We decided to test domain-based interactome mapping on 800 proteins required for C. However, domain-based Y2H mapping has not been carried out systematically at the scale of a biological process or the whole proteome. The Y2H system is ideally suited to identify binary interactions between proteins, and has been used to define interaction domains of individual proteins. Since current knowledge of protein domains is often limited to sequence conservation, new experimental strategies are required to accurately describe large numbers of interaction domains. Thus, a more precise description of protein-protein interaction networks requires information on the discrete domains that mediate these interactions. However, such high-throughput assays typically model interactions between full-length proteins, which fails to reflect that most proteins are composed of multiple distinct domains and motifs ( Bornberg-Bauer et al., 2005 Liu and Rost, 2004 Pawson and Nash, 2003). Hence, there have been major efforts at systematically identifying protein-protein interactions using yeast two-hybrid (Y2H) and affinity pull-down mass spectrometry (AP/MS) approaches ( Formstecher et al., 2005 Gavin et al., 2002 Giot et al., 2003 Ho et al., 2002 Ito et al., 2001 Krogan et al., 2006 Li et al., 2004 Rual et al., 2005 Stelzl et al., 2005 Uetz et al., 2000 Walhout et al., 2000). Physical interactions between proteins are crucial in most biological processes.
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