A proteomic investigation of isolated soy proteins with variable effects in experimental and clinical studies.
(49/9620)
Dietary preparations of soy proteins used for clinical studies, particularly of hypercholesterolemia, in Europe and the United States were the subject of a proteomic comparison because differences in their composition may explain variability in experimental and clinical results. After two-dimensional electrophoresis, identities of the protein components (globulin subunits and their breakdown products) were established by matrix-assisted laser desorption/ionization mass spectrometry. The soy concentrates (Cholsoy/Croksoy), which were used in most of the Italian and Swiss studies in which reductions in cholesterolemia occurred, exhibited a predominance of breakdown products of the 7S globulin and mainly intact 11S globulin subunits. Soy isolates used in the United States (SUPRO) showed none of the major components corresponding to 7S globulin subunits; only some of the light chains of 11S were intact, and heavy chains of 11S also were fragmented. Ethanol- and nonethanol-treated SUPRO products showed considerable variability in their isoflavone concentrations and there seemed to be differential protein recoveries due to ethanol processing. These findings indicate differences in the protein composition of soy products used in clinical studies. We suggest that standardization should be improved before products are assessed for clinical outcome studies. (+info)
PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data.
(50/9620)
PlasmoDB (http://PlasmoDB.org) is the official database of the Plasmodium falciparum genome sequencing consortium. This resource incorporates the recently completed P. falciparum genome sequence and annotation, as well as draft sequence and annotation emerging from other Plasmodium sequencing projects. PlasmoDB currently houses information from five parasite species and provides tools for intra- and inter-species comparisons. Sequence information is integrated with other genomic-scale data emerging from the Plasmodium research community, including gene expression analysis from EST, SAGE and microarray projects and proteomics studies. The relational schema used to build PlasmoDB, GUS (Genomics Unified Schema) employs a highly structured format to accommodate the diverse data types generated by sequence and expression projects. A variety of tools allow researchers to formulate complex, biologically-based, queries of the database. A stand-alone version of the database is also available on CD-ROM (P. falciparum GenePlot), facilitating access to the data in situations where internet access is difficult (e.g. by malaria researchers working in the field). The goal of PlasmoDB is to facilitate utilization of the vast quantities of genomic-scale data produced by the global malaria research community. The software used to develop PlasmoDB has been used to create a second Apicomplexan parasite genome database, ToxoDB (http://ToxoDB.org). (+info)
The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003.
(51/9620)
The SWISS-PROT protein knowledgebase (http://www.expasy.org/sprot/ and http://www.ebi.ac.uk/swissprot/) connects amino acid sequences with the current knowledge in the Life Sciences. Each protein entry provides an interdisciplinary overview of relevant information by bringing together experimental results, computed features and sometimes even contradictory conclusions. Detailed expertise that goes beyond the scope of SWISS-PROT is made available via direct links to specialised databases. SWISS-PROT provides annotated entries for all species, but concentrates on the annotation of entries from human (the HPI project) and other model organisms to ensure the presence of high quality annotation for representative members of all protein families. Part of the annotation can be transferred to other family members, as is already done for microbes by the High-quality Automated and Manual Annotation of microbial Proteomes (HAMAP) project. Protein families and groups of proteins are regularly reviewed to keep up with current scientific findings. Complementarily, TrEMBL strives to comprise all protein sequences that are not yet represented in SWISS-PROT, by incorporating a perpetually increasing level of mostly automated annotation. Researchers are welcome to contribute their knowledge to the scientific community by submitting relevant findings to SWISS-PROT at [email protected]. (+info)
An automated method for finding molecular complexes in large protein interaction networks.
(52/9620)
BACKGROUND: Recent advances in proteomics technologies such as two-hybrid, phage display and mass spectrometry have enabled us to create a detailed map of biomolecular interaction networks. Initial mapping efforts have already produced a wealth of data. As the size of the interaction set increases, databases and computational methods will be required to store, visualize and analyze the information in order to effectively aid in knowledge discovery. RESULTS: This paper describes a novel graph theoretic clustering algorithm, "Molecular Complex Detection" (MCODE), that detects densely connected regions in large protein-protein interaction networks that may represent molecular complexes. The method is based on vertex weighting by local neighborhood density and outward traversal from a locally dense seed protein to isolate the dense regions according to given parameters. The algorithm has the advantage over other graph clustering methods of having a directed mode that allows fine-tuning of clusters of interest without considering the rest of the network and allows examination of cluster interconnectivity, which is relevant for protein networks. Protein interaction and complex information from the yeast Saccharomyces cerevisiae was used for evaluation. CONCLUSION: Dense regions of protein interaction networks can be found, based solely on connectivity data, many of which correspond to known protein complexes. The algorithm is not affected by a known high rate of false positives in data from high-throughput interaction techniques. The program is available from ftp://ftp.mshri.on.ca/pub/BIND/Tools/MCODE. (+info)
Proteomic analysis of the cellular proteins induced by adaptive concentrations of hydrogen peroxide in human U937 cells.
(53/9620)
When cells are first exposed to low levels of oxidative stress, they develop a resistance to a subsequent challenge of the same stress, even at higher levels. Although some protein(s) induced by oxidative stress likely mediated this adaptive response, the nature of these proteins is unknown. In this study, the total proteins extracted from human U937 leukemia cells exposed to 50 micromM H(2)O(2) for 24 h to induce an optimal protective response were analyzed by two-dimensional polyacrylamide gel electrophoresis. H(2)O(2) treatment induced elevation of level of 34 protein spots. An analysis of these spots by a matrix associated laser desorption/ionization time-of-flight mass spectrometry identified 28 of the H(2)O(2)-induced proteins. These include proteins involved in energy metabolism, translation and RNA processing, chaperoning or mediating protein folding, cellular signaling, and redox regulation, as well as a mitochondrial channel component, and an actin-bundling protein. Therefore, it appears that the cellular adaptation to oxidative stress is a complex process, and is accompanied by a modulation of diverse cellular functions. (+info)
Detection and analysis of urinary peptides by on-line liquid chromatography and mass spectrometry: application to patients with renal Fanconi syndrome.
(54/9620)
Urinary proteomics has become a topical and potentially valuable field of study in relation to normal and abnormal renal function. Filtered bioactive peptides present in high concentration in the nephron of patients with tubular proteinuria may have downstream effects on renal tubular function. In renal Fanconi syndromes, such as Dent's disease, peptides implicated in altered tubular function or injury have recently been measured in urine by immunochemical methods. However, the limited availability of antibodies means that only certain peptides can be detected in this way. We have used nanoflow liquid chromatography and tandem mass spectrometry (nanoLC-MS/MS) as a complementary technique to analyse urinary peptides. Urine was desalted by solid-phase extraction (SPE) and its peptides were then separated from neutral and acidic compounds by strong cation-exchange chromatography (SCX), which was also used to fractionate the peptide mixture. Fractions from the SCX step were separated further by reversed-phase LC and analysed on-line by MS/MS. Extraction by SPE showed a good recovery of small peptides. We detected over 100 molecular species in urine samples from three individuals with Dent's disease. In addition to plasma and known urinary proteins, we identified some novel proteins and potentially bioactive peptides in urine from these patients, which were not present in normal urine. These data show that nanoLC-MS/MS complements existing techniques for the identification of polypeptides in urine. This approach is a potentially powerful tool to discover new markers and/or causative factors in renal disease; in addition, its sensitivity may also make it applicable to the direct ultramicroanalysis of renal tubule fluid. (+info)
Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics.
(55/9620)
Identifying the genes responsible for human diseases requires combining information about gene position with clues about biological function. The recent availability of whole-genome data sets of RNA and protein expression provides powerful new sources of functional insight. Here we illustrate how such data sets can expedite disease-gene discovery, by using them to identify the gene causing Leigh syndrome, French-Canadian type (LSFC, Online Mendelian Inheritance in Man no. 220111), a human cytochrome c oxidase deficiency that maps to chromosome 2p16-21. Using four public RNA expression data sets, we assigned to all human genes a "score" reflecting their similarity in RNA-expression profiles to known mitochondrial genes. Using a large survey of organellar proteomics, we similarly classified human genes according to the likelihood of their protein product being associated with the mitochondrion. By intersecting this information with the relevant genomic region, we identified a single clear candidate gene, LRPPRC. Resequencing identified two mutations on two independent haplotypes, providing definitive genetic proof that LRPPRC indeed causes LSFC. LRPPRC encodes an mRNA-binding protein likely involved with mtDNA transcript processing, suggesting an additional mechanism of mitochondrial pathophysiology. Similar strategies to integrate diverse genomic information can be applied likewise to other disease pathways and will become increasingly powerful with the growing wealth of diverse, functional genomics data. (+info)
Proteomics of light-harvesting proteins in different plant species. Analysis and comparison by liquid chromatography-electrospray ionization mass spectrometry. Photosystem II.
(56/9620)
An overview of the intact molecular masses and the hydrophobic properties of the photosystem II (PSII) light-harvesting proteins in 14 different plant species is presented. The protein separation and identification was achieved by means of reversed-phase high-performance liquid chromatography-electrospray ionization-mass spectrometry. The good correspondence of the molecular masses measured by reversed-phase high-performance liquid chromatography-electrospray ionization-mass spectrometry with those deduced from the DNA sequence (0.008%-0.016% relative deviation in Arabidopsis) enabled the identification of the different protein types. Utilizing this correlation, it was possible in several cases to spot a gene product for the previously cloned genes. In PSII, all antenna proteins show hydrophobic properties considerably different within the same as well as among various species, in contrast to observations made previously with PSI. These differences might reflect a tuning of protein-protein interactions that play a role in inducing different supramolecular organizations of PSII: within the same species as a consequence of short-term adaptations, and among species for seasonal species adaptation. The relative antenna stoichiometry was readily established on the basis of relative peak areas of the separated proteins in the ultraviolet chromatograms. The correspondence found between the high copy number of genes with the gene products reveals that the genes are not silent in their protein expression. Moreover, the high copy number of gene products as well as protein heterogeneity observed in PSII suggest a possible plant strategy to realize the high degree of organization and interconnection of the light-harvesting systems under any environmental conditions. (+info)