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Data files were parsed with UNIX scripts, which extracted pairs of genes consisting of one repressor and one or more binding partners.

In keeping with previous results, we found that LCR-containing proteins tend to have more binding partners across different PPI networks than proteins that have no LCRs.

A final mechanism through which pre-assembly of a complex can mediate cooperative interactions is configurational pre-organization, which involves distinct binding sites on multivalent ligands that can form multiple discrete interactions with one or more binding partners (5, 7).

These questions have been considered in numerous studies of protein protein interactions, but, unfortunately, although our understanding of the energetics of rigid-body interactions has grown considerably, the situation is greatly complicated when the flexibility of one or more binding partners must be considered.

Similar(56)

Our results show that LCRs are preferentially located towards sequence extremities, and that proteins with LCRs in their sequence extremities have more protein binding partners than proteins with LCRs in their central regions.

It will be very interesting to establish whether LIMP-2 acts as a more general binding partner for lysosomal hydrolases.

More than 30 binding partners have been reported for NHERF1 and 2 (Shenolikar et al., 2004), some are shared by more than one NHERF isoform (Yun et al., 1998; Sun et al., 2000), while others are NHERF isoform-specific (Shenolikar et al., 2004).

More importantly, most binding partners are yet to be mapped to specific isoforms.

For example, more than two binding partners might be necessary to stabilize protein protein interactions.

Since the Tudor domain of TDRD3 can specifically recognize methylated arginine motifs in proteins (16, 17), we speculated that TDRD3 might be recruited to SGs through methyl-dependent interactions with one or more of its binding partners.

The proteins have numerous functions, and more than 100 binding partners have been identified in metabolic pathways for signal transduction, cell cycle regulation, apoptosis, stress responses, and malignant transformation (Darling et al., 2005).

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