也处于堆积无序状态,即复合物按两种取向进行堆积：Ｔａ∶ＭａＭｂ∶Ｔｂ和Ｔｂ∶ＭｂＭａ∶Ｔａ（Ｔａ,Ｔｂ为胰蛋白酶,Ｍａ为抑制剂结合环Ⅰ,Ｍｂ为抑制剂结合环Ⅱ）。但四方晶体结构比三方晶体结构多测定了一个抑制剂残基Ｐｒｏ１１的位置,同时,四方晶体中的抑制剂不存在膺β－折叠片层结构,其构象与三方晶体中的抑制剂相比有所变化。分析表明抑制剂的两个刚性的结构域之间的连接肽具有一定的柔性,并因此形成不同的晶型。此外,绿豆抑制剂与其他Ｂｏｗｍａｎ－Ｂｉｒｋ抑制剂相比,分子的两个双股的反平行β－折叠片层和抑制活性位点所在的结合环的结构具有很高的保守性     

Structure of beta-ketoacyl-[acyl carrier protein] reductase from Escherichia coli: negative cooperativity and its structural basis.

The structure of beta-ketoacyl-[acyl carrier protein] reductase (FabG) from Escherichia coli was determined via the multiwavelength anomalous diffraction technique using a selenomethionine-labeled crystal containing 88 selenium sites in the asymmetric unit. The comparison of the E. coli FabG structure with the homologous Brassica napus FabG.NADP(+) binary complex reveals that cofactor binding causes a substantial conformational change in the protein. This conformational change puts all three active-site residues (Ser 138, Tyr 151, and Lys 155) into their active configurations and provides a structural mechanism for allosteric communication between the active sites in the homotetramer. FabG exhibits negative cooperative binding of NADPH, and this effect is enhanced by the presence of acyl carrier protein (ACP). NADPH binding also increases the affinity and decreases the maximum binding of ACP to FabG. Thus, unlike other members of the short-chain dehydrogenase/reductase superfamily, FabG undergoes a substantial conformational change upon cofactor binding that organizes the active-site triad and alters the affinity of the other substrate-binding sites in the tetrameric enzyme.     

Independent tyrosyl contributions to the CD of Ff gene 5 protein and the distinctive effects of Y41H and Y41F mutants on protein-protein cooperative interactions

The gene 5 protein (g5p) of the Ff virus contains five Tyr, individual mutants of which have now all been characterized by CD spectroscopy. The protein has a dominant tyrosyl 229-nm L(a) CD band that is shown to be approximately the sum of the five individual Tyr contributions. Tyr41 is particularly important in contributing to the high cooperativity with which the g5p binds to ssDNA, and Y41F and Y41H mutants are known to differ in dimer-dimer packing interactions in crystal structures. We compared the solution structures and binding properties of the Y41F and Y41H mutants using CD spectroscopy. Secondary structures of the mutants were similar by CD analyses and close to those derived from the crystal structures. However, there were significant differences in the binding properties of the two mutant proteins. The Y41H protein had an especially low binding affinity and perturbed the spectrum of poly[d(A)] in 2 mM Na(+) much less than did Y41F and the wild-type gene 5 proteins. Moreover, a change in the Tyr 229 nm band, assigned to the perturbation of Tyr34 at the dimer-dimer interface, was absent in titrations with the Y41H mutant under low salt conditions. In contrast, titrations with the Y41H mutant in 50 mM Na(+) exhibited typical CD changes of both the nucleic acid and the Tyr 229-nm band. Thus, protein-protein and g5p-ssDNA interactions appeared to be mutually influenced by ionic strength, indicative of correlated changes in the ssDNA binding and cooperativity loops of the protein or of indirect structural constraints.     

A conserved tyrosine residue of Saccharomyces cerevisiae leukotriene A4 hydrolase stabilizes the transition state of the peptidase activity

Saccharomyces cerevisiae leukotriene A4 hydrolase (LTA4H) is a bifunctional aminopeptidase/epoxide hydrolase and a member of the M1 family of metallopeptidases. In order to obtain a more thorough understanding of the aminopeptidase activity of the enzyme, two conserved tyrosine residues, Tyr244 and Tyr456, were altered to phenylalanine and the mutant proteins characterized by determining KM and kcat for various amino acid beta-naphthylamide substrates. While mutation of Tyr456 exhibited minimal effect on catalysis, mutation of Tyr244 caused an overall 25-100-fold reduction in catalytic activity for all substrates tested. Furthermore, LTA4H Y244F exhibited a 40-fold decrease in affinity for RB-3014, a transition state analog inhibitor, implicating Tyr244 in transition state stabilization.     

3-Nitrotyrosine as a spectroscopic probe for investigating protein protein interactions

3-Nitrotyrosine (NT) is approximately 10(3)-fold more acidic than Tyr, and its absorption properties are strongly pH-dependent. NT absorbs radiation in the wavelength range where Tyr and Trp emit fluorescence (300-450 nm), and it is essentially nonfluorescent. Therefore, NT may function as an energy acceptor in resonance energy transfer (FRET) studies for investigating ligand protein interactions. Here, the potentialities of NT were tested on the hirudin thrombin system, a well-characterized protease inhibitor pair of key pharmacological importance. We synthesized two analogs of the N-terminal domain (residues 1-47) of hirudin: Y3NT, in which Tyr3 was replaced by NT, and S2R/Y3NT, containing the substitutions Ser2 --> Arg and Tyr3 --> NT. The binding of these analogs to thrombin was investigated at pH 8 by FRET and UV/Vis-absorption spectroscopy. Upon hirudin binding, the fluorescence of thrombin was reduced by approximately 50%, due to the energy transfer occurring between the Trp residues of the enzyme (i.e., the donors) and the single NT of the inhibitor (i.e., the acceptor). The changes in the absorption spectra of the enzyme inhibitor complex indicate that the phenate moiety of NT in the free state becomes protonated to phenol in the thrombin-bound form. Our results indicate that the incorporation of NT can be effectively used to detect protein protein interactions with sensitivity in the low nanomolar range, to uncover subtle structural features at the ligand protein interface, and to obtain reliable Kd values for structure activity relationship studies. Furthermore, advances in chemical and genetic methods, useful for incorporating noncoded amino acids into proteins, highlight the broad applicability of NT in biotechnology and pharmacological screening.     

Structural similarities between thiamin-binding protein and thiaminase-I suggest a common ancestor

ATP-binding cassette (ABC) transporters are responsible for the transport of a wide variety of water-soluble molecules and ions into prokaryotic cells. In Gram-negative bacteria, periplasmic-binding proteins deliver ions or molecules such as thiamin to the membrane-bound ABC transporter. The gene for the thiamin-binding protein tbpA has been identified in both Escherichia coli and Salmonella typhimurium. Here we report the crystal structure of TbpA from E. coli with bound thiamin monophosphate. The structure was determined at 2.25 A resolution using single-wavelength anomalous diffraction experiments, despite the presence of nonmerohedral twinning. The crystal structure shows that TbpA belongs to the group II periplasmic-binding protein family. Equilibrium binding measurements showed similar dissociation constants for thiamin, thiamin monophosphate, and thiamin pyrophosphate. Analysis of the binding site by molecular modeling demonstrated how TbpA binds all three forms of thiamin. A comparison of TbpA and thiaminase-I, a thiamin-degrading enzyme, revealed structural similarity between the two proteins, especially in domain 1, suggesting that the two proteins evolved from a common ancestor.     

Synthesis of 2-,4,-6-, and/or 7-substituted quinoline derivatives as human dihydroorotate dehydrogenase (hDHODH) inhibitors and anticancer agents: 3D QSAR-assisted design

Following our research for human dihydroorotate dehydrogenase (hDHODH) inhibitors as anticancer agents, herein we describe 3D QSAR-based design, synthesis and in vitro screening of 2-,4,-6-, and/or 7-substituted quinoline derivatives as hDHODH inhibitors and anticancer agents. We have designed 2-,4,-6-, and/or 7-substituted quinoline derivatives and predicted their hDHODH inhibitory activity based on 3D QSAR study on 45 substituted quinoline derivatives as hDHODH inhibitors, and also predicted toxicity. Designed compounds were docked into the binding site of hDHODH. Designed compounds which showed good predictive activity, no toxicity, and good docking score were selected for the synthesis, and in vitro screening as hDHODH inhibitors in an enzyme inhibition assay, and anticancer agents in MTT assay against cancer cell lines (HT-29 and MDA-MB-231). Synthesized compounds 7 and 14 demonstrated IC₅₀ value of 1.56?µM and 1.22?µM, against hDHODH, respectively, and these are our lead compounds for the development of new hDHODH inhibitors and anticancer agents.     

Expression and characterization of rat soluble catechol-O-methyltransferase fusion protein

Rat soluble catechol-O-methyltransferase cDNA was cloned into the pCAL-n-FLAG vector and expressed in Escherichia coli as a fusion protein with a calmodulin-binding peptide tag. The recombinant protein, comprising up to 30% of the total protein in the soluble fraction of E. coli, was purified by calmodulin affinity chromatography and gel filtration. Up to 16 mg of pure recombinant enzyme was recovered per liter of culture. Recombinant catechol-O-methyltransferase, in the bacterial soluble fraction, exhibited the same affinity for adrenaline as rat liver soluble catechol-O-methyltransferase (K(m) 428 [246, 609] microM and 531 [330, 732] microM, respectively), as well as the same affinity for the methyl donor, S-adenosyl-l-methionine (K(m) 27 [9, 45] microM and 38 [21, 55] microM, respectively). In addition, both the recombinant and the liver enzymes displayed the same sensitivity to the inhibitor 3,5-dinitrocatechol (IC(50) 132 [44, 397] nM and 74 [38, 143] nM, respectively), and both had the same catalytic number, respectively, 10.1 +/- 1.5 min(-1) and 8.3 +/- 0.3 min(-1). The purified recombinant enzyme also displayed the same affinity for the substrate as the purified rat liver catechol-O-methyltransferase (K(m) 336 [75, 597] microM and 439 [168, 711] microM, respectively) as well as the same inhibitor sensitivity (IC(50) 44 [19, 101] nM and 61 [33, 111] nM, respectively). This recombinant form of catechol-O-methyltransferase is kinetically identical to the rat liver enzyme. This system provides an easy and quick way of obtaining large amounts of soluble catechol-O-methyltransferase for both pharmacological and structural studies.     

Modulation of the affinity of the single-stranded DNA-binding protein of Escherichia coli (E. coli SSB) to poly(dT) by site-directed mutagenesis

A vector for site-directed mutagenesis and overproduction of the Escherichia coli single-stranded-DNA-binding protein (E. coli SSB) was constructed. An E. coli strain carrying this vector produces up to 400 mg pure protein from 25 g wet cells. The vector was used to mutate specifically the Phe60 residue of E. coli SSB. Phe60 had been proposed to be located near the single-stranded-DNA-binding site. Substitution of the Phe60 residue by Val, Ser, Leu, His, Tyr and Trp gave proteins with no or only minor conformational changes, as detected by NMR spectroscopy. The affinity of the mutant E. coli SSB proteins for single-stranded DNA decreased in the order Trp greater than Phe (wild-type) greater than Tyr greater than Leu greater than His greater than Val greater than Ser, leading to the conclusion that position 60 is a site of hydrophobic interaction of the protein with DNA.     

Crystal structure of the stromelysin catalytic domain at 2.0 A resolution: inhibitor-induced conformational changes.

Matrix metalloproteinases are believed to play an important role in pathological conditions such as osteoarthritis, rheumatoid arthritis and tumor invasion. Stromelysin is a zinc-dependent proteinase and a member of the matrix metalloproteinase family. We have solved the crystal structure of an active uninhibited form of truncated stromelysin and a complex with a hydroxamate-based inhibitor. The catalytic domain of the enzyme of residues 83-255 is an active fragment. Two crystallographically independent molecules, A and B, associate as a dimer in the crystals. There are three alpha-helices and one twisted, five-strand beta-sheet in each molecule, as well as one catalytic Zn, one structural Zn and three structural Ca ions. The active site of stromelysin is located in a large, hydrophobic cleft. In particular, the S1' specificity site is a deep and highly hydrophobic cavity. The structure of a hydroxamate-phosphinamide-type inhibitor-bound stromelysin complex, formed by diffusion soaking, has been solved as part of our structure-based design strategy. The most important feature we observed is an inhibitor-induced conformational change in the S1' cavity which is triggered by Tyr223. In the uninhibited enzyme structure, Tyr223 completely covers the S1' cavity, while in the complex, the P1' group of the inhibitor displaces the Tyr223 in order to fit into the S1' cavity. Furthermore, the displacement of Tyr223 induces a major conformational change of the entire loop from residue 222 to residue 231. This finding provides direct evidence that Tyr223 plays the role of gatekeeper of the S1' cavity. Another important intermolecular interaction occurs at the active sit of molecule A, in which the C-terminal tail (residues 251-255) from molecule B inserts. The C-terminal tail interacts extensively with the active site of molecule A, and the last residue (Thr255) coordinated to the catalytic zinc as the fourth ligand, much like a product inhibitor would. The inhibitor-induced conformational change and the intermolecular C-terminal-zinc coordination are significant in understanding the structure-activity relationships of the enzyme.     

Identification of contacts between topoisomerase I and its target DNA by site-specific photocrosslinking.

Vaccinia DNA topoisomerase, a eukaryotic type I enzyme, binds and cleaves duplex DNA at sites containing the sequence 5''-(T/C)CCTT. We report the identification of Tyr70 as the site of contact between the enzyme and the +4C base of its target site. This was accomplished by UV-crosslinking topoisomerase to bromocytosine-substituted DNA, followed by isolation and sequencing of peptide-DNA photoadducts. A model for the topoisomerase-DNA interface is proposed, based on the crystal structure of a 9 kDa N-terminal tryptic fragment. The protein domain fits into the DNA major groove such that Tyr70 is positioned close to the +4C base and Tyr72 is situated near the +3C base. Mutational analysis indicates that Tyr70 and Tyr72 contribute to site recognition during covalent catalysis. We propose, based on this and other studies of the vaccinia protein, that DNA backbone recognition and reaction chemistry are performed by a relatively well-conserved 20 kDa C-terminal portion of the vaccinia enzyme, whereas discrimination of the DNA sequence at the cleavage site is accomplished by a separate N-terminal domain, which is less conserved between viral and cellular proteins. Division of function among distinct structural modules may explain the different site specificities of the eukaryotic type I topoisomerases.