Cellular Proteins Interact

Apart from subunit-subunit interactions within the CSN, a considerable number of cellular proteins interact with CSN subunits (see Figure 13.1). Although the physiological relevance of many of the identified interactions is questionable, most of them might be attributed to a role of the CSN complex in signal transduction and ubiquitin-dependent proteolysis. 

Models also can assist in experimental design and the determination of the limits of experimental systems. For example, it is known that three proteins mediate the interaction of HIV with cells namely, the chemokine receptor CCR5, the cellular protein CD4, and the viral coat protein gpl20. An extremely useful experimental system to study this interaction is one in which radioactive CD4, prebound to soluble gpl20, is allowed to bind to cellular receptor CCR5. This system can be used to screen for... 

The ankyrin repeat motif is one of the most common protein-protein interaction domains. Ankyrin repeats are modules of about 33 amino acids repeated in tandem. They are found in a large number of proteins with diverse cellular functions such as transcriptional regulators, signal transducers, cell-cycle regulators, and cytoskeletal proteins. 

In response to a rise up calcium, SI00 proteins interact with distinct target proteins and some members relocate to different cellular compartments and are implicated in multiple intracellular and extracellular activities. 

SUMOylation. Figure 1 SUMOylation is a reversible and regulated process. Target protein modification by SUMO can be initiated and terminated by different cues. Sumoylation leads to changes in the behavior of the modified protein, for example, different cellular localization, enhanced/reduced activity, or increased stability. These changes are due to alterations either in protein interactions or protein folding. 

The ultimate goal of microarray-based expression analysis is to acquire a comprehension of the entire cellular process, in order to exploit and to standardize the multidi-menisional relations between genotype and phenotype. However, an increasingly important parameter, which has not yet been substantially taken into account, is the role of cellular translation. This means that mRNA expression data need to be correlated with the assortment of proteins actually present in the cell. One approach is based on the use of microarrays containing double-stranded DNA probes for the analysis of DNA-protein interaction and, thus, the detection and identification of DNA-binding proteins by means of fluorescence [130] or mass spectrometry analysis [131]. Moreover, substantial efforts are currently under way to develop protein, antibody, or even cell arrays, applicable to the cor-... 

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).

Screening the molecular heterogeneity of receptor expression in endothelial cell surfaces is required for the development of vascular-targeted therapies. First, as opposed to targeting purified proteins as discussed above, membrane-bound receptors are more likely to preserve their functional conformation, which can be lost upon purification and immobilization outside the context of intact cells. Moreover, many cell surface receptors require the cell membrane microenvironment to function so that protein-protein interaction may occur. Finally, combinatorial approaches may allow the selection of cell membrane ligands in a functional assay and without any bias about the cellular surface receptor. Therefore, even as yet unidentified receptors may be targeted. 

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