Intersubunit Interactions in Human Cytidine Deaminase

Abstract

In order to design new efficient cytidine based drugs, an intersubunit interactions study related to the active site has been performed on the wild-type cytidine deaminase (CDA) and on the mutant enzyme F137W/W113F. F137 is the homologous to the Bacillus subtilis CDA F125 involved in the subunit interactions. In presence of the dissociating agent SDS, wild-type human CDA dissociate into enzymatically inactive monomers without intermediate forms via a non-cooperative transition. Extensive dialysis or dilution of the inactivated monomers restores completely the activity. The presence of the strong human CDA competitive inhibitor 5-fluorozebularine disfavour dissociation of the tetramer into subunits in the wild-type CDA but not in mutant enzyme F137W/W113F.     

小鼠APOBEC3的结构与功能分析

随着对APOBEC3抗病毒功能的深入研究以及其在癌症中的表现,APOBEC3已成为当前的热点.小鼠只有一个APOBEC3基因,而人类有七个APOBEC3基因,人类APOBEC3G是其中研究最明确的抗病毒蛋白.利用生物信息学方法对两个蛋白进行序列比对、亲疏水性分析、亚细胞定位预测、二级结构及高级结构分析以及相互作用分析....     

Crystal structure determination and dynamic studies of Mycobacterium tuberculosis Cytidine deaminase in complex with products

Cytidine deaminase (CDA) is a key enzyme in the pyrimidine salvage pathway. It is involved in the hydrolytic deamination of cytidine or 2′-deoxycytidine to uridine or 2′-deoxyuridine, respectively. Here we report the crystal structures of Mycobacterium tuberculosis CDA (MtCDA) in complex with uridine (2.4 Å resolution) and deoxyuridine (1.9 Å resolution). Molecular dynamics (MD) simulation was performed to analyze the physically relevant motions involved in the protein–ligand recognition process, showing that structural flexibility of some protein regions are important to product binding. In addition, MD simulations allowed the analysis of the stability of tetrameric MtCDA structure. These findings open-up the possibility to use MtCDA as a target in future studies aiming to the rational design of new inhibitor of MtCDA-catalyzed chemical reaction with potential anti-proliferative activity on cell growth of M. tuberculosis, the major causative agent of tuberculosis.     

Length of the hypermutation motif DGYW/WRCH in the focus of statistical limits. Implications for a double-motif or extended motif recognition models

The motif DGYW/WRCH (Mh) and its frequently discussed simplified derivative GYW/WRC (Mhs) are involved in immunoglobulin (Ig) hypermutation. Both these motifs appear to be markedly shorter than the corresponding conventionally predicted minima of valid sequence lengths (MVSL). The same conclusion concerning both Mh and Mhs can also be obtained in the combined case including a less strict semi-empirically defined w-value and one nucleotide length tolerance related to MVSL. Such disagreement indicates considerably low information content in Mh and Mhs when evaluating these motifs as alphabetical structures (words). This fact raises a question of actually recognized structures (presumably longer than Mh and Mhs). Interestingly, both Mh and Mhs dimers or pairs of closely located Mh or Mhs achieve confirmation of length validity in the case of w=0.05, suggesting thus double-motif recognition as one of statistically consistent explanations. This possibility is also in agreement with the results of our model sequence study of mRNA derived from variable Ig gene sequences (rIgV) with respect to the most frequently occurring structures formed by motif overlaps in all model sequence sets. On the other hand, additional superior occurrence of motif pairs at a structurally important distance of a single DNA thread was found in the conserved domain (cd00099) related sequences of Elasmobranchii origin and less markedly in the corresponding human rIgV, but not in a randomly selected human subset of rIgV. The data are discussed with respect to statistical evaluation and structural properties of hypermutation motifs or the competent enzyme, i.e. activation-induced cytidine deaminase.     

高表达人源SP15对小鼠生长和生殖的影响

目的:探究高表达人源SP15对小鼠生长和生殖的影响,为研究NYD-SP15在生物体中的功能提供动物模型。方法:将人源NYD-SP15 cDNA以及Cre序列插入PCAG启动子下游,构建NYD-SP15转基因表达载体,并通过原核注射,构建全身性表达NYD-SP15的转基因小鼠;将获得的NYD-SP15转基因小鼠与C57/BL6小鼠交配,PCR鉴定转基因小鼠是否有Cre插入,筛选出人源NYD-SP15表达的小鼠,统计转基因小鼠体重变化和后代阳性情况。结果:通过PCR鉴定及公司测序验证,我们成功构建了NYD-SP15转基因过表达载体。并通过PCR鉴定小鼠基因型,筛选出可以表达人NYD-SP15的转基因小鼠。比较转基因小鼠与同窝野生型小鼠体重,发现转基因小鼠体重与同窝野生型小鼠相比无明显区别,说明在体内过表达NYD-SP15对小鼠体重无明显影响。通过对后代阳性小鼠出生情况统计发现F2代阳性小鼠出生率较F1代明显降低。结论:人源NYD-SP15在小鼠体内能正常表达,对其生长无明显影响,但其后代阳性出生率呈逐代下降趋势,推测该原因可能与NYD-SP15在睾丸中表达有关。     

Binding and structural studies of the complexes of type 1 ribosome inactivating protein from Momordica balsamina with cytosine,cytidine, and cytidine diphosphate

The type 1 ribosome inactivating protein from Momordica balsamina (MbRIP1) has been shown to interact with purine bases, adenine and guanine of RNA/DNA. We report here the binding and structural studies of MbRIP1 with a pyrimidine base, cytosine; cytosine containing nucleoside, cytidine; and cytosine containing nucleotide, cytidine diphosphate. All three compounds bound to MbRIP1 at the active site with dissociation constants of 10^?4 M–10^?7 M. As reported earlier, in the structure of native MbRIP1, there are 10 water molecules in the substrate binding site. Upon binding of cytosine to MbRIP1, four water molecules were dislodged from the substrate binding site while five water molecules were dislodged when cytidine bound to MbRIP1. Seven water molecules were dislocated when cytidine diphosphate bound to MbRIP1. This showed that cytidine diphosphate occupied a larger space in the substrate binding site enhancing the buried surface area thus making it a relatively better inhibitor of MbRIP1 as compared to cytosine and cytidine. The key residues involved in the recognition of cytosine, cytidine and cytidine diphosphate were Ile71, Glu85, Tyr111 and Arg163. The orientation of cytosine in the cleft is different from that of adenine or guanine indicating a notable difference in the modes of binding of purine and pyrimidine bases. Since adenine containing nucleosides/nucleotides are suitable substrates, the cytosine containing nucleosides/nucleotides may act as inhibitors.     

CDA基因沉默对人慢性髓系白血病细胞增殖和凋亡的影响

目的:探讨胞苷脱氨酶(CDA)基因沉默在治疗人慢性髓系白血病(CML)中的潜在价值.方法:通过RT-PCR和Western blot检测CML患者和造血干细胞移植供体的骨髓单个核细胞中的CDA表达.对CML KCL-22细胞系转染shRNA和过表达CDA的pBS/U6-Neo质粒来诱导CDA基因沉默或过表达.通过细胞计...     

Quantitative immunoblot assay for assessment of liposomal antibody conjugation efficiency.

Routine direct assessment of immunoglobulin (Ig)-liposome(lp) conjugation efficiency has been impeded by phospholipid interference with standard protein and immunoassay methods. Rabbit IgG conjugated to anionic liposomes was quantitated in immunoblots using computer image analysis techniques. Lp-coupled Ig was separated from free Ig by dialysis in disposable Spectra/Por units (MWCO 300 kDa). Differential Lowry protein assay (DLA) of the thiolated Ig reactant and the dialyzate provided an estimate of conjugation efficiency that was compared to the results of the immunoblot assay (IBA). The color response of Ig-lp in the IBA was about an order of magnitude greater than rabbit IgG alone, requiring the synthesis of an Ig-lp standard in which the Ig conjugation efficiency was assessed by radiotracer methodology. The use of the same standard in three colorimetric protein assays verified the accuracy of the IBA and demonstrated that the colorimetric assays could be employed to determine Ig-lp conjugation efficiency. In terms of sensitivity and specificity, however, the IBA is better suited for routine assessment of laboratory-scale Ig-lp conjugation efficiencies. The DLA was found to be an unsatisfactory measure of conjugation efficiencies because an interfering substance was apparently released by Ig-lp preparations.     

The iscS gene deficiency affects the expression of pyrimidine metabolism genes

Inactivation of iscS encoding cysteine desulfurase results in a slow growth phenotype associated with the deficiency of iron-sulfur clusters, thiamine, NAD, and tRNA thionucleosides in Escherichia coli. However, the other roles of iscSin vivo are unknown. By using differential screening strategies, we identified 2 pyrimidine salvage enzymes, namely, uridine phosphorylase and cytidine deaminase, which were down-regulated in the iscS mutant. Both enzymes are positively regulated by the cAMP receptor protein (CRP). We also identified a novel protein complex, namely, YeiT-YeiA, whose expression level was decreased in the iscS mutant. The recombinant YeiT-YeiA complex exhibited NADH-dependent dihydropyrimidine dehydrogenase activity, indicating its role in pyrimidine metabolism. The presence of a CRP-binding consensus sequence on the 5′-upstream of the yeiT-YeiA gene suggests its regulation by CRP. These results provide a clue to the possible role of iscS in pyrimidine metabolism by gene regulation.     

Ubiquinone binding protein used for determination of coenzyme Q

The conventional method of assaying for the ubiquinone (CoQ) content of biological samples is to partition CoQ into an organic phase and separate it from contaminants by high-performance liquid chromatography (HPLC). HPLC is an accurate method of quantifying CoQ content but is not ideal for routine clinical analyses. This paper describes the development of a rapid method for assaying the CoQ content of biological samples based on the binding of CoQ to a CoQ binding peptide. The 14-amino acid binding peptide was chemically synthesized, and conditions for immobilizing the peptide on microfuge tubes were established. CoQ could be selectively bound to the immobilized peptide, eluted, and determined spectrophotometrically. Limits of detection for the method were 0.25 to 5 nmol CoQ. To test biological samples, CoQ was isolated from cultures of Saccharomyces cerevisiae grown in oleic acid medium. The recovery of CoQ samples using the binding assay ranged from 99 to 102% of the values obtained with HPLC. The assay described here provides an inexpensive, rapid method for determining the CoQ content of large numbers of biological samples in a variety of laboratory settings.     

Cyclic, trinuclear PdII complex of cytidine with pronounced double cone structure

Reaction of PdII(tmeda) (tmeda=N,N,N',N'-tetramethylethylenediamine) with the RNA nucleoside cytidine (Cytd) yields a cyclic nucleoside complex containing three metal entities and three cytidine anions, with metal cross-links involving N(3) and N(4)H(-) sites. [{Pd(Cytd(-)-N3,N4)(tmeda)}3](ClO4)3.6H2O has a characteristic double cone structure with the methyl groups of the tmeda ligands representing the lower rim and the ribose moieties forming the upper rim. The Pd3 triangle is equilateral (5.193(1)A). In the solid state structure, one of the ClO(4)(-) counter ions links the lower and the upper rims of adjacent cones, thereby leading to a 1D chain. No host-guest chemistry has been detected with a series of N-heterocyclic ligands in water.     

纳米抗体技术应用的最新进展

纳米抗体作为一种可塑性强、较为新颖的抗原识别和调控的工具,具备小尺寸、易表达和筛选及改造、高亲性和稳定性等优势,能够识别传统抗体难以识别的较为隐匿的抗原表位,在诊断治疗各种疾病及检测方面的应用不断深入,且在基础研究中也发挥着不可替代的作用。文中主要介绍了纳米抗体及其衍生结构在小分子化合物及病原微生物检测和疾病的诊断,以及在疾病靶向治疗,细胞、分子成像领域的相关进展,此外还综述了在蛋白质构象研究领域展现的广阔前景。     

重组钩端螺旋体外膜蛋白酶联免疫吸附(ELISA)检测方法的建立

目的建立以重组外膜蛋白为基础的钩端螺旋体抗体间接ELISA检测方法。方法以基因重组技术获取重组钩端螺旋体外膜蛋白LipL32,以该蛋白为抗原,特异的钩体抗血清进行ELISA方阵滴定、交叉性试验、阻断试验,并对北京地区的70份犬血清使用建立的ELISA方法以及德国Virion公司的全菌体钩端螺旋体ELISA试剂盒进行相互验证。结果方阵滴定试验确立以100ng/孔为抗原包被浓度,1∶160为血清稀释度。交叉性试验具有广泛性、阻断试验标明该方法特异性强、灵敏度高。两种方法数据经χ2检验,两者检出率之间差异不显著。结论重组LipL32蛋白具有结合活性。初步建立了以重组LipL32蛋白为抗原的钩端螺旋体抗体间接ELISA检测方法。     

Cytotoxic activity of 2',2'-difluorodeoxycytidine, 5-aza-2'-deoxycytidine and cytosine arabinoside in cells transduced with deoxycytidine kinase gene

Deoxycytidine nucleoside analogs must be first phosphorylated to become active anticancer drugs. The rate-limiting enzyme in this pathway is deoxycytidine kinase (dCK). Cells deficient in this enzyme are resistant to these analogs. To evaluate the potential of dCK to be used as suicide gene for deoxycytidine nucleoside analogs, we transduced both human A-549 lung carcinoma and murine NIH3T3 fibroblast cell lines with this gene. The dCK-transduced cells showed an increase in cytotoxicity to the analogs, cytosine arabinoside (ARA-C), and 5-aza-2'-deoxycytidine (5-AZA-CdR). Unexpectedly, the related analog, 2',2'-difluorodeoxycytidine (dFdC), was less cytotoxic to the dCK-transduced cells than the wild-type cells. For the A-549-dCK cells, the phosphorylation of dFdC by dCK was much greater than control cells. In accord with the elevated enzyme activity, we observed a 6-fold increased dFdC incorporation into DNA and a more pronounced inhibition of DNA synthesis in the A-549-dCK cells. In an attempt to clarify the mechanism of dFdC, we investigated its action on A549 and 3T3 cells transduced with both cytidine deaminase (CD) and dCK. We reported previously that overexpression of CD confers drug resistance to deoxycytidine analogs. In this study, when the CD-transduced cells were also transduced with dCK they became relatively more sensitive to dFdC. In addition, we observed that dFdU, the deaminated form of dFdC, was cytotoxic to the A-549-dCK cells, but not the wild-type cells. Our working hypothesis to explain these results is that the mitochondrial thymidine kinase (TK2), an enzyme reported to phosphorylate dFdC, acts as an important modulator of dFdC-induced cell toxicity. These findings may further clarify the action of dFdC and the mechanism by which it induces cell death.