Proteomic profiling of human urine using multi-dimensional protein identification technology

Human urine samples are ideal for proteomic profiling and have tremendous potential as sources of biomarkers. Multi-dimensional protein identification technology (MudPIT) is an effective approach to analyzing human urine or other fluids dominated by diverse metabolites. MudPIT analysis was used to identify 87 proteins in just 15 ml of human urine. A high throughput, reproducible, and sensitive technology, MudPIT may soon be used for more proteomic analyses of metabolites.     

Proteomic applications of surface plasmon resonance biosensors: analysis of protein arrays

Proteomics is one of the most important issues in the post-genomic area, because it can greatly contribute to identifying protein biomarkers for disease diagnosis and drug screening. Protein array is a key technology for proteome researches and has been analyzed by various methods including fluorescence, mass spectrometry, atomic force microscopy and surface plasmon resonance (SPR). SPR biosensor is a promising technology in proteomics, since it has various advantages including real-time measurement of biomolecular interactions without labeling and the simple optical system for the device. SPR biosensors have a strong potential for analyzing proteomes by SPR imaging and SPR spectroscopic imaging, even though the challenge is to produce proteins on a proteomic scale.     

3,4-dimethylbenzyl radical formed in a corona discharge of 1,2,4-trimethylbenzene

A precursor, 1,2,4-trimethylbenzene, seeded in a large amount of an inert carrier gas, helium, was electrically discharged in a corona-excited supersonic expansion using a pinhole-type glass nozzle. The blue-green colored fluorescence emanating from the downstream jet was recorded with a long path monochromator to observe the vibronic emission spectrum of the benzyl-type radical formed. Analysis of the spectrum suggests that the most dominant product of the corona discharge is the 3,4-dimethylbenzyl radical formed by extracting a hydrogen atom from the methyl group at the 4-position. The electronic energies of the D1 and D2 states and the vibrational mode frequencies of the 3,4-dimethylbenzyl radical were accurately obtained for the first time by comparison with those from an ab initio calculation as well as those of the known vibrational mode frequencies of the precursor.     

Impact of the nanoparticle-protein corona on colloidal stability and protein structure

In biological fluids, proteins may associate with nanoparticles (NPs), leading to the formation of a so-called "protein corona" largely defining the biological identity of the particle. Here, we present a novel approach to assess apparent binding affinities for the adsorption/desorption of proteins to silver NPs based on the impact of the corona formation on the agglomeration kinetics of the colloid. Affinities derived from circular dichroism measurements complement these results, simultaneously elucidating structural changes in the adsorbed protein. Employing human serum albumin as a model, apparent affinities in the nanomolar regime resulted from both approaches. Collectively, our findings now allow discrimination between the formation of protein mono- and multilayers on NP surfaces.     

Catalytic approach to the estimation of the influence of carbon nanomaterial structures on surface functional groups

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Formation of a protein corona around nanoparticles

In biofluids, nanoparticles rapidly become surrounded by a protein corona. This phenomenon started to attract attention 10 years ago. Since then, this subfield of colloid and interface science was among the most rapidly expanding and progressing. Owing to its strong relation to biology and applications, this area is rich in various questions to explore. The reviews of the corresponding experiments are already numerous. Herein, I focus on the related theory including conventional mean-field kinetic models, dynamic density functional theory, Monte Carlo simulations, and molecular dynamics simulations. The key concept here is that the formation of a protein corona depends on the interplay of competition of different proteins for the location near the nanoparticle–solution interface (Vroman effect) and denaturation at this interface. Although this concept is not new, many details of this interplay are still open for debate.     

Proteomic profiling of pancreatic ductal carcinoma cell lines treated with trichostatin-A

A pancreatic adenocarcinoma cell line (Paca44) was treated with trichostatin-A (TSA), a potent inhibitor of histone deacetylases, in order to evaluate the effect of this drug on protein expression. Master maps of control and treated Paca44 cells were generated by analysis with the PDQuest software. The comparison between such maps showed up- and downregulation of 51 polypeptide chains, out of a total of 700 spots detected by a medium-sensitivity stain, micellar Coomassie Brilliant Blue. Fingerprinting by matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF)-mass spectrometry analysis enabled the identification of 22 of these spots. Among these proteins, of particular interest are the two downregulated proteins nucleophosmin and translationally controlled tumor protein, as well as the upregulated proteins programmed cell death protein 5 (also designated as TFAR19) and stathmin (oncoprotein 18). The modulation of these four proteins is consistent with our observation that TSA is able to inhibit cell growth of Paca44 by causing cell cycle arrest at the G2 phase and apoptotic cell death.     

Proteomic profiling of the photo-oxidation of silk fibroin: implications for historic tin-weighted silk

The stability of silk proteins to ultraviolet light is an issue of significant concern in both the appearance retention of silk-derived products and the preservation of historic silk textiles. Until now, evaluation of silk degradation has only been performed at the holistic, rather than molecular level. This article describes the first proteomic profiling of silk photo-oxidation, characterizing protein primary level modification leading to coloration changes, and evaluating the effects of tin weighting on photodegradation. Heavy-chain fibroin, the main proteinaceous component of the silk thread, is a repetitive, highly crystalline protein with a content rich in tyrosine. Photoproducts of tyrosine were characterized and the levels of oxidative modification at the protein primary structural level correlated with changes in coloration and tensile strength. The effect of tin as a weighting agent used on historical fabrics was examined. Tin-weighted fabrics were evaluated following two treatments (pink and dynamite) and proteomic analysis revealed a significant increase in oxidatively modified amino acid residues within the pink-treated silk. These findings offer new insight into the molecular-level oxidation of silk proteins under UV exposure, and the effects of silk treatments in either exacerbating or ameliorating this degradation.     

Proteomic profiling of human colon cancer cells treated with the histone deacetylase inhibitor belinostat

The anticancer drug belinostat is a hydroxamate histone deacetylase inhibitor that has shown significant antitumour activity in various tumour models and also in clinical trials. In this study, we utilized a proteomic approach in order to evaluate the effect of this drug on protein expression in the human colon cancer cell line HCT116. Protein extracts from untreated HCT116 cells, and cells grown for 24 h in the presence of 1 and 10 μM belinostat were analysed by 2‐D gel electrophoresis. Proteins were visualized by colloidal Coomassie blue staining and quantitative analysis of gel images revealed 45 unique differentially expressed proteins that were identified by LC‐MSMS analysis. Among these proteins, of particular interest are the downregulated proteins nucleophosmin and stratifin, and the upregulated proteins nucleolin, gelsolin, heterogeneous nuclear ribonucleoprotein K, annexin 1, and HSP90B that all were related to the proto‐oncogene proteins p53, Myc, activator protein 1, and c‐fos protein. The modulation of these proteins is consistent with the observations that belinostat is able to inhibit clonogenic cell growth of HCT116 cells and the biological role of these proteins will be discussed.     

Oxidation of polyethylene surface by corona discharge and the subsequent graft polymerization

Oxidation of a polyethylene (PE) surface by corona discharge and the subsequent graft polymerization of acrylamide (AAm) were studied. The maximum amount of peroxides introduced by corona treatment at a voltage of 15 kV was about 2.3 × 10^?9 mol cm^?2. The decomposition rate of peroxide and the dependence of graft amount on the storage period of the corona-treated PE films showed that there were several kinds of peroxides, the labile one being mainly responsible for the initiation of graft polymerization. When the corona-treated film was brought into contact with a deaerated aqueous solution of AAm, graft polymerization took place more strongly with the treatment time, but was reduced after passing a maximum. Although the x-ray photoelectron spectroscopic analyses of the corona-treated PE films showed homogeneous oxidation of the outer polymer surface by corona discharge, optical microscopy on the cross section of the grafted film revealed the graft polymerization to be limited to a very thin surface region.     

Proteomic dissection of biological pathways/processes through profiling protein-protein interaction networks

Cellular functions, either under the normal or pathological conditions or under different stresses, are the results of the coordinated action of multiple proteins interacting in macromolecular complexes or assemblies. The precise determination of the specific composition of protein complexes, especially using scalable and high-throughput methods, represents a systematic approach toward revealing particular cellular biological functions. In this regard, the direct profiling protein-protein interactions (PPIs...     

The influence of aging on surface free energy of corona treated packaging films

In packaging, plastic films are very often applied as overprinting materials. The printing properties of plastic films depend on the value of the surface free energy. Usually, during storage but before printing, the surface free energy is decreasing as a result of ageing. The aim of this study was to analyse the influence of elevated temperature and UV radiation on ageing properties and variation of the free surface energy for three commercially available plastic films: polyethylene, polypropylene and polyethylene terephthalate. The investigation was done experimentally, and the surface free energy was calculated using two approaches, Owens-Wendt and van Oss-Chaudhury-Good. The time change of polar fractions was also analysed. The calculation results were compared and it was concluded that UV radiation causes more changes in surface free energy than elevated temperature. In some cases, surface free energy values calculated with the applied methods show similar trends.     

非手性的棒状分子在非手性表面形成的风车团簇

利用低温STM研究了非手性的棒状并五苯分子在Bi（111）表面形成的手性风车团簇.在团簇内部,并五苯分子分别沿Bi（111）的3个对称轴方向平行排列,形成6个不同的分子带.在每个分子带中,相邻分子之间有一个滑移错位.当平行排列的分子数多于4时,滑移错位发生反向,形成弯曲的风车扇叶.我们认为,分子的滑移错位来自于分子之间的π-π相互作用;而滑移错位的反向是团簇内部的吸引力导致的密堆积的结果.这两种作用的竞争是形成手性风车团簇的微观机制.     

Proteomic profiling of mature leaves from oil palm (Elaeis guineensis Jacq.)

Oil palm is one of the most productive oil bearing crops grown in Southeast Asia. Due to the dwindling availability of agricultural land and increasing demand for high yielding oil palm seedlings, clonal propagation is vital to the oil palm industry. Most commonly, leaf explants are used for in vitro micropropagation of oil palm and to optimize this process it is important to unravel the physiological and molecular mechanisms underlying somatic embryo production from leaves. In this study, a proteomic approach was used to determine protein abundance of mature oil palm leaves. To do this, leaf proteins were extracted using TCA/acetone precipitation protocol and separated by 2DE. A total of 191 protein spots were observed on the 2D gels and 67 of the most abundant protein spots that were consistently observed were selected for further analysis with 35 successfully identified using MALDI TOF/TOF MS. The majority of proteins were classified as being involved in photosynthesis, metabolism, cellular biogenesis, stress response, and transport. This study provides the first proteomic assessment of oil palm leaves in this important oil crop and demonstrates the successful identification of selected proteins spots using the Malaysian Palm Oil Board (MPOB) Elaeis guineensis EST and NCBI‐protein databases. The MS data have been deposited in the ProteomeXchange Consortium database with the data set identifier PXD001307.     

Proteomic profiling of a snake venom using high mass detection MALDI-TOF mass spectrometry

Proteomic profiling involves identification and quantification of protein components in complex biological systems. Most of the mass profiling studies performed with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) have been restricted to peptides and small proteins (<20 kDa) because the sensitivity of the standard ion detectors decreases with increasing ion mass. Here we perform a protein profiling study of the snake venom Sistrurus miliarius barbouri, comparing 2D gel electrophoresis and reversed-phase high-performance liquid chromatography (HPLC) with a high mass cryodetector MALDI-TOF instrument (Macromizer), whose detector displays an uniform sensitivity with mass. Our results show that such MS approach can render superior analysis of protein complexity compared with that obtained with the electrophoretic and chromatographic approaches. The summation of ion impacts allows relative quantification of different proteins, and the number of ion counts correlates with the peak areas in the reversed-phase HPLC. Furthermore, the sensitivity reached with the high mass cryodetection MS technology clearly exceeds the detection limit of standard high-sensitivity staining methods.     

An overview on enrichment methods for cell surface proteome profiling

Cell surface proteins are essential for many important biological processes, including cell–cell interactions, signal transduction, and molecular transportation. With the characteristics of low abundance, high hydrophobicity, and high heterogeneity, it is difficult to get a comprehensive view of cell surface proteome by direct analysis. Thus, it is important to selectively enrich the cell surface proteins before liquid chromatography with mass spectrometry analysis. In recent years, a variety of enrichment methods have been developed. Based on the separation mechanism, these methods could be mainly classified into three types. The first type is based on their difference in the physicochemical property, such as size, density, charge, and hydrophobicity. The second one is based on the bimolecular affinity interaction with lectin or antibody. And the third type is based on the chemical covalent coupling to free side groups of surface‐exposed proteins or carbohydrate chains, such as primary amines, carboxyl groups, glycan side chains. In addition, metabolic labeling and enzymatic reaction‐based methods have also been employed to selectively isolate cell surface proteins. In this review, we will provide a comprehensive overview of the enrichment methods for cell surface proteome profiling.     

Glass transition of crosslinked polystyrene shells formed on the surface of calcium carbonate whisker

Glass transition of core/shell capsules consisting of calcium carbonate whisker as a core and crosslinked polystyrene as a shell was studied by differential scanning calorimetry. The thickness of the crosslinked shell was in the range of 26–81 nm. The crosslinked shells were revealed to show higher glass transition temperatures (T_g) than the corresponding bulk values. It was revealed that a thicker shell exhibits a lower T_g than a thinner shell, and that capsules without core (hollow capsules) exhibit lower T_g's than the corresponding core/shell capsules. These results suggest that the interfacial molecular interaction plays a role in the segmental relaxation, which is responsible for the glass transition. The difference in T_g between the core/shell and hollow samples was reduced when a coupling agent, methacrylic acid 3‐(trimethoxysilyl)propyl ester, was not included. This also suggests the interfacial effect on T_g. However, the results still suggest that the enhancement of T_g for the present crosslinked shells is not only due to the interfacial effect but also to the effects of chain configuration and heterogeneous crosslink. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 2475–2485, 2006     

Cell surface glycoprotein profiling of cancer cells based on bioorthogonal chemistry

Bioorthogonal chemistry refers to chemical reactions that can occur within a living system without altering native biochemical processes. Applications of this concept extend to studies on a group of biomolecules that includes glycans, proteins, and lipids. In this study, a strategy for isolating cell surface glycoproteins and based on bioorthogonal chemistry was employed to identify new cancer-related glycoproteins. A novel alkyne reagent containing one disulfide bond was synthesized for the enrichment of glycoproteins metabolized with peracetylated N-azidoacetylmannosamine, which was applied on three different cancer cell lines, and all isolated proteins were analyzed by high-performance liquid chromatography-tandem mass spectrometry. The strategy of purifying cell surface glycoproteins introduced in this article was shown to be reliable, and a total of 56 cell surface glycoproteins were identified. Neuronal cell adhesion molecule was found uniquely expressed in A549 lung adenocarcinoma, and its expression in non-small-cell lung carcinomas was detected by immunohistochemistry. Furthermore, a significant increase of neuronal cell adhesion molecule expression was identified in non-small-cell lung adenocarcinoma compared with adjacent noncancerous tissues, and could be a novel potential target and marker in cancer treatment and detection.