稳定同位素化学标记结合质谱技术在定量蛋白质组学中的应用

传统的蛋白质组定量策略主要是通过双向凝胶电泳来进行相对定量。由于该方法不能对相对分子质量极高或极低、等电点极酸或极碱和含量低的蛋白质以及膜蛋白质等进行有效分离和检测,所以已不能适应目前蛋白质组研究深入发展的需要。近年来,定量蛋白质组学的发展主要是以同位素亲和标签试剂为代表的、以质谱检测为核心的稳定同位素化学标记方法。稳定同位素化学标记结合质谱技术,使定量蛋白质组的分析更趋简单、准确和快速,具有良好的发展前景。本文对稳定同位素化学标记结合质谱技术在定量蛋白质组学中的研究进展进行了评述。     

系统生物学中的数学模型方法及其应用

综述了当前在系统生物学研究领域中常用数学模型的建立和研究方法,介绍了通量平衡分析、基元通量模式、生化系统理论,以及代谢控制分析等模型的理论基础和发展背景,讨论了这些模型之间的联系、区别,以及适用范围,并总结了这些模型在分析代谢网络结构、优化代谢途径、指导菌种改进以提高琥珀酸、色氨酸、乙醇等重要化工品生产率和转化率中的实际应用。     

樟芝的药用保健价值及开发应用(综述)

樟芝是一种原产于台湾的药用真菌,具有解毒抗癌、保肝强心、提高免疫力等功效。本文介绍樟芝的生物学特性、主要化学成分及药用保健价值,并对今后樟芝的开发应用提出建议。     

Comparative morphology of Van der Vecht's organ in Polistes social parasites: host ecology and adaptation of the parasite

Camouflage strategies are common in insect social parasites. Being accepted into an alien colony as a dominant nestmate favours behavioural and morphological adaptations to mimic a specific odour. In Polistes social parasites, abdominal tegumental glands are involved in this camouflage strategy. These glands secreting cuticular hydrocarbons are connected with a modified cuticular area of the last gastral sternite of female wasps, named Van der Vecht's organ, whose secretion is involved in rank and dominance recognition. The size of this exocrine area has been demonstrated to be under selective pressure in Polistes, as a response to an efficient dominance recognition. Because chemical and behavioural integration differs between parasitic species, we carried out a comparison of Van der Vecht's organ size between the three Polistes social parasites and their respective hosts. The parasites Polistes sulcifer and Polistes semenowi, capable of a rapid chemical mimicry and specialized to exploit a lowland host, also show an enlarged Van der Vecht's organ. Conversely, the parasite Polistes atrimandibularis, specialized on a mountain species and showing a slow chemical integration, has a smaller organ. The time available for the parasite to tune up its chemical mimicry, before the emergence of workers to be accepted as a dominant nestmate, appears to be the most important selective pressure acting on the size of this abdominal organ. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013 , 109 , 313–319.     

Grand Molecular Dynamics: A Method for Open Systems

We present a new molecular dynamics method for studying the dynamics of open systems. The method couples a classical system to a chemical potential reservior. In the formulation, following the extended system dynamics approach, we introduce a variable, v to represent the coupling to the chemical potential reservoir. The new variable governs the dynamics of the variation of number of particles in the system. The number of particles is determined by taking the integer part of v. The fractional part of the new variable is used to scale the potential energy and the kinetic energy of an additional particle: i.e., we introduce a fractional particle. We give the ansatz Lagrangians and equations of motion for both the isothermal and the adiabatic forms of grand molecular dynamics. The averages calculated over the trajectories generated by these equations of motion represent the classical grand canonical ensemble (μVT) and the constant chemical potential adiabatic ensemble (μVL) averages, respectively. The microcanonical phase space densities of the adiabatic and isothermal forms the molecular dynamics method are shown to be equivalent to adiabatic constant chemical potential ensemble, and grand canonical ensemble partition functions. We also discuss the extension to multi-component systems, molecular fluids, ionic solutions and the problems and solutions associated with the implementation of the method. The statistical expressions for thermodynamic functions such as specific heat; adiabatic bulk modulus, Grüneissen parameter and number fluctuations are derived. These expressions are used to analyse trajectories of constant chemical potential systems.     

Combined strategies for liposome characterization during in vitro digestion

Three types of pyranine (HPTS)-containing liposomes were prepared by high-pressure homogenization under optimized conditions. At 37°C, they were 1) fluid-state vesicles made from soybean phosphatidylcholine (SPC), 2) gel-state liposomes made from hydrogenated SPC (HSPC), and 3) solid-disordered membranes obtained from HSPC and cholesterol (HSPC-Chol). These liposome formulations were characterized before, during, and after in vitro digestion, which involved the presence of pH gradients, enzymes, and bile salts. Mean sizes and size distributions of the vesicles were determined by DLS; ³¹P-NMR (nuclear magnetic resonance) was used to quantify lyso-PC forms; internal pH was monitored throughout digestion with two different fluorescent pH probes; and changes in bilayer permeability and HPTS encapsulation were determined by size-exclusion chromatography and fluorimetry. Differential scanning calorimetry analysis was also performed in order to study the effect of digestion on HSPC vesicles. SPC liposomes were physically stable during digestion; they presented 8% lyso-forms and an HPTS encapsulation around 85% after in vitro digestion. However, they were extremely permeable to ions, so that the internal pH immediately equilibrated with the bulk pH. HSPC liposomes were the most affected by the digestive process. Even though they were chemically stable, as inferred from the low lyso-PC content, very important changes in their size distribution were observed. A final 50% HPTS leakage was quantified after in vitro digestion. Nevertheless, they were the least permeable to protons under pH gradients. HSPC-Chol vesicles presented intermediate permeability to protons, having their internal pH decreased from approximately 6.8 to 4.6 after 1 hour of incubation at pH 2. This was the most chemically stable formulation and showed the highest encapsulation, even after in vitro digestion. Therefore, HSPC-Chol liposomes would be the most adequate choice for the design of lipid products for oral administration.     

Characterization of Carbonic Anhydrase Isozyme CA2, Which Is the CAH2 Gene Product,in Chlamydomonas reinhardtii

From high-CO₂ (5% CO₂) grown unicellular green alga, Chlamydomonas reinhardtii, carbonic anhydrase (CA) was isolated by affinity chromatography and characterized. Isolated CA was identified as an isozyme (CA2) which is the product from the second gene CAH2 by peptide sequencing. The CA2 was inactivated by dithiothreitol. This treatment caused dissociation of CA2 into the large (38 kDa) and small subunits (4243 Da). The molecular mass of the CA2 holoenzyme measured by low-angle laser light-scattering photometry and precision differential refractometry combined with gel-filtration HPLC was 87.9 kDa. These results and gene structure indicate that CA2 is a heterotetramer consisting of two large and two small subunits linked by disulfide bonds like CA1, which is the CAH1 gene product. The speciffc activity of CA2 purified by anion-exchange HPLC was 3300 units per mg protein, which was approximately 1.6 times higher than that of CA1. Therefore, it was concluded that two structurally related isozymes, CA1 and CA2, are present in the wild type cells of C. reinhardtii and differentially regulated by the atmospheric CO₂ concentration.     

A probabilistic model for secondary structure prediction from protein chemical shifts

Protein chemical shifts encode detailed structural information that is difficult and computationally costly to describe at a fundamental level. Statistical and machine learning approaches have been used to infer correlations between chemical shifts and secondary structure from experimental chemical shifts. These methods range from simple statistics such as the chemical shift index to complex methods using neural networks. Notwithstanding their higher accuracy, more complex approaches tend to obscure the relationship between secondary structure and chemical shift and often involve many parameters that need to be trained. We present hidden Markov models (HMMs) with Gaussian emission probabilities to model the dependence between protein chemical shifts and secondary structure. The continuous emission probabilities are modeled as conditional probabilities for a given amino acid and secondary structure type. Using these distributions as outputs of first‐ and second‐order HMMs, we achieve a prediction accuracy of 82.3%, which is competitive with existing methods for predicting secondary structure from protein chemical shifts. Incorporation of sequence‐based secondary structure prediction into our HMM improves the prediction accuracy to 84.0%. Our findings suggest that an HMM with correlated Gaussian distributions conditioned on the secondary structure provides an adequate generative model of chemical shifts. Proteins 2013; © 2012 Wiley Periodicals, Inc.     

Substrate‐shielding and hydrolytic reaction in hydrolases

In general, transferases undergo large structural changes and sequester substrate molecules, to shield them from water. By contrast, hydrolases exhibit only small structural changes, and expose substrate molecules to water. However, some hydrolases deeply bury their substrates within the proteins. To clarify the relationship between substrate‐shielding and enzymatic functions, we investigated 70 representative hydrolase structures, and examined the relative accessible surface areas of their substrates. As compared to the hydrolases employing the single displacement reaction, the hydrolases employing the double displacement reaction bury the substrate within the proteins. The exo hydrolases display significantly more substrate‐shielding from water than the endo hydrolases. It suggests that the substrate‐shielding is related to the chemical reaction mechanism of the hydrolases and the substrate specificity. Proteins 2013; © 2012 Wiley Periodicals, Inc.