Network interaction

The dibenzobicyclo[2.2.2]octatriene system (71) essentially involves interaction of three composite n orbitals, i.e., the olefinic n orbital as the reaction center, and two aromatic k orbitals. A simplified interaction network, i.e., two n component systems free from steric bias, is intriguing. In this context the facial selectivities of... 

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cyto-scape a software environment for integrated models of biomolecular interaction networks. Genome Res 2003 13 2498-504. 

Finally, the networks of protein-protein interactions defined by these studies provide a global view of how cellular processes are coordinated. As described below, protein interaction networks from S. cerevisiae indicate that interactions occur not only between proteins involved in certain cellular processes but also between proteins involved in different processes. These links may be crucial for sharing information and thereby coordinating global responses to environmental stimuli. 

Figure 5.4. Example of a small region of a hypothetical protein interaction network. Each letter represents a different yeast protein. The white boxes and gray boxes represent genes that are involved in the same function while the hatched boxes indicate proteins of unknown function. The A protein is likely to be involved in the same process as the white box protein and the J protein is likely to be involved in the same process as the gray box proteins because of the multiple interactions within the network. The connection between the E and I proteins indicates communication between the cellular processes. Figure adapted from Hazbun and Fields (2001).

A fascinating future area of study will be experimental and computational evaluation of the dynamics of protein networks. For example, how do protein complexes and interaction networks change in response to environmental signals or developmental states How do the networks of... 

The lifetime of the excited state of fluorophores may be altered by physical and biochemical properties of its environment. Fluorescence lifetime imaging microscopy (FLIM) is thus a powerful analytical tool for the quantitative mapping of fluorescent molecules that reports, for instance, on local ion concentration, pH, and viscosity, the fluorescence lifetime of a donor fluorophore, Forster resonance energy transfer can be also imaged by FLIM. This provides a robust method for mapping protein-protein interactions and for probing the complexity of molecular interaction networks. 

Schachter V. Bioinformatics of large-scale protein interaction networks. Biotechniques 2002 32(Suppl.) S16-S27. 

Zhang H,Tang X, Munske GR, et al. In vivo identification of the outer membrane protein OmcA-MtrC interaction network in Shewanella oneidensis MR-1 cells using novel hydrophobic chemical cross-linkers. J. Proteome Res. 2008 7 1712-1720. 

Guerrero C, Tagwerker C, Kaiser P, et al. An integrated mass spectrometry-based proteomic approach quantitative analysis of tandem affinity-purified in vivo cross-linked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network. Mol. Cell. Proteomics. 2006 5 366-378. 

Fig. 17 A view of the interaction network on [Cp W(dnut)2] showing the dmit dmit (circles) and the Cp dmit (squares) interactions...

The experimental exploration and confirmation of protein functions are relatively slow processes and always require dedicated experiments. The analysis of protein-protein associations as such improved remarkably in quality and speed. This is accompanied by the creation of new databases that will reflect the network of interacting proteins (the Protein Function and Metabolic Pathway project, http //bioinformer.ebi. ac.uk 80/newsletter/archives/4/pfmp.html, and the Biomolecular Interaction Network Database project http //bioinfo.mshri.on.ca/ BIND/). These activities contribute to the idea that cellular mechanisms can be better understood when they are seen as a multicomponent networked process. 

Fig. 1. The generalized protein-protein interaction network that includes (A) direct protein-protein interactions such as in the signal transduction pathway, (B) enzyme-enzyme relations in the metabolic pathway, and (C) transcription factor-expressed gene product relations in the gene regulatory pathway. The interactions in (B) and (C) are termed indirect protein-protein interactions.

The generalized protein-protein interaction network as defined here is actually a graph consisting of nodes for proteins (or RNAs) and edges... 

Table V shows a classification of binary relations gene-gene relations, protein-protein relations, and other molecule-molecule relations. Different sets of binary relations can then be related to different types of graphs. For example, the generalized protein-protein interaction network is equivalent to a set of protein-protein binary relations. The KEGG metabolic pathway is a generalized protein-protein network, but it is also a network of chemical compounds that can be converted to a set of com-...

Alfarano, C., Andrade, C.E., Anthony, R, Bahroos, N., Bajec, M., Bantoft, R, Betel, D., Bobechko, B., Boutilier, R, Burgess, E., et al, (2005) The Biomolecular Interaction Network Database and Related Tools 2005 Update. Nucl Acids Res, 33, D418 24. 

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