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Results for “proteome mapping”

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At least 757 records · Page 42Linked to original sources
PubMed2005

Identification of critical heterodimer protein interface parameters by multi-dimensional scaling in euclidian space.

Protein subunit dimers are either homodimers (consisting of identical polypeptides) or heterodimers (consisting of different polypeptides). Protein dimers are involved in several cellular processes and an understanding of their molecular principle in complexations (subunit-subunit interaction) is essential. This is generally studied using 3D structures of homodimers and heterodimers determined by X-ray crystallography. However, the current knowledge on subunit interaction is limited due to lack of sufficient 3D dimer structures. It is our interest to study heterodimers using 3D structures to identify interaction parameters that would help in the development of a model to predict heterodimer interaction sites just from protein sequences. The efficiency of such models depends on the weighted contribution of numerous parameters characterizing heterodimer interfaces. Therefore, we studied the salient features of 111 interface parameters in 65 heterodimer structures. In this study, we applied multi-dimensional scaling for dimensionality reduction on these parameters to select the most critical ones that best characterize heterodimer interfaces. The significance of these parameters in subunit interaction is discussed.

Computational Biology↗
PubMed2004

[Differential analysis of two-dimension gel electrophoresis profiles of human lung squamous carcinoma and tumor-adjacent tissue].

BACKGROUND & OBJECTIVE: Carcinogenesis of lung squamous carcinoma is a complex process involving multiple events and steps. Though some molecular pathogenesis studies on human lung cancer have been undertaken successfully in gene (DNA) and transcription (mRNA) levels, the carcinogenic mechanism is still unclear. At present, there is no special molecular marker for early-stage diagnosis and prognosis evaluation. The objective of this study was to establish two-dimensional electrophoresis profiles with high resolution and reproducibility from human lung squamous carcinoma tissue and paired normal tumor-adjacent bronchial epithelial tissue, and to identify differential expression proteins. METHODS: The total proteins of human lung squamous carcinoma tissue and paired normal tumor-adjacent bronchial epithelial tissue were separated by immobilized pH gradient (IPG)-based two-dimensional gel electrophoresis (2-DE). The differential expression proteins were analyzed using image analysis software, then identified using mass spectrometry and database searching. RESULTS: (1) For tumor tissues, the average protein spots of 3 gels were 1349+/-67; and 1235+/-48 spots were matched with the average matching rate of 91.5%. For control, the average protein spots of 3 gels were 1297+/-73; and 1183+/-56 spots were matched with the average matching rate of 91.2%. The average position deviation of matched spots was 0.873+/-0.125 mm in IEF direction, and 1.025+/-0.213 mm in SDS-PAGE direction. (2) A total of 1069+/-45 spots were matched between the electrophoretic maps of 15 human lung squamous carcinoma tissue and paired normal tumor-adjacent bronchial epithelial tissue. Forty differential proteins were identified by peptide mass fingerprint(PMF), some proteins were the products of oncogenes, and the others involve in the regulation of cell cycle and signal transduction. CONCLUSION: In this study, the well-resolved, reproducible 2-DE patterns of human lung squamous carcinoma and adjacent normal bronchial epithelial tissues were established and certain differential proteins were characterized. These data will be helpful for screening the biomarker to further study on human lung squamous carcinoma.

Amino Acid Sequence↗
PubMed2004

[Two-dimensional polyacrylamide gel electrophoresis analysis of apoptosis in K562 cells induced by harringtonine].

BACKGROUND & OBJECTIVE: Harringtonine (HT),an anti-tumor drug,has been widely used to treat acute or chronic myeloid leukemia,and obtained satisfactory effects. Studies showed that the anti-tumor activity of HT is related with the apoptosis-inducing effect,but the molecular mechanisms remain unclear. This study was to analyze the protein maps contributed to the apoptosis in K562 cells induced by HT,and to screen the apoptosis-associated proteins. METHODS: Flow cytometry was used to distinguish K562 cells of early apoptosis stage from those of late apoptosis stage through Annexin V and PI staining. Two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) was used to separate and compare the HT-induced apoptotic K562 cells and control K562 cells. RESULTS: When K562 cells were treated with 10 microg/ml HT for 5,a nd 24 hours,percentages of early apoptotic cells (Annexin V+/PI-) were 28.3%, and 18.1%(P< 0.01), while percentages of late apoptotic cells (Annexin V+/PI+) were 9.1%,and 20.2% (P< 0.01), respectively. Statistical analysis showed (1300+/-50) protein spots were resolved with a match rate of (88.3+/-2.0)% in control K562 cells. Ten protein spots in late apoptotic cells displayed changes in expression after induction of HT for 24 hours (P< 0.01), of which 8 showed higher expression, 1 decreased,and 1 only expressed in control k562 cells. CONCLUSION: These proteins may be apoptosis-associated proteins of K562 cells induced by HT.

Antineoplastic Agents, Phytogenic↗
PubMed2004

[Two-dimensional electrophoretic separation of subproteomes in adult rat hippocampal subregions after membrane protein enrichment with sequential extraction].

OBJECTIVE: To establish a method for analysis of the subproteomes following membrane protein enrichment, so as to investigate the differences in cytosolic and membrane protein/peptide contents among different hippocampal subregions (CA1, CA3 and dentate gyrus) of rats. METHODS: The hippocampal subregions were isolated by microdissection, and after membrane protein enrichment with protein solubility-based sequential sample extraction, subproteome profiling was accomplished using modified two-dimensional electrophoresis and silver staining method compatible with high-performance mass spectrometry, which displayed cytosolic or membrane proteins/peptides separately. The efficacy of the electrophoresis was evaluated by image analyzing software. RESULTS: The membrane proteins were enriched by 8 folds, and around 30% more spots were shown on the integrated dentate gyrus map than on the conventional map obtained by one-step protein extraction. Such improvement could also be seen in protein mapping of CA1 and CA3 regions. CONCLUSION: When analyzing hippocampal subregions sequential extraction and two-dimensional electrophoresis more effectively separate and display enriched membrane protein/peptides, which may play important roles in such cellular events as signal transduction.

Animals↗
PubMed2003

Initial large-scale exploration of protein-protein interactions in human brain.

Study of protein interaction networks is crucial to post-genomic systems biology. Aided by high-throughput screening technologies, biologists are rapidly accumulating protein-protein interaction data. Using a random yeast two-hybrid (R2H) process, we have performed large-scale yeast two-hybrid searches with approximately fifty thousand random human brain cDNA bait fragments against a human brain cDNA prey fragment library. From these searches, we have identified 13,656 unique protein-protein interaction pairs involving 4,473 distinct known human loci. In this paper, we have performed our initial characterization of the protein interaction network in human brain tissue. We have classified and characterized all identified interactions based on Gene Ontology (GO) annotation of interacting loci. We have also described the "scale-free" topological structure of the network.

Brain↗
PubMed2006

[Application of serum protein fingerprint model and support vector machine in diagnosis of thyroid cancer].

OBJECTIVE: To detect new biomarkers and to establish a serum protein fingerprint model for early detection and diagnosis of thyroid cancer. METHODS: The serum samples of 40 thyroid cancer patients, 9 thyroid adenoma patient, and 32 healthy individuals were randomly divided into 2 sets: training set (n = 66, including 32 thyroid cancer patients, 9 thyroid adenoma patients, and 25 healthy individuals) and test set (n = 15). The serum protein were bound to WCX2 chip and tested by surface enhanced laser desorption/ionization time of flight-mass spectrometry (SELDI-TOF-MS). The data of spectra were analyzed by support vector machine (SVM) to establish a diagnostic model. RESULTS: The detective model combined with 3 biomarkers could differentiate the serum of thyroid cancer from that of healthy individual with a specificity of 86% and a sensitivity of 100%. The diagnostic model combined with 3 biomarkers could differentiate thyroid cancer from thyroid adenoma with a specificity of 88.9% and a sensitivity of 96.9%. The positive predictive value to differentiate papillary thyroid carcinoma from the thyroid cancer of other types was 97%, and the positive predictive value of thyroid carcinoma of other pathological types was 71%. CONCLUSION: The combination of SELDI with bioinformatics tools is a novel, effective, and highly specific and sensitive method for thyroid cancer detection and diagnosis.

Biomarkers, Tumor↗
PubMed2004

Two-dimensional reference map of Agrobacterium tumefaciens proteins.

Proteomics based on two-dimensional (2-D) gel electrophoresis of proteins followed by spot identification with mass spectrometry is a commonly used method for physiological studies. Physiological proteomics requires 2-D reference maps, on which most of the main proteins are identified. We present a reference map for the bacterial plant pathogen Agrobacterium tumefaciens proteins, which contains more than 300 entries with an isoelectric point (pI) between 4 and 7. The quantitative study of the proteins in the analytical window of the master gel demonstrated unique features, in comparison with other bacteria. In addition, a theoretical analysis of several protein parameters was performed and compared with the experimental results. A comparison of the theoretical molecular weight (MW) of the proteins and their theoretical pI with their vertical and horizontal migration distances, respectively, pointed out the existence of several proteins that strongly diverted from the graph trend-line. These proteins were clearly subjected to post-translational modifications, which changed their pI and/or MW. Additional support for post-translational modifications comes from the identification of multiple spots of the same gene products. Post-translational modifications appear to be more common than expected, at least for soluble proteins, as more than 10% of the proteins were associated with multiple spots.

Agrobacterium tumefaciens↗
PubMed2006

Mapping the antigenicity of the parasites in Leishmania donovani infection by proteome serology.

BACKGROUND: Leishmaniasis defines a cluster of protozoal diseases with diverse clinical manifestations. The visceral form caused by Leishmania donovani is the most severe. So far, no vaccines exist for visceral leishmaniasis despite indications of naturally developing immunity, and sensitive immunodiagnostics are still at early stages of development. METHODOLOGY/PRINCIPLE FINDINGS: Establishing a proteome-serological methodology, we mapped the antigenicity of the parasites and the specificities of the immune responses in human leishmaniasis. Using 2-dimensional Western blot analyses with sera and parasites isolated from patients in India, we detected immune responses with widely divergent specificities for up to 330 different leishmanial antigens. 68 antigens were assigned to proteins in silver- and fluorochrome-stained gels. The antigenicity of these proteins did not correlate with the expression levels of the proteins. Although some antigens are shared among different parasite isolates, there are extensive differences and no immunodominant antigens, but indications of antigenic drift in the parasites. Six antigens were identified by mass spectrometry. CONCLUSIONS/SIGNIFICANCE: Proteomics-based dissection of the serospecificities of leishmaniasis patients provides a comprehensive inventory of the complexity and interindividual heterogeneity of the host-responses to and variations in the antigenicity of the Leishmania parasites. This information can be instrumental in the development of vaccines and new immune monitoring and diagnostic devices.

Adolescent↗
PubMed2004

Two-dimensional maps and databases of the human macrophage proteome and secretome.

Macrophages exert a crucial, but still incompletely known, role in complex disorders such inflammatory, immunological, and infectious diseases. A differential proteomic approach should help to elucidate the macrophage dysfunctions involved in these diseases. With this goal in mind, we established the first two-dimensional maps of the human macrophage proteome and secretome. Intracellular and secreted proteins were extracted from monocyte-derived macrophages obtained from healthy donors (n = 16), and separated by two-dimensional gel electrophoresis. Silver-stained gels were analyzed using Progenesis software. A high level of between-gel reproducibility was obtained, allowing us to generate two patterns specific of the macrophage proteome and secretome, respectively. A total of 127 and 66 distinct intracellular and secreted polypeptide spots, corresponding to 100 and 38 different proteins, respectively, were identified by matrix assisted laser desorption/ionisation-mass spectrometry. The two-dimensional reference maps and databases resulting from this study confirm that macrophages are involved in a wide range of biological functions, and that they provide a useful tool for a wide array of investigators involved in macrophage biology, allowing to investigate the macrophage protein changes associated with various disorders or environmental stimuli.

Databases, Protein↗