Current Proteomics - Volume 1, Issue 2, 2004
Volume 1, Issue 2, 2004
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Mining for Protein Kinase Substrates: Integration of Biochemistry, Genetics and Proteomics
Authors: Benjamin K. Benton, Christian Rommel, Mark Velleca and Christian PasqualiThe inhibition of protein phosphorylation is proving to be a powerful therapeutic approach to treat a number of disorders. As more protein kinase inhibitors are developed, critical issues of drug and target specificity must be addressed. While a remarkable amount of information exists for the regulation of protein kinase function, relatively little is known about the substrates they phosphorylate. Classical protein kinase substrate identification approaches have been hampered largely due to high background phosphorylation in cellular lysates and the laborious methods required identifying and purifying both the protein kinases and their substrates. Recent advances in biochemistry, bioinformatics and proteomics have addressed many of these issues. A particularly powerful method to identify direct protein kinase substrates combines standard proteomics with a unique chemical genetics approach. Identification of new protein kinase substrates by such chemical-genetic and other emerging technologies may provide the next generation of drug targets for multiple therapeutic areas.
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Evaluation of Proteomic Techniques: Applications and Potential
Authors: Bernd H. A. Rehm and Frank ReineckeProteomics, the parallel separation, identification and quantification of all proteins produced by a tissue or cell culture, together with the analysis of protein properties like posttranslational modifications and interactions, provides more detailed information about the biological system under study than the determination of the static genome or expression profiling based on mRNA. To benefit fully from the power of proteomics, some of the inherent problems have to be solved. Most methods of protein separation fail to recover all proteins. Protein abundance spans several orders of magnitude and there is no amplification method, analogous to the polymerase chain reaction method for amplifying genes. In order to overcome these problems, proteomic technologies have to be very sensitive as well as to cover a broad dynamic range. Advantages and disadvantages of different established and emerging methods used for protein separation and identification are discussed and the evolving chip-based approaches are evaluated. Results of proteomic experiments consist of far more than a mere sequence of nucleic-acid bases or amino acids. The essential information of a proteomic approach is difficult to extract, standardise and integrate into databases. This, however, is necessary to allow laboratory and organism independent use of experimental data. Discussion on related databases and data integration are presented.
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Characteristic Alterations of Nuclear Structure and Chromatin Organisation of Cancer Cells Addressed by Proteome Analysis**
More LessHistological assessment of nuclear morphology is a standard procedure in clinical practice. The implications of altered nuclear structure accompanying neoplastic disease are still not fully understood. Nuclear matrix proteins were considered as structural units defining the shape of nuclei. Consequently, it was assumed that nuclei displaying characteristics of cancer cells would exhibit specific nuclear matrix proteins. The nuclear proteome was investigated by various approaches, including analyses of preparations of whole nuclei, the nuclear matrix and of subnuclear compartments. Proteome alterations related to cancer were mainly investigated by comparative two dimensional polyacrylamide gel analyses. This review provides an overview of results achieved by this and other proteome analysis approaches, highlighting some implications of technical and analytical details. The contribution and future potential of proteomics to the further understanding of the chromatin regulation and mechanisms affecting nuclei during cell transformation will be discussed with regard to important advances accomplished by current techniques.
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Proteomic Approaches in Plant Biology
Proteomic approaches play an important role in the study of complex biological systems. The application of proteomic technologies in plant science has been strongly supported by the completion of genome sequence projects of the model plants Arabidopsis thaliana and rice. This review focuses on the state of proteomic technologies with special emphasis on their application in plant biology. An overview of recent developments in 2-dimensional gel electrophoresis and liquid chromatography-based multidimensional protein identification technology, MudPIT is provided. These techniques are commonly combined with mass spectrometric methods for identification of proteins. Furthermore, protein expression profiling by antibody arrays and the selection of required recombinant antibodies by phage display are described. Interaction studies, using functional protein microarrays or the yeast two-hybrid system are presented as powerful techniques to gain insights into the function of proteins. Advantages and limitations of the described methods as well as their current and potential future applications in plant research are discussed.
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Bioinformatics of Botulin Neurotoxin Structures
Authors: Shawn M. McDonald, Michael J. Dudek and Kal RamnarayanThe botulinum neurotoxins [BoNT] can be subdivided into immunologically distinct serotypes A-G and are multidomain proteins that are released by pathogenic strains of Clostridium botulinum. Each neurotoxin contains a catalytic domain that is a metalloprotease and cleaves a specific site on one of three proteins involved in synaptic vesicle fusion. Substrate cleavage leads to loss of neurotransmitter release and thus to paralysis, a common symptom in the disease botulism. In this article we have provided an extensive literature review of BoNT structure and function, as well as homology modeling and docking methods. Building upon the known three-dimensional structures of BoNT / A and BoNT / B, we have generated 3D homology models for the catalytic domains of the remaining serotypes. The models, along with the known BoNT / A and BoNT / B crystal structures, have been used in molecular docking experiments using AutoDock to predict binding of five small molecules that are known as weak inhibitors of BoNTs. These docking calculations have been discussed in relation to recent free energy calculations on a BoNT-peptide complex as well as with regard to the known substrate specificity of the seven BoNT serotypes. The results of the docking calculations reveal energetic and structural differences among the BoNT serotypes and provide new information about substrate specificity for future computer-aided drug design efforts to develop more potent BoNT inhibitors.
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The Protein Profile of Fibroblasts: The Role of Proteomics
Authors: Daniela Quaglino, Federica Boraldi, Luca Bini and Nicola VolpiFibroblasts represent one of the most widely used cell types to investigate the biology of connective tissues in normal and pathologic conditions. Aim of the present review is to emphasize, in the light of the current literature, the importance of fibroblast proteomics as a powerful resource for functional genomics in health and disease. Only very recently, proteomic techniques has been applied to characterise human dermal fibroblasts, but few data are available concerning fibroblasts of various animal origins or derived from different tissues. Functional proteomic methods have been successfully used in order i) to investigate changes in protein synthesis resulting from stimulation of fibroblasts with exogenous and endogenous factors and in the presence of conditioned media; ii) to identify the underlying mechanisms that modulate fibroblast protein profile during senescence; iii) to obtain increased knowledge about the pathogenesis of diseases such as peribronchial fibrosis; iv) to better understand the molecular basis of biocompatibility. In addition, comparison of data obtained by proteome analysis, on in vitro aged human embryo fibroblasts and on in vitro cultured human fibroblasts from subjects of different ages, allowed differences and similarities of the aging process in different models to be highlighted. Although the number of proteomic studies has exponentially increased during the past couple of years, several proteins are still under-represented in most proteome maps, i.e. membrane, low abundant and basic proteins. Since a comprehensive proteomic approach must use a technology platform that is not biased against any protein class and is able to resolve co- and post-translationally modified forms of proteins, we exemplify here the major technical improvements in protein separation and identification. Moreover, glycosylation is the most common type of post-translational protein modification, and a special emphasis is therefore placed on the expanding role of glycomics.
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Volumes & issues
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Volume 21 (2024)
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Volume 20 (2023)
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Volume 19 (2022)
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Volume 18 (2021)
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Volume 17 (2020)
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Volume 16 (2019)
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Volume 15 (2018)
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Volume 14 (2017)
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Volume 13 (2016)
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Volume 12 (2015)
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Volume 11 (2014)
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Volume 10 (2013)
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Volume 9 (2012)
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Volume 8 (2011)
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Volume 7 (2010)
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Volume 6 (2009)
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Volume 5 (2008)
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Volume 4 (2007)
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Volume 3 (2006)
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Volume 2 (2005)
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Volume 1 (2004)
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