The interactome: predicting the protein-protein interactions in cells.
ABSTRACT The term Interactome describes the set of all molecular interactions in cells, especially in the context of protein-protein interactions. These interactions are crucial for most cellular processes, so the full representation of the interaction repertoire is needed to understand the cell molecular machinery at the system biology level. In this short review, we compare various methods for predicting protein-protein interactions using sequence and structure information. The ultimate goal of those approaches is to present the complete methodology for the automatic selection of interaction partners using their amino acid sequences and/or three dimensional structures, if known. Apart from a description of each method, details of the software or web interface needed for high throughput prediction on the whole genome scale are also provided. The proposed validation of the theoretical methods using experimental data would be a better assessment of their accuracy.
Article: Plant Protein Interactomes.[Show abstract] [Hide abstract]
ABSTRACT: Protein-protein interactions are a critical element of biological systems, and the analysis of interaction partners can provide valuable hints about unknown functions of a protein. In recent years, several large-scale protein interaction studies have begun to unravel the complex networks through which plant proteins exert their functions. Two major classes of experimental approaches are used for protein interaction mapping: analysis of direct interactions using binary methods such as yeast two-hybrid or split ubiquitin, and analysis of protein complexes through affinity purification followed by mass spectrometry. In addition, bioinformatics predictions can suggest interactions that have evaded detection by other methods or those of proteins that have not been investigated. Here we review the major approaches to construct, analyze, use, and carry out quality control on plant protein interactome networks. We present experimental and computational approaches for large-scale mapping, methods for validation or smaller-scale functional studies, important bioinformatics resources, and findings from recently published large-scale plant interactome network maps. Expected final online publication date for the Annual Review of Plant Biology Volume 64 is April 29, 2013. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.Annual Review of Plant Biology 01/2013; · 18.71 Impact Factor
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ABSTRACT: Highly concentrated urine may induce a harmful effect on the urinary bladder. Therefore, we considered osmolarity of the urine as a basic pathomechanism of mucosal damage. The influence of both cyclophosphamide (CYP) and hyperosmolar stimuli (HS) on the urothelium are not well described. The purpose was to evaluate the effect of CYP and HS on rat urothelial cultured cells (RUCC). 15 Wistar rats were used for RUCC preparation. RUCC were exposed to HS (2080 and 3222 mOsm/l NaCl) for 15 min and CYP (1 mg/ml) for 4 hrs. APC-labelled annexin V was used to quantitatively determine the percentage of apoptotic cells and propidium iodide (PI) as a standard flow cytometric viability probe to distinguish necrotic cells from viable ones. Annexin V-APC (+), annexin V-APC and PI (+), and PI (+) cells were analysed as apoptotic, dead, and necrotic cells, respectively. The results were presented in percentage values. The flow cytometric analysis was done on a FACSCalibur Flow Cytometer using Cell-Quest software. Treatment with 2080 and 3222 mOsm/l HS resulted in 23.7 ± 3.9% and 26.0 ± 1.5% apoptotic cells, respectively, 14.3 ± 1.4% and 19.4 ± 2.7% necrotic cells, respectively and 60.5 ± 1.4% and 48.6 ± 5.3% dead cells, respectively. The effect of CYP on RUCC was similar to the effect of HS. After CYP the apoptotic and necrotic cells were 23.1 ± 0.3% and 17.9 ± 7.4%, respectively. The percentage of dead cells was 57.7 ± 10.8%. CYP and HS induced apoptosis and necrosis in RUCC. 3222 mOsm/l HS had the most harmful effect based on the percentage of necrotic and apoptotic cells.Cellular & Molecular Biology Letters 01/2012; 17(2):196-205. · 1.95 Impact Factor
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ABSTRACT: The kinetics of protein interactions are essential determinants in many cellular processes such as signal transduction and transcriptional regulation. Many proteins involved in these functions contain intrinsic disordered regions. This makes conformational flexibility become an unneglectable factor when studying the binding kinetic of these proteins. Compared with the binding of rigid proteins that is limited by diffusions, the binding mechanisms of proteins with internal flexibility are much more complicated. Using a small protein that contains two domains and a connecting loop as a testing system, we developed a multiscale simulation framework to study the role of flexible linkers in regulating kinetics of protein binding. The association and dissociation processes were implemented by a coarse-grained Monte-Carlo algorithm, while the conformational changes of the flexible linker were captured from all-atom molecular dynamic simulations. Our simulations illustrated that the presence of the extended domain linker can enhance the rate of protein association. On the other hand, the full-length flexible molecule is more difficult to dissociate than its two rigid domains but much easier than the molecule with a rigid linker. Overall, our studies demonstrated that both kinetics and thermodynamics of protein binding are closely modulated by the dynamic features of linker regions. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.Proteins Structure Function and Bioinformatics 05/2014; · 3.34 Impact Factor