Mechanism of adenylate kinase. Structural and functional demonstration of arginine-138 as a key catalytic residue that cannot be replaced by lysine

Replacement of the arginine-138 of adenylate kinase (AK) by lysine or methionine resulted in a decrease in kcat by a factor of 10(4), increases in Km by a factor of 10-20, and relatively little changes in dissociation constants. Proton nuclear magnetic resonance (NMR) studies were then undertaken to obtain structural information for quantitative interpretation of the kinetic data. Since the lysine mutant (R138K) represents a conservative mutation with surprisingly large effects on kinetics, structural studies were focused on the wild type (WT) and R138K. The results and conclusions are summarized as follows: (i) The aromatic spin systems of WT and R138K were assigned from total correlated spectroscopy (TOCSY). Comparison of the chemical shifts of aromatic protons, one-dimensional spectra, TOCSY, and nuclear Overhauser enhanced spectroscopy (NOESY) indicated that the conformation of R138K was almost unperturbed relative to that of WT. Thus Arg-138 is not important for the tertiary structure. (ii) Proton NMR titrations with AMP and MgATP suggested that substrate binding affinities and substrate-induced conformational changes are nearly identical between WT and R138K. Thus arginine-138 should not be involved in stabilizing the first substrate in the binary complex. (iii) Notable differences were observed between the proton NMR spectra of the WT and R138K complexes with the reaction mixture, which agrees with the perturbation in the Km values of R138K. The differences were analyzed in detail by using a "static reaction mixture'--p1, p5-bis(5'-adenosyl)pentaphosphate (MgAP5A). The aromatic spin systems of WT + MgAP5A and R138K + MgAP5A were partially assigned from various two-dimensional spectra.(ABSTRACT TRUNCATED AT 250 WORDS)     

Mechanism of adenylate kinase. Are the essential lysines essential?

Using site-specific mutagenesis, we have probed the structural and functional roles of lysine-21 and lysine-27 of adenylate kinase (AK) from chicken muscle expressed in Escherichia coli. The two residues were chosen since according to the nuclear magnetic resonance (NMR) model [Mildvan, A. S., & Fry, D. C. (1987) Adv. Enzymol. 58, 241-313], they are located near the alpha- and the gamma-phosphates, respectively, of adenosine 5'-triphosphate (ATP) in the AK-MgATP complex. In addition, a lysine residue (Lys-21 in the case of AK) along with a glycine-rich loop is considered "essential" in the catalysis of kinases and other nucleotide binding proteins. The Lys-27 to methionine (K27M) mutant showed only slight increases in kcat and Km, but a substantial increase (1.8 kcal/mol) in the free energy of unfolding, relative to the WT AK. For proper interpretation of the steady-state kinetic data, viscosity-dependent kinetics was used to show that the chemical step is partially rate-limiting in the catalysis of AK. Computer modeling suggested that the folded form of K27M could gain stability (relative to the wild type) via hydrophobic interactions of Met-27 with Val-179 and Phe-183 and/or formation of a charge-transfer complex between Met-27 and Phe-183. The latter was supported by an upfield shift of the methyl protons of Met-27 in 1H NMR. Other than this, the 1H NMR spectrum of K27M is very similar to that of WT, suggesting little perturbation in the global or even local conformations.(ABSTRACT TRUNCATED AT 250 WORDS)     

Vibrational spectroscopy of bacteriorhodopsin mutants. Evidence for the interaction of aspartic acid 212 with tyrosine 185 and possible role in the proton pump mechanism

The role of Asp-212 in the proton pumping mechanism of bacteriorhodopsin (bR) has been studied by a combination of site-directed mutagenesis and Fourier transform infrared difference spectroscopy. Difference spectra were recorded at low temperature for the bR----K and bR----M photoreactions of the mutants Asp-212----Glu, Asp-212----Asn, and Asp-212----Ala. Despite an increased proportion of the 13-cis form of bR (normally associated with dark adaptation), all of the mutants exhibited a light-adapted form containing as a principal component the normal all-trans retinal chromophore. The absence of a shift in the retinal C = C stretching frequency in these mutants indicates that Asp-212 is not a major determinant of the visible absorption wavelength maximum in light-adapted bR. It is unlikely that Asp-212 is the acceptor group for the Schiff base proton since both the Asp-212----Glu and Asp-212----Ala mutants formed an M intermediate. All of the Asp-212 mutants were missing a Fourier transform infrared difference band that had been assigned previously to protonation changes of Tyr-185. These results are discussed in terms of a model in which Tyr-185 and Asp-212 form a polarizable hydrogen bond and are positioned near the C13-Schiff base portion of the chromophore. These 2 residues may be involved in stabilizing the relative orientation of the F and G helices and isomerizing the retinal in a regioselective manner about the C13 = C14 double bond.     

南美蟛蜞菊内参基因Actin的克隆及其分析

看家基因Actin常被用作定量、半定量PCR试验的内参基因.为研究其他基因在南美蟛蜞菊响应环境变化的表达调控机制,根据GenBank上已登录的肌动蛋白基因(Actin)的同源核苷酸保守序列,设计特异性引物,利用RT-PCR的方法克隆获得了南美蟛蜞菊Actin基因的全长序列,并将该序列命名为WtAct.序列分析结果表明W...     

Ontogenetic trait variation and metacommunity effects influence species relative abundances during tree community assembly

Predicting species abundance is one of the most fundamental pursuits of ecology. Combining the information encoded in functional traits and metacommunities provides a new perspective to predict the abundance of species in communities. We applied a community assembly via trait selection model to predict quadrat-scale species abundances using functional trait variation on ontogenetic stages and metacommunity information for over 490 plant species in a subtropical forest and a lowland tropical forest in Yunnan, China. The relative importance of trait-based selection, mass effects, and stochasticity in shaping local species abundances is evaluated using different null models. We found both mass effects and trait selection contribute to local abundance patterns. Trait selection was detectable at all studied spatial scales (0.04–1 ha), with its strength stronger at larger scales and in the subtropical forest. In contrast, the importance of stochasticity decreased with spatial scale. A significant mass effect of the metacommunity was observed at small spatial scales. Our results indicate that tree community assembly is primarily driven by ontogenetic traits and metacommunity effects. Our findings also demonstrate that including ontogenetic trait variation into predictive frameworks allows ecologists to infer ecological mechanisms operating in community assembly at the individual level.     

高致病性2型猪链球菌plcR基因敲除株的构建及其相关生物学特性的研究

【目的】构建高致病性2型猪链球菌05ZYH33菌株plcR基因敲除株,通过比较突变株与野生株生物学特性的差异,研究plcR基因在2型猪链球菌致病过程中的作用。【方法】利用同源重组技术敲除plcR基因,多重交叉PCR及RT-PCR鉴定并测序验证。比较野生株与突变株基本生物学特性的差异,小鼠攻毒实验分析plcR基因缺失对细菌毒力的影响。【结果】经RT-PCR证实05SSU0241与05SSU0242共转录,通过多重交叉PCR及RT-PCR证实成功构建plcR基因缺失突变株,基本生物学特性显示突变株的生长速率、菌落形态、溶血活性均无显著改变,小鼠致病性试验结果显示,野生株攻毒的小鼠死亡率为70%,突变株攻毒的小鼠死亡率为40%,毒力较野生株显著降低。【结论】plcR基因作为2型猪链球菌有毒株基因组中特有的外源基因,在细菌致病过程中具有重要作用。     

进口竹荚鱼中单核细胞增生李斯特菌的鉴定及其鞭毛蛋白的原核表达

【目的】对进口竹荚鱼中分离的一株病原菌S1-2进行鉴定,并在大肠杆菌中表达其鞭毛蛋白。【方法】采用全自动微生物鉴定仪和革兰氏阳性菌鉴定卡进行生理生化反应测试,利用iap基因实时荧光PCR特异性扩增检测病原菌。通过PCR技术扩增病原菌S1-2的鞭毛蛋白flaA基因,克隆筛选和测序鉴定后,构建该基因的原核表达质粒pET22b-flaA,镍柱法纯化表达产物,通过免疫印迹鉴定其免疫原性。【结果】分离病原菌为革兰氏阳性菌,生理生化特征与单核细胞增生李斯特菌(Listeria monocytogenes)的相似性为99%,协同溶血实验在靠近金黄色葡萄球菌的接种端溶血增强。SDS-PAGE结果表明融合表达产物分子量约为32 kD,Western blot结果表明重组表达的鞭毛蛋白具有免疫原性。【结论】flaA基因的原核表达为制备单核细胞增生李斯特菌的单克隆抗体及其检测方法的建立奠定了基础。     

江苏省县域森林生态安全评价及空间计量分析

通过考察生态区位因素对森林生态安全的影响,建立评价指标体系,研究其空间相关性的内在效应机制,从而实现森林生态安全的评价与监测。以江苏省80个区县为研究对象,基于2000—2015年面板数据,运用熵权法、专家法及模糊物元法计算森林生态安全指数,然后结合气象类指标及地形类指标计算生态区位系数,再用该系数修正森林ESI,同时结合Arc GIS技术、空间相关性分析、SLM与SEM模型得出如下结论:(1)人口密度、单位面积能源消耗量、退耕还林面积占比等指标权重最大;(2)生态区位系数高值区主要分布在江苏南部少数地区,低值区主要分布在江苏东北部;(3)苏南地区森林生态安全状况整体好于苏北及中东部地区;(4) 2000—2015年,江苏省67.5%的区县森林ESI呈现出较明显下降趋势,反映出江苏省森林生态安全发展状况不容乐观;(5)江苏省县域森林ESI整体空间相关性显著(P≤0.01),但2000—2015年空间聚集程度有所下降,且Low-Low聚类显著性更强;(6)森林ESI在江苏省县域间为扩散效应与回流效应并存。     

乳粉中嗜热菌污染研究进展

嗜热菌是乳粉中的常见污染菌,是影响乳粉品质的一个重要因素。本文综述乳粉中嗜热菌的种类、污染源对乳品工业的危害及其控制手段的研究进展,为国内相关领域研究提供参考。     

粤北南岭大宝山矿流域山水林田湖草修复阻力与优先级分析

遵循“防源、控流、治汇”理念,以粤北南岭大宝山矿区作为风险源,以所在流域为研究区,分析研究区主要阻力因素,采用最小累积阻力模型建立区域生态阻力面;利用Jenks自然断点法,分析生态修复优先级,提出分区治理重点和对策。研究结果表明：研究区综合阻力系数处于9-32之间,各评价指标的阻力面空间分布格局相似,其阻力值呈现出东南部大,西北部小的空间格局;长期的矿业开采污染了流域生态环境,且距离矿区越近的区域生态修复的优先性越高。将研究区分为4个优先级区,各区修复优先性依次为Ⅰ区 > Ⅱ区 > Ⅲ区 > Ⅳ区。Ⅰ区重点在于治水,提高pH、降低重金属有效态含量和增加地表植被覆盖度。Ⅱ区重点在于河流治理与治土,确保污染减排,增强拦泥库的废水调节。Ⅲ区、Ⅳ区核心在治土,逐步改善土壤条件。研究结果为修复项目在时空尺度上落地和科学治理提供科学依据。