Interaction partners

Catenins are defined as cytoplasmic interaction partners of cadherins that form a chain of proteins ( catena, latin for chain), which connects cadherins to the actin cytoskeleton. 

Of special meaning for ionic reactions like cationic polymerization is the consideration of the interaction between reactants and solvent. This was attained by use of the extended solvent continuum model introduced by Huron and Claverie 69,70). Specific interactions between molecule and solvent cannot be taken into account by this model. For the above reason, the solvent is not considered to be an interacting partner, rather as a factor influencing the reacting species (see part 2.3.4). 

As an example of this nonlinear character we may consider two pairs of compounds, naphthalene versus quinoline and indole versus benzimidazole (Fig. 11.5). In both pairs of compounds the second differs from the first by a mutahon of an aromahc -CH group to an aromahc nitrogen, which introduces a strong H-bond acceptor into the molecule. In quinoline, which has no H-bond donor, the acceptor has no favorable interaction partner in the supercooled liquid or crystalline state, while it can make strong H-bonds with the solvent in water. Therefore, log Sw of quinoline is about 2 log units higher [35, 36] than that of naphthalene, i.e. the introduction of the H-bond acceptor strongly increases solubility in this... 

As targets become increasing more complex, the assays used to measure them become complex as well. This is most evident in the current assays which measure protein-protein interactions. Most involve tagging the interacting partners with a variety of either FRET partners or F-Q pairs, or measuring via FP changes [48]. 

A current limitation of assigning protein function based on interaction partners is the relative lack of knowledge about the function of proteins within a genome. For example, of the 554 proteins of unknown function within the large network identified by Schwikowki et al. (2000), only 69 had two or more partners of known function. As knowledge of the function of proteins within the genome improves, this approach will become much more powerful. 

A molecular field involves mapping the chemical forces between an interacting partner and a target (macro)molecule. As the information contained in 3D molecular fields is related to the interacting molecular partners, the amount of information in molecular interaction fields (MIFs) is in general superior to other mono-dimensionally or bi-dimensionally computed molecular descriptors. 

Figure 28.1 A small segment of the yeast interactome. The spheres represent proteins and the interconnecting lines are identified protein interactions. Many proteins are seen to interact with one or two other proteins, but some can have over a dozen other interacting partners.

The techniques developed to study protein interactions can be divided into a number of major categories (Table 31.1), including bioconjugation, protein interaction mapping, affinity capture, two-hybrid techniques, protein probing, and instrumental analysis (i.e., NMR, crystallography, mass spectrometry, and surface plasmon resonance). Many of these methods are dependent on the use of an initial bioconjugation step to discern key information on protein interaction partners. 

Many of the methods developed to study protein interactions use the bait/prey model to detect interacting partners (Phizicky and Fields, 1995 Archakov et al., 2003 Piehler, 2005). The bait protein is a purified protein (often recombinant) that is used to lure and capture a putative interacting protein or biomolecule. The bait protein may be immobilized to a solid phase for affinity separations or be used in solution. It also may be fusion tagged (i.e., GST or 6X His) or labeled with a detectable molecule, such as a fluorescent probe. It often is the case... 

Figure 28.2 DSS can capture protein interacting partners through amide bond crosslinks.

Finally, knowledge of the peptide masses that resulted from the PIR conjugation provides information to identify the parent proteins from which they originated. Peptide mass and sequence databases now are sufficiently developed to provide rapid confirmation of protein-protein interaction partners. 

When fewer than three hydrogen bonds exist to satisfy the oxygen valence of a siloxy group, as for example in some hydrous layer silicates mentioned above, then they need to be stronger (yielding a low-field shift in proton NMR) and/or additional interaction partners should be present. 

MS can perform large-scale analyses of protein interactions. Interacting partners of proteins in complexes can be purified by several strategies including affinity chromatography and immunoprecipi-tation with antibodies specific to the bait protein. The purified components can then be subjected to LC-MS/MS and proteins within the complex identified. Using a variety of approaches including... 

Expression of a recombinant protein using an inducible vector system would permit expression at endogenous levels to simulate physiologic levels of expression of a protein of interest. Tandem affinity purification strategies have recently been employed and facilitate the analyses of highly interactive proteins when the bait protein is expressed at endogenous levels. Immunoaffinity or immunoprecipitation followed by LC-MS/MS does not readily permit determination of the stoichiometry of interacting partners. Additionally, when compared to yeast hybrid experiments, it is difficult to determine whether interactions are binary when identified in complexes by MS/MS. 

As noted above, many natively unfolded proteins become folded in the presence of an appropriate interaction partner. Fungal prion domains subscribe to this paradigm whereby the partner is itself (each other) and the interaction represents homotypic polymerization into amyloid. 

A similar scenario is assumed for Sup35p (Chien etal., 2004 Glover et al., 1997). The inactivation of Ure2p and by inference also of Sup35p in the prion states comes from steric constraints. One such mechanism would be steric blocking, that is, the binding sites for the interaction partners are not accessible in filaments. 

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