Solution structure, mutagenesis, and NH exchange studies of the MutT enzyme–Mg-8-oxo-dGMP complex

The MutT pyrophosphohydrolase from E. coli (129 residues) catalyzes the hydrolysis of nucleoside triphosphates (NTP), including 8-oxo-dGTP, by substitution at Pβ, to yield NMP and pyrophosphate. The product, 8-oxo-dGMP is an unusually tight binding, slowly exchanging inhibitor with a K_D=52 nM, (ΔG°=−9.8 kcal/mol) which is 6.1 kcal/mol tighter than the binding of dGMP (ΔG°=−3.7 kcal/mol). The higher affinity for 8-oxo-dGMP results from a more favorable ΔH_binding (−32 kcal/mol) despite an unfavorable −TΔS°_binding (+22 kcal/mol). The solution structure of the MutT–Mg²⁺-8-oxo-dGMP complex shows a narrowed, hydrophobic nucleotide-binding cleft with Asn-119 and Arg-78 among the few polar residues. The N119A, N119D, R78K and R78A single mutations, and the R78K+N119A double mutant all showed largely intact active sites, on the basis of small changes in the kinetic parameters of dGTP hydrolysis and in ¹H–¹⁵N HSQC spectra. However, the N119A mutation profoundly weakened the active site binding of 8-oxo-dGMP by 4.3 kcal/mol (1650-fold). The N119D mutation also weakened 8-oxo-dGMP binding but only by 2.1 kcal/mol (37-fold), suggesting that Asn-119 functioned both as a hydrogen bond donor to C8=O, and a hydrogen bond acceptor from N7H of 8-oxo-dGMP, while aspartate at position −119 functioned as an acceptor of a single hydrogen bond. Much smaller weakening effects (0.3–0.4 kcal/mol) on the binding of dGMP and dAMP were found, indicating specific hydrogen bonding of Asn-119 to 8-oxo-dGMP. While formation of the wild type MutT–Mg²⁺-8-oxo-dGMP complex slowed the backbone NH exchange rates of 45 residues distributed throughout the protein, the same complex of the N119A mutant slowed the exchange rates of only 11 residues at or near the active site, indicating an increase in conformational flexibility of the N119A mutant. The R78K and R78A mutations weakened the binding of 8-oxo-dGMP by 1.7 and 1.1 kcal/mol, respectively, indicating a lesser role of Arg-78 than of Asn-119 in the selective binding of 8-oxo-dGMP, likely donating a single hydrogen bond to its C6=O. The R78K+N119A double mutant weakened the binding of 8-oxo-dGMP (K_I^slope=3.1 mM) by 6.5±0.2 kcal/mol which overlaps, within error with the sum of the effects of the two single mutants (6.0±0.3 kcal/mol). Such additive effects of the two single mutants in the double mutant are most simply explained by the independent functioning of Asn-119 and Arg-78 in the binding of 8-oxo-dGMP. Independent functioning of these two residues in nucleotide binding is consistent with their locations in the MutT–Mg²⁺-8-oxo-dGMP complex, on opposite sides of the active site cleft, with a distance of 8.4±0.5 Å between their side chain nitrogens.     

THE EFFECTS OF PERFUSION OF LATERAL VENTRICLE WITH CaCl_2 ON THE FEBRILE RESPONSE AND cAMP CONTENT IN PLASMA AND CEREBROSPINAL FLUID DURING LP-INDUCED FEVER

Artificial cerebrospinal fluid (c.s.f.) containing 40 mmol/L excess calcium was perfus-ed through the lateral ventricles of New Zealand white rabbits in order to reduce the Na~+/Ca~(++) ratio in the brain and the effects on both the febrile response and adenosine cyclic mo-nophosphate (cAMP) concentration in plasma and c.s.f, during leucocytic pyrogen (LP)-induced fever were observed. The results showed that cAMP concentration in c.s.f, increas-ed significantly during LP-induced fever while the cAMP level in Plasma remained unchang-ed, and the perfusion of artificial c.s,f, containing 40 mmol/L excess calcium can signif-icantly inhibit not only the febrile response but also the increase in c.s.f, cAMP level,while there appears no effect on plasma cAMP concentration, thus demonstrating that theincrease of Na~+/Ca~(++) ratio causing the increase of cAMP content in the brain may be anessential link in the pathogenesis of LP-induced fever.     

Biotechnological storage and utilization of entrapped solar energy

Our laboratory has recently developed a device employing immobilized F₀F₁ adenosine triphosphatase (ATPase) that allows synthesis of adenosine triphosphate (ATP) from adenosine 5′-diphosphate and inorganic phosphate using solar energy. We present estimates of total solar energy received by Earth’s land area and demonstrate that its efficient capture may allow conversion of solar energy and storage into bonds of biochemicals using devices harboring either immobilized ATPase or NADH dehydrogenase. Capture and storage of solar energy into biochemicals may also enable fixation of CO₂ emanating from polluting units. The cofactors ATP and NADH synthesized using solar energy could be used for regeneration of acceptor d-ribulose-1,5-bisphosphate from 3-phosphoglycerate formed during CO₂ fixation.     

高效液相色谱法测定地顶孢霉培养物中的腺苷

建立测定虫草源饲料添加剂地顶孢霉培养物中腺苷含量的高效液相色谱方法。样品经过研碎、超声处理,离心、过滤后上机测定。腺苷的最佳提取条件:以超纯水为浸提液,用超声波浸提,浸提温度为40℃,浸提时间为55 min。使用Waters Spherisorb ODS2柱(150 mm×3.9 mm,5μm),以甲醇-0.01 mol/L磷酸二氢钾混合液(10∶90)为流动相,流量为1.0 mL/min,进样体积为20μL,检测波长为254 nm。腺苷的质量浓度在0.5~100μg/mL范围内与色谱峰面积成良好的线性关系,相关系数为0.9990。样品测定结果的相对标准偏差为1.65%(n=6),3水平加标的平均回收率为98.19%。该方法简便、快捷,可准确测定虫草饲料添加剂地顶孢霉培养物中腺苷的含量。     

New methods for data analysis of isothermal titration calorimetry

Heat divided by ligand concentration vs. heat, similar to the Scatchard plot, was introduced to obtain the equilibrium constant (K) and the enthalpy of binding (DH) using isothermal titration calorimetry data. Values of K and DH obtained by this linear pseudo-Scatchard plot for a system with a set of independent binding sites (such as binding fluoride ions on urease and monosaccharide methyl a-D-mannopyranoside on concavalin A) were remarkably like that obtained from a normal fitting Wiseman method and other our technical methods. On applying this graphical method to study the binding of copper ion on myelin basic protein (MBP), a concave downward curve obtained was consistent with the positive cooperativity in the binding. A graphical fitting by simple method for determination of thermodynamic parameters was also introduced. This method is general, without any assumption and restriction made in previous method. This general method was applied to the product inhibition study of adenosine deaminase. This revised version was published online in July 2006 with corrections to the Cover Date.     

毛细管区带电泳法测定冬虫夏草中的腺苷、腺嘌呤和尿嘧啶

建立了毛细管区带电泳法测定天然和人工冬虫夏草中腺苷、腺嘌呤和尿嘧啶含量的分析方法。采用15mmol/L硼砂＋14mmol/L磷酸二氢钠＋5％（V／V）甲醇（pH＝9.5）作为缓冲体系，在电压为18kV和检测波长为254nm的条件下，冬虫夏草提取液中的腺苷、腺嘌呤和尿嘧啶实现了基线分离。定量分析表明，3种成分的校正峰面积与质量浓度呈较好的线性关系(r≥0.9991）。考察了缓冲溶液的pH值、浓度及有机改性剂对腺苷、腺嘌呤和尿嘧啶迁移行为的影响。     

Molecule-binding dependent assembly of split aptamer and γ-cyclodextrin: A sensitive excimer signaling approach for aptamer biosensors

A highly sensitive and selective fluorescence aptamer biosensors for the determination of adenosine triphosphate (ATP) was developed. Binding of a target with splitting aptamers labeled with pyrene molecules form stable pyrene dimer in the γ-cyclodextrin (γ-CD) cavity, yielding a strong excimer emission. We have found that inclusion of pyrene dimer in γ-cyclodextrin cavity not only exhibits additive increases in quantum yield and emission lifetime of the excimer, but also facilitates target-induced fusion of the splitting aptamers to form the aptamer/target complex. As proof-of-principle, the approach was applied to fluorescence detection of adenosine triphosphate. With an anti-ATP aptamer, the approach exhibits excimer fluorescence response toward ATP with a maximum signal-to-background ratio of 32.1 and remarkably low detection limit of 80 nM ATP in buffer solution. Moreover, due to the additive fluorescence lifetime of excimer induced by γ-cyclodextrin, time-resolved measurements could be conveniently used to detect as low as 0.5 μM ATP in blood serum quantitatively.     

An ultrasensitive quantum dots fluorescent polarization immunoassay based on the antibody modified Au nanoparticles amplifying for the detection of adenosine triphosphate

In this work, an ultrasensitive fluorescent polarization immunoassay (FPIA) method based on the quantum dot/aptamer/antibody/gold nanoparticles ensemble has been developed for the detection of adenosine triphosphate (ATP). DNA hybridization is formed when ATP is present in the PBS solution containing the DNA-conjugated quantum dots (QDs) and antibody-AuNPs. The substantial sensitivity improvement of the antibody-AuNPs-enhanced method is mainly attributed to the slower rotation of fluorescent unit when QDs-labeled oligonucleotides hybridize with antibody modified the gold nanoparticle. As a result, the fluorescent polarization (FP) values of the system increase significantly. Under the optimal conditions, a linear response with ATP concentration is ranged from 8 × 10⁻¹² M to 2.40 × 10⁻⁴ M. The detection limit reached as low as 1.8 pM. The developed work provides a sensitive and selective immunoassay protocol for ATP detection, which could be applied in more bioanalytical systems.     

Resonant-Mie-scattering of aggregates of phosphomolybdate and papaverine for measuring activities and screening inhibitors of cyclic nucleotide phosphodiesterase isozymes

A resonant-light-scattering (RLS) method was proposed to quantify phosphate for screening inhibitors of isozymes of cyclic nucleotide phosphodiesterase (PDE). In acidified mixtures of phosphate, papaverine and molybdate, there were aggregates exhibiting micrometre sizes, no absorbance peaks over 360 nm but strong RLS peaks at 392 nm; Mie scattering thus accounted for the RLS signals. When papaverine was added before molybdate to acidified samples of phosphate, RLS signals at 392 nm were stable from 5 to 25 min since the addition of molybdate; after optimization, phosphate from 0.40 to 3.60 μM was quantifiable. This RLS method tolerated 60 mg L⁻¹ proteins besides common PDE inhibitors and dimethyl sulfoxide in acidified samples of phosphate; the integration of this RLS method with the coupled action of a phosphomonoesterase on PDE product was thus rational to measure PDE activities without the removal of proteins in samples. By quantifying activities of a truncated mutant of human PDE4B2 via this RLS method, Michaelis–Menten constant, inhibition constants of rolipram, papaverine and theophylline varied over three magnitudes and were consistent with those estimated by an improved malachite green assay of phosphate, respectively. Hence, this novel RLS method was promising for screening inhibitors of PDE isozymes.     

Synthesis of an o-Nitrobenzyl Attached A1 Adenosine Receptor Antagonist,a Prodrug Approach

Abstract

The o-nitrobenzyl group, possessing distinct advantage of being photolabile under mild conditions, was successfully connected to 8-(5,6-epoxynorbornan-2-yl)-1,3-dipropylxanthine (5), a high specific A₁ adenosine receptor antagonist. The resulting compound 4 would have potential use as a prodrug.