一种规模化蛋白质组分离和鉴定新方法研究及其应用

建立了一种规模化的蛋白质组分离和鉴定新方法。通过对在生命发育过程中具有重要研究价值的人胎肝线粒体蛋白质组的分离分析，表明与毛细管液-质联用的不同分离方法的组合可以增大检测动态范围和分辨率。研究共鉴定了2977个肽段，归属于915种蛋白质。去除批次间冗余后，鉴定的蛋白质为477种，其中291种为唯一蛋白质，186种为蛋白质簇，144种蛋白质明确定位于人胎肝线粒体中。所鉴定蛋白质的分子量分布范围为7000Da～330000 Da，pI值分布在4．0～11．89，克服了两维凝胶电泳在分子量和pH方面的歧视性问题。实验中发现的蛋白质簇以及确定一种蛋白质需要最少肽段数的问题还需要进一步研究。     

Cysteine and histidine shuffling: mixing and matching cysteine and histidine residues in zinc finger proteins to afford different folds and function

Zinc finger proteins utilize zinc for structural purposes: zinc binds to a combination of cysteine and histidine ligands in a tetrahedral coordination geometry facilitating protein folding and function. While much is known about the classical zinc finger proteins, which utilize a Cys(2)His(2) ligand set to coordinate zinc and fold into an anti-parallel beta sheet/alpha helical fold, there are thirteen other families of 'non-classical' zinc finger proteins for which relationships between metal coordination and protein structure/function are less defined. This 'Perspective' article focuses on two classes of these non-classical zinc finger proteins: Cys(3)His type zinc finger proteins and Cys(2)His(2)Cys type zinc finger proteins. These proteins bind zinc in a tetrahedral geometry, like the classical zinc finger proteins, yet they adopt completely different folds and target different oligonucleotides. Our current understanding of the relationships between ligand set, metal ion, fold and function for these non-classical zinc fingers is discussed.     

NMR of membrane-associated peptides and proteins

In living cells, membrane proteins are essential to signal transduction, nutrient use, and energy exchange between the cell and environment. Due to challenges in protein expression, purification and crystallization, deposition of membrane protein structures in the Protein Data Bank lags far behind existing structures for soluble proteins. This review describes recent advances in solution NMR allowing the study of a select set of peripheral and integral membrane proteins. Surface-binding proteins discussed include amphitropic proteins, antimicrobial and anticancer peptides, the HIV-1 gp41 peptides, human alpha-synuclein and apolipoproteins. Also discussed are transmembrane proteins including bacterial outer membrane beta-barrel proteins and oligomeric alpha-helical proteins. These structural studies are possible due to solubilization of the proteins in membrane-mimetic constructs such as detergent micelles and bicelles. In addition to protein dynamics, protein-lipid interactions such as those between arginines and phosphatidylglycerols have been detected directly by NMR. These examples illustrate the unique role solution NMR spectroscopy plays in structural biology of membrane proteins.     

A rat brain protein expression map including cytosolic and enriched mitochondrial and microsomal fractions

Proteomics is a powerful tool to screen brain protein expression but the methodology is hampered by low abundance of proteins or compartmentalization or overload of high-abundance proteins. It was therefore the aim of the study to determine the expression of brain proteins by using enriched cellular subfractions and pre-electrophoretic chromatographical separation of brain homogenates. We used two-dimensional electrophoresis with subsequent matrix-assisted laser desorption/ionization (MALDI) detection and characterization of brain proteins. Subfractionation into cytosolic, mitochondrial and microsomal compartments was performed by ultracentrifugation. Pre-electrophoretic fractionation of the cytosolic fractions was carried out by ion exchange column chromatography. We detected and identified a large series of 437 proteins in rat brain and have shown proteins specific for the individual subcellular compartments. These proteins included housekeeping, signaling, cytoskeletal, intermediary metabolism, antioxidant proteins on the one and neuron and synaptosomal specific proteins on the other hand. Using fractionations of brain homogenates we were able to improve the power of the method on forming the basis for brain protein expressional studies and providing a reference map as a powerful tool for the neuroscientist.     

Gelation and interfacial behaviour of vegetable proteins

Recent studies on gelation and interfacial properties of vegetable proteins are reviewed. Attention is focused on legume proteins, mainly soy proteins, and on wheat proteins. The rheological properties of vegetable protein gels as a function of heating time or temperature is discussed as well as the interfacial gelation upon adsorption of soy and wheat proteins at the air/water interface. It is shown that modification of proteins improves protein functionality and application.     

快速老化模型小鼠血清蛋白质组学分析比较

以6月及12月龄SAMP 8及同龄SAMR 1为研究对象, 应用双向凝胶电泳法, 分析比较了快速老化模型小鼠(Senescence accelerated mice, SAM)的快速老化亚系SAMP 8及抗快速老化亚系SAMR 1血清蛋白表达的差异. 与同龄SAMR 1比较, 6月龄SAMP 8血清中有15个蛋白点表达显著上调, 3个蛋白点表达显著下调, 7个蛋白点只在SAMP 8中有表达; 12月龄SAMP 8血清中有9个蛋白点表达显著上调, 7个蛋白点表达显著下调, 12个蛋白点只在SAMP 8中有表达. 应用质谱进行肽质量指纹图谱分析和数据库检索共鉴定了19种蛋白质. 其中6个蛋白只在6月龄SAMP 8中表达, 4个蛋白只在12月龄SAMP 8中表达. 此外, 在6月龄及12月龄SAMP 8血清差异蛋白中, 存在9个共同的差异蛋白, 按照功能可分为4类: (1) 免疫相关蛋白; (2) 老化相关蛋白; (3) 糖代谢及神经元凋亡相关蛋白; (4) 其它蛋白. 上述研究结果显示, SAMP 8和SAMR 1血清蛋白表达存在明显差异, 其中一些差异蛋白可能是SAMP 8老化进程中相关病理生理变化的重要原因.     

Shape transitions in lipid membranes and protein mediated vesicle fusion and fission

In the cell, the plasma membrane is often densely decorated by transmembrane proteins. The morphology and dynamics of the membrane are strongly influenced by the presence of proteins. In this paper, we use a coarse-grained model to explore the composite membrane-protein system and develop a simulation methodology based on thermodynamic integration to examine free energy changes during membrane shape transitions. The authors show that a critical concentration of conical membrane proteins or proteins with nonzero spontaneous curvature can drive the formation of small vesicles. The driving force of vesicle budding stems from the preference of proteins to gather in regions of high curvature. A sufficiently high concentration of proteins therefore can influence the topology of the membrane. The biological significance of our results is discussed.     

An effective and in-situ method based tresyl-functionalized porous polymer material for enrichment and digestion of membrane proteins and its application in extraction tips

Membrane proteins are one of promising targets for drug discovery because of the unique properties in physiological processes. Due to their low abundance and extremely hydrophobic nature, the analysis of membrane proteins is still a great challenge. In this work, an effective and in-situ method were developed to enrich and digest membrane proteins by adopting tresyl-functionalized porous polymer material. With tresyl groups, the material can effectively immobilize membrane proteins via covalent bonding on the surface. The material became a facile carrier to enrich membrane proteins from the rat liver in detergents and organic solvents owing to its outstanding binding capacity and excellent biocompatibility. Moreover, it was further applied in extraction tips to capture and in-situ digest the pretreatment membrane proteins in two different solutions. A total of 600 membrane proteins (51% of total protein groups) and 359 transmembrane proteins were identified by nano-LC-ESI-MS/MS in 4% sodium dodecyl sulfate (SDS), and similar results were achieved in the 60% methanol solution. All these results demonstrated that the new approach is of great promise for large-scale characterization of membrane proteins.     

Chemistry and function of human plasma proteins

Human blood plasma contains a large number of proteins. New analytical and preparative techniques have so far permitted the isolation of more than one hundred such proteins; about ninety percent of these were first characterized in the last 30 years. The plasma proteins include components of the clotting and complement systems as well as proteinase inhibitors, immunoglobulins, lipoproteins, and carrier proteins. The biological function of some of the plasma proteins is not yet known. Deficiency of one or more plasma proteins usually causes serious health disorders, the best known example being hemophilia. Several biologically active proteins can be gained from blood plasma; these proteins—for example the blood clotting factors—are of great prophylactic and therapeutic importance and allow a better exploitation of the valuable plasma than can be obtained by means of transfusion.     

Shape, flexibility and packing of proteins and nucleic acids in complexes

Determining the change in topological properties like shape, flexibility and packing of proteins and nucleic acids on complexation is important in characterizing the role of induced structural changes and various interactions which control the functional specificity of proteins and nucleic acids. To this end, we have analyzed and compared the three dimensional structures of several protein-protein, protein-DNA and protein-RNA complexes available in the Protein Data Bank (PDB) and the Nucleic Acid Data Bank (NDB). The size of complexed proteins and nucleic acids, as measured by the radius of gyration, follows Flory's scaling law. The change in the scaling exponents for proteins, RNA and DNA reflects the changes in their respective sizes due to complexation. The anisotropy in the shape of proteins, DNA and RNA in complexes is measured by considering the asphericity and shape parameter, which are calculated from the eigenvalues of the moment of inertia tensor. The distribution of asphericity and shape shows that complexed proteins are mostly spherically symmetrical, while DNA and RNA in complexed states are largely prolate and considerably more aspherical compared to the proteins. Persistence length characterizes the intrinsic flexibility/rigidity of proteins and nucleic acids. The flexibility of all biomolecules decreases with the chain length. For small DNA molecules (6-147 base pairs), persistence length is larger compared to RNA and proteins in protein-protein and protein-RNA complexes. The flexibility of DNA increases, while RNA decreases, in their respective complexed states as compared to that of proteins which remain almost unchanged. The two body contact analysis confirms that the side-chain-backbone contacts are predominant compared to sidechain-sidechain and backbone-backbone contacts in the complexed proteins. The average packing density of proteins decreases in their complexed states, which is measured by the mean value of the contact density of their alpha carbon atoms. The average number of hydrogen bonds are found to be less in the interface region of protein-protein complexes compared to that in protein-DNA and protein-RNA complexes.     

Analysis of expression and comparative profile of normal placental tissue proteins and those in preeclampsia patients using proteomic approaches

Preeclampsia (PE) is a complex and serious condition of pregnancy. Trophoblasts in human placenta can be separated and collected by laser capture micro-dissection (LCM). Protein in trophoblasts have been extracted and separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), finally 962 unique proteins are identified by liquid chromatography coupled to mass spectrometry (LC-MS/MS). Comparison of differential expressed proteins in normal and those in PE are investigated. Two-dimensional electrophoresis (2DE) and MS were used to identify differential expressed proteins. 13 differential expressed proteins include signal transduction protein, molecular chaperone, cell skeleton proteins are identified, in which 3 proteins are down-regulated and 10 proteins are up-regulated. They might be correlated with the cause of PE.     

4-(2-苄氧基乙氧基羰基)氧杂环丁-2-酮的合成及表征

通过16例人肺鳞癌和小细胞肺癌组织中表达蛋白的二维电泳分离和质谱分析,经数据库检索鉴定了53个蛋白,其中24个蛋白与肺癌发病机制相关,4个蛋白在其它癌症中有报道,表达呈现差异的蛋白点有44个,其中34个在表达量上有差异,lO个蛋白在鳞癌和小细胞癌间表现为有和无的关系,蛋白功能分析提示人肺鳞癌与小细胞癌的蛋白质组表达存在差异,分析这些差异蛋白有利于肺癌分型及其生物标志物研究。     

Quantification of chitinase and thaumatin-like proteins in grape juices and wines

Chitinases and thaumatin-like proteins are important grape proteins as they have a great influence on wine quality. The quantification of these proteins in grape juices and wines, along with their purification, is therefore crucial to study their intrinsic characteristics and the exact role they play in wines. The main isoforms of these two proteins from Chardonnay grape juice were thus purified by liquid chromatography. Two fast protein liquid chromatography (FLPC) steps allowed the fractionation and purification of the juice proteins, using cation exchange and hydrophobic interaction media. A further high-performance liquid chromatography (HPLC) step was used to achieve higher purity levels. Fraction assessment was achieved by mass spectrometry. Fraction purity was determined by HPLC to detect the presence of protein contaminants, and by nuclear magnetic resonance (NMR) spectroscopy to detect the presence of organic contaminants. Once pure fractions of lyophilized chitinase and thaumatin-like protein were obtained, ultra-HPLC (UHPLC) and enzyme-linked immunosorbent assay (ELISA) calibration curves were constructed. The quantification of these proteins in different grape juice and wine samples was thus achieved for the first time with both techniques through comparison with the purified protein calibration curve. UHPLC and ELISA showed very consistent results (less than 16% deviation for both proteins) and either could be considered to provide an accurate and reliable quantification of proteins in the oenology field.     

Extensive fractionation and identification of proteins within nasal lavage fluids from allergic rhinitis and asthmatic chronic rhinosinusitis patients

Allergic rhinitis (AR), chronic rhinosinusitis (CRS), and asthma are prevalent airway diseases that can have a substantial impact on a patient's quality of life. MS analyses of biological fluids can effectively screen for proteins associated with disease processes, however, initial detection of diagnostic proteins is difficult due to protein complexity and dynamic range. To enhance the detection of lower abundance proteins, intact nasal lavage fluid (NLF) proteins from nonpolypoid AR and from asthmatic CRS patients were extensively fractionated prior to LC/MS/MS analysis. Pooled NLF samples were processed to remove low molecular weight molecules and high abundance plasma proteins. Anion exchange (AX) chromatography followed by RP‐LC further separated the remaining intact NLF proteins. The resulting fractions were digested with trypsin and the peptides analyzed by LC/MS/MS. Spectra were searched with MASCOT, SEQUEST, and X!Tandem to obtain peptide identifications and subsequently analyzed by Scaffold software to identify parent proteins with at least 99% confidence. The 197 identified proteins are compared to those previously cited in the literature and the workflow evaluated to determine the usefulness for the detection of lower abundance proteins. This is the first extensive list of NLF proteins generated from CRS patients with coexisting asthma.     

Separation and characterization of proteins from green and etiolated shoots of rice (Oryza sativa L.): towards a rice proteome

Proteins extracted from green and etiolated shoots of rice were separated by two-dimensional polyacrylamide gel electrophoresis and relative molecular weights and isoelectric points were determined. The separated proteins were electroblotted onto a polyvinylidene difluoride membrane and 85 proteins were analyzed by a gas-phase protein sequencer. The N-terminal amino acid sequences of 21 out of 85 proteins were determined in this manner. N-terminal regions of the remaining proteins could not be sequenced. The internal amino acid sequences of proteins were determined by sequence analysis of peptides obtained by the Cleveland peptide mapping method and compared with those of known plant and animal protein sequences to understand the nature of the proteins. Green shoots revealed the presence of photosynthetic proteins as expected; however, as etiolated shoots were not photosynthetic, only precursors of the photosynthetic proteins were identified. Interestingly, the presence of L-ascorbate peroxidase only in etiolated shoots suggests a cellular protectant function for this antioxidant enzyme in the etiolating shoots. Using this experimental approach, we could identify the major proteins involved in growth regulation in photosynthetic green shoots as well as in etiolating rice seedlings.     

Methods for imaging and analyses of intracellular organelles using fluorescent and luminescent proteins.

One of the important features of eukaryotic cells is the presence of intracellular compartments, organelles. Each organelle plays an essential role in the organelle-specific function; each cooperates with others for maintaining the vital activity of living cells. To analyze the organelle-specific functions, researchers have used many fluorescent and luminescent reporter proteins extensively. The reporter proteins have provided unprecedented insights into the movement of proteins and their interactions in the organelles. In this review, we summarize recently validated methods for visualizing protein localization, dynamics and protein-protein interactions, and for identifying a series of proteins localized in organelles using newly developed reporter proteins.     

Current developments on beta-barrel membrane proteins: sequence and structure analysis, discrimination and prediction

beta-barrel membrane proteins perform a variety of functions, such as mediating non-specific, passive transport of ions and small molecules, selectively passing the molecules like maltose and sucrose and are involved in voltage dependent anion channels. Understanding the structural features of beta-barrel membrane proteins and detecting them in genomic sequences are challenging tasks in structural and functional genomics. In this review, with the survey of experimentally known amino acid sequences and structures, the characteristic features of amino acid residues in beta-barrel membrane proteins and novel parameters for understanding their folding and stability will be described. The development of statistical methods and machine learning techniques for discriminating beta-barrel membrane proteins from other folding types of globular and membrane proteins will be explained along with their relative importance. Further, different methods including hydrophobicity profiles, rule based approach, amino acid properties, neural networks, hidden Markov models etc. for predicting membrane spanning segments of beta-barrel membrane proteins will be discussed. In addition, the applications of discrimination techniques for detecting beta-barrel membrane proteins in genomic sequences will be outlined. In essence, this comprehensive review would provide an overall picture about beta-barrel membrane proteins starting from the construction of datasets to genome-wide applications.     

New and missing proteins in the electromagnetic and thermal stimulation of biosynthesis

Electromagnetic (EM) or thermal stress (HS) result in altered patterns of biosynthesis that are characterized by new and missing proteins. With both EM and HS stresses, proportionally more new low molecular weight (MW) proteins are synthesized and the distribution of their mass is skewed to lower molecular weights. These observations suggest that the new proteins could be the result of an interruption (i.e., early termination) of biosynthesis. The missing proteins are distributed as the control proteins in unexposed samples and are largely negative for all molecular weights. In contrast, the new proteins are distributed symmetrically with regard to 6.0 < pI < 6.5, and smaller molecules are more highly charged, both positively and negatively. The number of new proteins divided by the amount of new protein, a measure of diversity of product, increases with the frequency or repeat rate of the EM stimulation while the number of missing proteins decreases. These data are in accord with the electrochemical model in that interference should increase with both the frequency of the EM and the charge on the molecules, and result in smaller polypeptides than in the control cells. The results on HS appear to follow the same pattern as the EM experiments, indicating that electrochemical properties affect the responses to thermal stimuli.     

Cullin-based ubiquitin ligase and its control by NEDD8-conjugating system

Several studies have examined the importance of ubiquitin-like posttranslational modifiers (which consist of an unexpectedly large family). Of these, NEDD8 (also called Rub1, related to ubiquitin 1) with a high homology to ubiquitin is covalently linked to all members of cullin (Cul)-family proteins through an enzymatic cascade analogous to ubiquitylation. Cul-family proteins are scaffold proteins for a wide series of ubiquitin-protein ligase complexes, such as SCFs (Skp1, Cul-1, Roc1, and F-box proteins), which regulate the degradation of broad range of cellular proteins. Unlike ubiquitin, which mostly acts as a degradation signal for the target proteins, NEDD8 acts as an activation signal for Cul-family proteins; i.e., Cul-based ubiquitin-protein ligases. Accordingly, the NEDD8 conjugation pathway regulating Cul-protein function is responsible for a diverse array of biologically important processes, such as the cell cycle progression, signalling cascades and developmental programs. Furthermore, recent studies have revealed that the COP9/Signalosome complex interacts physically and genetically with Cul-family proteins, and catalyzes deconjugation of NEDD8 ligated to Cul-family proteins. This review summarizes recent advances in biochemical and genetic studies on how the NEDD8-modifying system regulates Cul-family proteins and their physiology.     

Modification of proteins with cyclodextrins prevents aggregation and surface adsorption and increases thermal stability

This work describes a general approach for preventing protein aggregation and surface adsorption by modifying proteins with β-cyclodextrins (βCD) via an efficient water-driven ligation. As compared to native unmodified proteins, the cyclodextrin-modified proteins (lysozyme and RNase A) exhibit significant reduction in aggregation, surface adsorption and increase in thermal stability. These results reveal a new chemistry for preventing protein aggregation and surface adsorption that is likely of different mechanisms than that by modifying proteins with poly(ethylene glycol).