The role of mammalian autophagy in protein metabolism

Autophagy is in principle a non-selective degradation system within cells, which is conserved in all eukaryotic cells. Autophagy is usually suppressed at low levels but can be upregulated during periods of nutrient starvation, which facilitates cell survival. In addition to this fundamental role, basal autophagy was recently revealed to be important for constitutive turnover of intracellular proteins and organelles. Autophagy has been considered to be involved also in presentation of endogenous antigens, degradation of invasive bacteria, tumor suppression, cell death and development. This review will discuss the biological significance of autophagy, particularly focusing on its implications in protein metabolism in mammals.     

Specificity of Cyanine Dye L-21 Aggregation in Solutions with Nucleic Acids

Optical spectroscopy experiments were used to study the features of cyanine dye 3,3′-dimethyl-9-(2-thienyl)-thiacarbocyanine iodide (L-21) aggregation in binary solutions DMF:Tris–HCl buffer (pH = 8) containing nucleic acids (DNA or RNA). The appearance of absorption and luminescence bands associated with J-aggregates and dimers that are formed within the minor groove of DNA has been observed. The model of L-21 J-aggregate structure is proposed. It has been found that dimers are the building blocks of L-21 J-aggregates. Disorientation in dimers caused by the minor groove curvature is reason of observation of Davydov splitting in absorption spectrum of L-21 J-aggregates. In the solution containing DNA the absorption and luminescence bands of L-21 J-aggregates exhibit the specific properties that allows the dye L-21 to be used as a fluorescent probe for DNA detection.     

亮氨酸与异亮氨酸的低频集体振动的太赫兹光谱研究

太赫兹(THz)波是指频率在0.1～10 THz频段的电磁波。太赫兹光谱技术不同于以往的检测手段,可以用于检测氨基酸同分异构体,反映物质的分子结构和构型,对食品安全和药品药性控制有着重要的意义。亮氨酸与异亮氨酸属于同系的同分异构体,它们具有近似的分子结构,但物理化学性质有很大的差别。生物大分子的太赫兹吸收与其分子间氢键和分子内氢键的振动和转动能级相关的偶极跃迁有关,可以利用分子偶极跃迁进行生物分子的指纹识别。采用太赫兹时域光谱(THz-TDS)和傅里叶红外光谱(FTIR),对亮氨酸和异亮氨酸进行了测量。在中红外波段亮氨酸与异亮氨酸的吸收光谱几乎完全重叠,而在太赫兹频波段可以观察到它们的光谱存在明显差异,因此太赫兹光谱能够作为快速准确鉴别这两种物质的方法。采用密度泛函理论(DFT)对亮氨酸和异亮氨酸的低频集体振动模式进行理论模拟,并对其太赫兹光谱进行研究和讨论。通过比较实验和理论结果,计算得到的峰位与实验结果可以互相印证。     

Effects of pressure and temperature on the solubility of monosodium L-glutamate monohydrate in water

Abstract

The solubility of monosodium L-glutamate monohydrate (MSG.H₂O) in water was measured at pressures in the range of 0.10-300MPa and 298.15K. The density of MSG solution at high concentrations and heat of solution at saturated concentration were also measured at atmospheric pressure. The solubility, m_s, increased with increasing pressure and the pressure coefficient, Θ_p, [?(? In m_s,? p)_T] at 0.10 MPa was (2.0 ± 0.1) × 10-¹⁰Pa-1. It agrees well with (2.1 ±0.2)× 10-¹⁰ Pa-¹ thermodynamically estimated using the partial molar volume, the activity coefficient of the solute in solution, and the molar volume of the crystal. The excellent agreement at 0.10MPa gives us confidence in the solubility data at higher pressures. The heat of solution data and other pertinent values were used to calculate the temperature coefficient of solubility, Θ_T [? (? In m_s/?(1/T))_p], by a thermodynamic equality. The resulting Θ_T compares well with the data directly measured by Ogawa.     

Passivation of aluminum with alkyl phosphonic acids for biochip applications

Self-assembly of decylphosphonic acid (DPA) and octadecylphosphonic acid (ODPA) was studied on aluminum films using XPS, ToF-SIMS and surface wettability. Modified aluminum films were tested for passivation against silanization and subsequent oligonucleotide attachment. Passivation ratios of at least 450:1 compared to unprotected aluminum were obtained, as quantified by attachment of radio-labeled oligos.     

氨基酸官能团的太赫兹振动模式研究

对比于氨基酸的红外分析法,太赫兹波的电子能量更低,可实现无损检测。氨基酸分子内原子振动、分子间氢键的作用、以及晶体中晶格的低频振动均处于太赫兹波段,使其在太赫兹波段具有吸收峰,且不同的氨基酸分子太赫兹吸收峰不同,故可用氨基酸在太赫兹波段的这种“指纹特性”实现氨基酸类物质的定性分析。量子化学分析方法可以应用量子力学的基本原理和方法,研究稳定和不稳定分子的结构、性能及其之间的关系,还可以针对分子与分子间的相互作用、相互碰撞及相互反应等问题进行研究。通过量子化学计算方法计算氨基酸分子的太赫兹吸收谱,可以为氨基酸分子的太赫兹吸收峰匹配分子振动模式,对氨基酸定性分析有一定参考性与指向性,并为实验获取的样品太赫兹时域光谱提供理论支撑,在实验获得太赫兹吸收谱的基础上进行量子化学计算,还能为实验结果进行验证。首先利用太赫兹时域光谱技术获取了谷氨酰胺、苏氨酸、组氨酸的太赫兹吸收谱,分别构建这三种氨基酸样品在实物中以两性离子形式存在的单分子构型,利用量子化学计算方法在完成结构优化后进行太赫兹吸收谱模拟计算。计算结果表明三种氨基酸单分子的太赫兹吸收谱计算结果与实验获取的太赫兹吸收谱差异较大,但在高频段吸收峰峰位基本吻合。通过GaussView分别查看了这三种氨基酸分子在太赫兹段内的吸收峰对应频率处的振转情况,发现在高频段内三种氨基酸分子官能团均只发生转动而未见振动,并且转动模式基本一致。通过对氨基酸官能团的太赫兹吸收谱进行量子化学计算,将官能团在高频段内吸收峰对应频率处的振转模式与三种氨基酸分子在该段内吸收峰对应频率处的振转模式做了对比。研究表明,在氨基酸单分子构型下由量子化学方法计算所得的太赫兹吸收谱中,高频段内计算得出的模拟吸收峰与实验获取的太赫兹吸收峰基本吻合;振转模式分析发现,谷氨酰胺、苏氨酸、组氨酸在太赫兹高频段内的氨基酸官能团振转模式相同,三种氨基酸分子在高频段内的吸收峰主要来源于氨基酸官能团。因此,结合量子化学计算与太赫兹吸收谱可以实现氨基酸类物质的定性分析。     

二元羧酸的化学结构与其抑制草酸钙结晶能力研究

采用X射线衍射(XRD)、傅里叶红外光谱(FTIR)和扫描电镜(SEM)研究了相距3个C—C键长具有不同取代基的二元羧酸对草酸钙(CaOxa)晶体生长的影响。这些二元酸包括丁二酸、顺丁二烯酸、反丁二烯酸、苹果酸、天冬氨酸和酒石酸。它们均能抑制一水草酸钙(COM)晶体的聚集,减小COM比表面积,并诱导二水草酸钙(COD)生成,其能力随二元酸上取代的—OH或—NH₂基数量增加而增强。从二元羧酸化学结构讨论了其影响草酸钙结晶效果的分子机理,对COM生长具有最佳抑制效果的羧酸是含有HOOC—CH(R)—CH₂—COOH(ROH或NH₂)分子的化合物。实验结果可为临床上寻找新的防石药物提供参考。     

Experimental evidence of chiral crown ether complexation with aromatic amino acids

The complexation of L ‐ and D ‐enantiomers of phenylglycine, phenylalanine, and tryptophan with D ‐mannonaphto‐crown‐6‐ether in methanol solution was studied by NMR and isothermal titration calorimetry (ITC) at 298.15 K. The total heat effects attributed to the binding phenomena were measured in the range of 1.8 to 7.7 mJ, and the complexation was found stereo‐specific. The binding topologies were estimated basing on ¹H 2D‐ROESY experiments. The analysis of Job plots obtained from ¹H NMR‐monitored titrations proved the coexistence of 1:1 and 1:2 (crown ether:amino acids) complexes, which thermodynamic parameters, K_s, ΔG, ΔH°, and TΔS were determined with the aid of ITC. The 1:1 complexes were found enthalpically stabilized, generally by electrostatic interactions between the charged NH group of amino acid and crown ether macrocyclic moiety, while the binding of the second amino acid molecule was driven entropically due to solvatophobic effect. Strong enthalpy–entropy compensation points towards the uniform binding mode of all complexes studied. The mode of complex formation was found solvent dependent. For phenylalanine guest studied in various solvent systems, in contrast to the aqueous media, the noticeable chiral recognition is observed in methanol solution, and the complex stoichiometry (1:2 ether:Phe) differs from the 2:1 one, determined previously for the same host‐guest system in water (J. Thermal. Anal. Cal. 2006; 83: 575–578). Copyright © 2007 John Wiley & Sons, Ltd.     

Adsorption of dicarboxylic acids onto nano‐structured silver surfaces – surface‐enhanced Raman scattering studies of pH‐dependent adsorption geometries

Understanding and shaping adsorption orientations of molecular compounds on nano‐structured metallic surfaces is an important issue across many areas of contemporary research including the design of nano‐structured surfaces and catalytic processes. Here, we used surface‐enhanced Raman spectroscopy to study these orientations on nano‐structured silver surfaces using dicarboxylic acids (maleic acid and fumaric acid) as model substances. Results revealed a clear pH dependence of the observed adsorption geometries of dicarboxylic acids correlating well with the dissociation states of the two acidic groups. Our data demonstrate the potential of the technique and contribute to an improved understanding of adsorption orientations of molecules at the interface between nano‐structured metal surfaces and a liquid phase. Copyright © 2012 John Wiley & Sons, Ltd.     

红外光谱结合二维相关分析研究堆肥过程腐殖酸演化规律

堆肥材料中腐殖酸的组成和结构直接影响堆肥产品品质和腐熟度。为研究堆肥腐殖酸的组成和形成过程,进行了生活垃圾堆肥并提取了不同堆肥阶段样品中的胡敏酸和富里酸,采用红外光谱和二维相关分析,探讨了堆肥过程胡敏酸、富里酸的组成、结构及随时间演化规律。红外光谱结果显示,堆肥胡敏酸组成复杂,在2 917～2 924,2 844～2 852,2 549,1 662,1 566,1 454,1 398,1 351,990～1 063,839,711 cm-1均出现了吸收峰;相对于胡敏酸,堆肥富里酸结构简单,仅在1 725,1 637,990 cm-1出现了吸收峰。上述吸收峰的出现表明堆肥胡敏酸和富里酸均含有木质素来源的苯环和糖类结构,但胡敏酸还含有丰富的脂族和蛋白类结构,这些在富里酸中含量较低;堆肥过程糖类、脂类、蛋白类及木质素结构均发生了降解,但是在胡敏酸和富里酸中它们的降解优先顺序不同。二维相关光谱分析结果表明,胡敏酸中降解先后顺序为脂肪类—蛋白类—多糖类和木质素,而富里酸中为蛋白质—多糖和脂肪类,降解过程均生成了羧酸、酮类和酯类结构,其中羧酸类物质一部分在堆肥中形成了碳酸盐。研究结果表明,红外光谱结合二维相关分析不仅可以获得堆肥腐殖酸官能团组成,还可以揭示堆肥过程这些官能团降解顺序,确定堆肥腐殖酸合成机制和动力学过程。