PDZ/PDZ interaction between PSD‐95 and nNOS neuronal proteins

N‐Methyl‐D‐aspartate (NMDA) receptors are key components in synaptic communication and are highly relevant in central nervous disorders, where they trigger excessive calcium entry into the neuronal cells causing harmful overproduction of nitric oxide by the neuronal nitric oxide synthase (nNOS) protein. Remarkably, NMDA receptor activation is aided by a second protein, postsynaptic density of 95 kDa (PSD95), forming the ternary protein complex NMDA/PSD95/nNOS. To minimize the potential side effects derived from blocking this ternary complex or either of its protein components, a promising approach points to the disruption of the PSD‐95/nNOS interaction which is mediated by a PDZ/PDZ domain complex. Since the rational development of molecules targeting such protein‐protein interaction relies on energetic and structural information herein, we include a thermodynamic and structural analysis of the PSD95‐PDZ2/nNOS‐PDZ. Two energetically relevant events are structurally linked to a “two‐faced” or two areas of recognition between both domains. First, the assembly of a four‐stranded antiparallel β‐sheet between the β hairpins of nNOS and of PSD95‐PDZ2, mainly enthalpic in nature, contributes 80% to the affinity. Second, binding is entropically reinforced by the hydrophobic interaction between side chains of the same nNOS β‐hairpin with the side chains of α2‐helix at the binding site of PSD95‐PDZ2, contributing the remaining 20% of the total affinity. These results suggest strategies for the future rational design of molecules able to disrupt this complex and constitute the first exhaustive thermodynamic analysis of a PDZ/PDZ interaction.     

樟子松人工林营建对土壤颗粒组成变化的影响

植被恢复是退化生态系统的主要恢复措施,也是人类改善区域生态环境较为重要和直接的活动。目前,针对不同植被恢复方式对干旱半干旱地区土壤理化性质及生物特征开展了大量研究。然而,关于科尔沁沙地樟子松人工林营建对土壤颗粒组成变化的影响却鲜有报道。因此,以辽宁省章古台地区不同生长阶段(包括幼龄林、中龄林、成熟林和过熟林)的20块樟子松人工林样地为研究对象(以临近的7块天然草地为对照),研究了沙地樟子松人工林营建对0—100 cm土层土壤颗粒组成变化的影响。结果表明:沙质草地营建樟子松人工林后,不同土层土壤细颗粒(0.05 mm)含量均呈增加趋势,并且在0—10 cm层增加趋势明显,随土层深度增加土壤细颗粒增加量逐渐降低(除幼龄林外),但樟子松林地土壤颗粒组成仍以砂粒为主,土壤粘粒和粉粒含量极低(仅占5%左右)。随着樟子松人工林林龄的增加,土壤细颗粒变化量在0—10 cm层逐渐升高,而在10—100 cm层并无显著变化趋势。土壤细颗粒含量的变化在10—100 cm层与土壤含水量呈显著正相关,在0—10、20—40 cm和80—100 cm层与土壤全钾极显著负相关,在20—60 cm层与土壤有机碳呈显著正相关,在10—40 cm和80—100 cm层分别与土壤全磷呈显著正相关和负相关。综上所述,樟子松人工林营建可有效提高土壤细颗粒含量且在土壤表层效果明显,但短期内并不会使土壤颗粒组成发生显著变化,樟子松林改善土壤颗粒组成的同时也会使其他土壤因子发生相应的变化。     

Formation and function of phosphatidylserine and phosphatidylethanolamine in mammalian cells

Phosphatidylserine (PS) and phosphatidylethanolamine (PE) are metabolically related membrane aminophospholipids. In mammalian cells, PS is required for targeting and function of several intracellular signaling proteins. Moreover, PS is asymmetrically distributed in the plasma membrane. Although PS is highly enriched in the cytoplasmic leaflet of plasma membranes, PS exposure on the cell surface initiates blood clotting and removal of apoptotic cells. PS is synthesized in mammalian cells by two distinct PS synthases that exchange serine for choline or ethanolamine in phosphatidylcholine (PC) or PE, respectively. Targeted disruption of each PS synthase individually in mice demonstrated that neither enzyme is required for viability whereas elimination of both synthases was embryonic lethal. Thus, mammalian cells require a threshold amount of PS. PE is synthesized in mammalian cells by four different pathways, the quantitatively most important of which are the CDP-ethanolamine pathway that produces PE in the ER, and PS decarboxylation that occurs in mitochondria. PS is made in ER membranes and is imported into mitochondria for decarboxylation to PE via a domain of the ER [mitochondria-associated membranes (MAM)] that transiently associates with mitochondria. Elimination of PS decarboxylase in mice caused mitochondrial defects and embryonic lethality. Global elimination of the CDP-ethanolamine pathway was also incompatible with mouse survival. Thus, PE made by each of these pathways has independent and necessary functions. In mammals PE is a substrate for methylation to PC in the liver, a substrate for anandamide synthesis, and supplies ethanolamine for glycosylphosphatidylinositol anchors of cell-surface signaling proteins. Thus, PS and PE participate in many previously unanticipated facets of mammalian cell biology. This article is part of a Special Issue entitled Phospholipids and Phospholipid Metabolism.     

Chronic morphine exposure and its abstinence alters dendritic spine morphology and upregulates Shank1

Exposure to chronic drugs of abuse has been reported to produce significant changes in postsynaptic protein profile, dendritic spine morphology and synaptic transmission. In the present study we demonstrate alterations in dendritic spine morphology in the frontal cortex and nucleus accumbens of mice following chronic morphine treatment as well as during abstinence for two months. Such alterations were accompanied with significant upregulation of the postsynaptic protein Shank1 in synaptosomal enriched fractions. mRNA levels of Shank1 was also markedly increased during morphine treatment and during withdrawal. Studies of the different postsynaptic proteins at the protein and mRNA levels showed significant alterations in the morphine treated groups compared to that of saline treated controls. Taken together, these observations suggest that Shank1 may have an important role in the regulation of spine morphology induced by chronic morphine leading to addiction.     

Applications and performance of a MALDI-ToF mass spectrometer with quadratic field reflectron technology

A new matrix-assisted laser desorption/ionization time of flight mass spectrometer (MALDI-ToF MS), developed specifically for the identification and characterization of proteins and peptides in proteomic investigations, is described. The mass spectrometer which can be integrated with the 2-D gel electrophoresis workflow is a bench-top instrument, enabling rapid, reliable and unattended protein identification in low-, as well as high-throughput proteomics applications. To obtain precise information on peptide sequences, the instrument utilizes a timed ion gate and a unique quadratic field reflectron (Z2 technology), allowing single-run, post-source decay (PSD) of selected peptides. In this study, the performance of the instrument in reflectron, PSD and linear mode, respectively, was investigated. The results showed that the limit of detection for a single peptide in reflectron mode was 125 amol with a signal to noise ratio exceeding 20. Average mass resolution for peptides larger than 2000 u was around 13,000 full width, half maximum (FWHM). The limit for protein identification during peptide mass fingerprinting (PMF) was 500 amol with a sequence coverage of 18%. Mass error during PMF analysis was less than 15 ppm for 17 out of 25 (68%) identified peptides. In PSD mode, a complete series of y-ions of a CAF-derivatized peptide could be obtained from 3.75 fmol of material. The average mass error of PSD-generated fragments was less than 0.14 u. Finally, in linear mode, intact proteins with molecular masses greater than 300,000 u were detected with mass errors below 0.2%.     

Novel inter-protein cross-link identified in the GGH-ecotin D137Y dimer

In the presence of a suitable oxidizing agent, the Ni(II) complex of glycyl-glycyl-histidine (GGH) mediates efficient and specific oxidative protein cross-linking. The fusion of GGH to the N terminus of a protein allows for the cross-linking reagent to be delivered in a site-specific fashion, making this system extremely useful for analyzing protein-protein contacts in complicated mixtures of biomolecules. Tyrosine residues have been postulated to be the primary amino acid target of this reaction, and using the dimeric serine protease inhibitor ecotin, we previously demonstrated that engineering a tyrosine at the protein interface of a dimer dramatically increased cross-linking efficiency. Cross-linking increased four-fold for GGH-ecotin D137Y in comparison to wild-type GGH-ecotin, presumably through bityrosine formation at the dimer interface. Here we report the first complete structural analysis of the cross-linked GGH-ecotin D137Y dimer. Using a combination of mass spectrometric and chemical derivatization methods, a sole novel cross-link between the N-terminal glycine residues and the engineered tyrosine at position 137 has been characterized. The dimer cross-link is localized to a single site without other protein modifications, but different reaction pathways produce structurally related products. We propose a mechanism that involves covalent bond formation between the protein backbone and a dopaquinone moiety derived from a specific tyrosine residue. This finding establishes that it is not necessary to have two tyrosine residues within close proximity in the protein interface to obtain high protein cross-linking yields, and suggests that the cross-linking reagent may be of more general utility than previously thought.     

A PDZ domain-based detection system for enzymatic assays

A time-resolved fluorescence resonance energy transfer (TR-FRET) detection method based on the formation of a PDZ domain.peptide ligand complex has been developed for enzymatic assays as an alternative to immuno-based detection strategies. The enzyme substrate is a "masked" biotinylated PDZ domain peptide ligand containing the consensus sequence Ser-X-Val-COOH. The critical residues in the binding consensus sequence of the ligand have been modified, for example, by phosphorylation of Ser or C-terminal extensions, providing binding-incompetent PDZ domain peptides. On processing by the corresponding enzyme, the binding epitope is exposed, and the product sequence is recognized specifically by Eu(3+) chelate-labeled GST-PDZ ([Eu(3+)]GST-PDZ) (GST-PDZ-glutathione S-transferase fused to PDZ domain). A ternary complex is subsequently formed by addition of allophycocyanin-labeled streptavidin ([XL665]SA), which binds to the biotinylated N terminus of the peptide, and detected by TR-FRET. Reported here are examples of the applicability of this detection strategy to three enzymatic systems, an endoprotease, an exoprotease, and a Ser/Thr phosphatase.     

突触后致密物基因与孤独症

孤独症是一种病因不明的广泛性发育障碍疾病,它是孤独症谱系障碍的代表疾病,发病年龄早,大多在3岁以内起病,以社会交往障碍,言语交流障碍,动作行为的重复刻板和兴趣范围狭窄为三大临床核心症状。孤独症发病率呈逐年增高趋势,我国患者量已超过一百万。但是迄今为止仍没有特异的方法与手段对孤独症进行彻底有效地诊治,为社会和家庭带来了沉重的负担,因此,其发病机制是迫切需要研究的难题。目前国际上公认为遗传因素在孤独症的发病中起着重要作用,但对于致病基因的确定仍不明确。突触后致密物(PSD)在中枢神经系统神经递质和信息的传递过程中起重要作用,影响学习记忆及认知相关功能,而孤独症患者存在认知相关功能损伤的表现,二者可能存在一定的联系。本文对PSD基因功能以及与孤独症关系的研究加以综述,希望有助于孤独症的病因学研究,以期早日改善该病的诊疗及预防。     

Power spectral density and coherence analysis of Alzheimer’s EEG

In this paper, we investigate the abnormalities of electroencephalograph (EEG) signals in the Alzheimer’s disease (AD) by analyzing 16-scalp electrodes EEG signals and make a comparison with the normal controls. The power spectral density (PSD) which represents the power distribution of EEG series in the frequency domain is used to evaluate the abnormalities of AD brain. Spectrum analysis based on autoregressive Burg method shows that the relative PSD of AD group is increased in the theta frequency band while significantly reduced in the alpha2 frequency bands, particularly in parietal, temporal, and occipital areas. Furthermore, the coherence of two EEG series among different electrodes is analyzed in the alpha2 frequency band. It is demonstrated that the pair-wise coherence between different brain areas in AD group are remarkably decreased. Interestingly, this decrease of pair-wise electrodes is much more significant in inter-hemispheric areas than that in intra-hemispheric areas. Moreover, the linear cortico-cortical functional connectivity can be extracted based on coherence matrix, from which it is shown that the functional connections are obviously decreased, the same variation trend as relative PSD. In addition, we combine both features of the relative PSD and the normalized degree of functional network to discriminate AD patients from the normal controls by applying a support vector machine model in the alpha2 frequency band. It is indicated that the two groups can be clearly classified by the combined feature. Importantly, the accuracy of the classification is higher than that of any one feature. The obtained results show that analysis of PSD and coherence-based functional network can be taken as a potential comprehensive measure to distinguish AD patients from the normal, which may benefit our understanding of the disease.     

Characterization of germin-like protein with polyphenol oxidase activity from Satsuma mandarine

Polyphenol oxidases (PPOs) catalyzing the oxygen dependent oxidation of phenols to quinones are ubiquitously distributed in plants and are assumed to be involved in plant defense against pests and pathogens. A protein with high PPO activity was identified in Satsuma mandarine, extracted with Tris–HCl buffer, purified by salt precipitation and column chromatography, and characterized by mass spectrometry as germin-like protein (GLP), which belongs to pathogenesis related protein (PR) family. In the present study, the structure and enzymatic properties of GLP were characterized using spectroscopy methods. Based on native PAGE analysis, the molecular weight of GLP was estimated to be 108 kDa and GLP was identified as a pentamer containing five subunits of 22 kDa. The optimum pH and temperature for PPO catalyzing activity of GLP was 6.5 and 65 °C, respectively. Kinetic constants were 0.0365 M and 0.0196 M with the substrates catechol and pyrogallol, respectively. The structural characterization of GLP provided better insights into the regions responsible for its PPO activity.