Domain interacting

Figure 9.7 Sequence specific interactions between TBP and the TATA box. Asn 69 and Thr 124 from one domain and the equivalent residues Asn 159 and Thr 215 from the second domain interact with the palindromic TATA sequence of the central region of the TATA box.

The individual domains of the two receptors both have structures similar to that of the glucocorticoid receptor, and they bind to DNA in a similar way, with their recognition helices in the major groove. The dimer contacts are, however, totally different. In the glucocorticoid receptor, which binds to a palindromic DNA sequence like the 434 repressor described in Chapter 8, the domains interact symmetrically in a head-to-head fashion equivalent... 

The variable domains associate in a strikingly different manner. It is obvious from Figure 15.11 that if they were associated in the same way as the constant domains, via the four-stranded p sheets, the CDR loops, which are linked mainly to the five-stranded p sheet, would be too far apart on the outside of each domain to contribute jointly to the antigen-binding site. Thus in the variable domains the five-stranded p sheets form the domain-domain interaction area (Figure 15.11). Furthermore, the relative orientation of the p strands in the two domains is closer to parallel than in the constant domains and the curvature of the five-stranded p sheets is such that they do not pack... 

The S domains form the viral shell by tight interactions in a manner predicted by the Caspar and Klug theory and shown in Figure 16.8. The P domains interact pairwise across the twofold axes and form protrusions on the surface. There are 30 twofold axes with icosahedral symmetry that relate the P domains of C subunits (green) and in addition 60 pseudotwofold axes relating the A (red) and B (blue) subunits (Figure 16.9). By this arrangement the 180 P domains form 90 dimeric protrusions. 

Figure 5.1. Yeast two-hybrid system. Interaction of proteins X and Y upstream of a reporter gene leads to transcriptional activation. Protein X is part of a fusion protein that binds to a site on DNA upstream of the reporter gene by means of a DNA binding domain. Protein Y is part of a fusion protein that contains a transcriptional activation domain. Interaction of proteins X and Y places the activation domain in the vicinity of the reporter gene and stimulates its transcription.

Nakagawa, T., Putai, K., Lashuel, H. A., Lo, I., Okamoto, K., Walz, T., Hayashi, Y., and Sheng, M. (2004). Quaternary structure, protein dynamics, and synaptic function of SAP97 controlled by L27 domain interactions. Neuron 44, 453—467. 

Derouiche, R., Benedetti, H., Lazzaroni, J.C., Lazdunski, C., and Lloubes, R. (1995) Protein complex within Escherichia coli inner membrane. TolA N-terminal domain interacts with TolQ and TolR proteins./. Biol. Chem. 270, 11078-11084. 

Hall, D.B., and Struhl, K. (2002) The VP16 activation domain interacts with multiple transcriptional components as determined by protein-protein cross-linking in vivo.]. Biol. Chem. 277, 46043-46050. 

Ishmael, F.T., Shier, V.K., Ishmael, S.S., and Bond, J.S. (2005) Intersubunit and domain interactions of the meprin B metalloproteinase Disulfide bonds and protein-protein interactions in the MAM and TRAF domains./. Biol. Chem. 280, 13895-13901. 

It is noteworthy that Src-induced increase in NR1-NR2A receptor activity is promoted by the coexpression of postsynaptic density protein known as PSD-95 [37]. PSD-95 is a scaffolding protein consisting of multiple protein-protein interaction domains - three N-terminal PDZ domains, an SH3 domain and a C-terminal guanyl-ate kinase domain. The first two PDZ domains interact with the NR2 C-terminal tails while the third PDZ domain... 

Although PTB domains and SH2 domains are both capable of phosphorylation-dependent binding [177], their ligand read-out and binding modes are substantially different. Specificity on PTB domain interaction is conferred by sequences N-terminal to pTyr (Fig. 12),rather than C-terminal as found for SH2 domains. PTB domains were identified based on their ability to recognize and bind -Asn-Pro-Any-pTyr- sequences [178]. 

Although the building blocks of the eukaryotic cytoskeleton appear to be ancient, the protein domains interacting with it appear to have emerged more recendy. Several actin-binding domain families, namely calponin homology, CH, actin depolymerisation factor (ADF), the Sla2p... 

Christensen, T., B. Svensson, and B.W. Sigurskjold. 1999. Thermodynamics of reversible and irreversible unfolding and domain interactions of glucoamylase from Aspergillus niger studied by differential scanning and isothermal titration calorimetry. Biochemistry 38 6300-6310. 

A third type of interaction is due to hydrophobic effects. These are the result of nonelectrostatic domains interacting. This type of interaction occurs mainly with the highly lipid-soluble drugs in the lipid part within the cytoplasm of the cell. 

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