Interaction protein complexes

The DRIP (Vitamin D3 receptor [VDR] interacting proteins) complex was purified using a VDR ligand-binding domain affinity matrix (Rachez et al., 1998). DRIP is needed for full transcriptional activity of VDR on naked DNA templates in vitro. Another complex, ARC (activator-recruited cofactor), was identified as a complex that enhances transcription activation by SREBP-la, VP16, and the p65 subunit of NF-kappaB using chromatin-assembled DNA templates (Naar et al., 1999). Characterization of the subunits of DRIP and ARC showed that the two complexes are highly related—if not identical—to each other and also to the TRAP/SMCC complexes (Rachez et al., 1999). 

Chiral Chromatography. Chiral chromatography is used for the analysis of enantiomers, most useful for separations of pharmaceuticals and biochemical compounds (see Biopolymers, analytical techniques). There are several types of chiral stationary phases those that use attractive interactions, metal ligands, inclusion complexes, and protein complexes. The separation of optical isomers has important ramifications, especially in biochemistry and pharmaceutical chemistry, where one form of a compound may be bioactive and the other inactive, inhibitory, or toxic. 

Cubic ternary complex model, a molecular model (J. Their. Biol 178, 151-167, 1996a 178, 169-182, 1996b 181, 381-397, 1996c) describing the coexistence of two receptor states that can interact with both G-proteins and ligands. The receptor/G-protein complexes may or may not produce a physiological response see Chapter 3.11. 

BH3 domain) of the BH3-only proteins binds to other Bcl-2 family members thereby influencing their conformation. This interaction facilitates the release of cytochrome C and other mitochondrial proteins from the intermembrane space of mitochondria. Despite much effort the exact biochemical mechanism which governs this release is not yet fully understood. The release of cytochrome C facilitates the formation of the apoptosome, the second platform for apoptosis initiation besides the DISC. At the apoptosome which is also a multi-protein complex the initiator caspase-9 is activated. At this point the two pathways converge. 

Biochemical characterization of clathrin-coated vesicles revealed that their major coat components are clathrin and various types of adaptor complexes. Clathrin assembles in triskelions that consist of three heavy chains of approximately 190 kDa and three light chains of 30 40 kDa. Four types of adaptor complexes have been identified to date, AP-1, AP-2, AP-3 and AP-4 (AP for adaptor protein). Whereas AP-1, AP-3 and AP-4 mediate sorting events at the TGN and/or endosomes, AP-2 is involved in endocytosis at the plasma membrane. Each adaptor complex is a hetero-tetrameric protein complex, and the term adaptin was extended to all subunits of these complexes. One complex is composed of two large adaptins (one each of y/a/S/s and [31-4, respectively, 90-130 kDa), one medium adaptin (pi -4, <50 kDa), and one small adaptin (ol-4, <20 kDa). In contrast to AP-1, AP-2 and AP-3, which interact directly with clathrin and are part of the clathrin-coated vesicles, AP-4 seems to be involved in budding of a certain type of non-clathrin-coated vesicles at the TGN. 

Protein-protein interaction domain that recognizes short sequences containing a phosphotyrosine. Hydrophobic residues N-terminal to the phosphotyrosine residue provide distinction from SH2 domains. Particularly important in assembling protein complexes at activated receptors. 

Fe protein MoFe protein complex from Avl + Av2 with MgADP/ MgATP and AlFj. This putative transition state complex is proving extremely useful in the analysis of the interactions between the two proteins and nucleotides. 

Sequences farther upstream from the start site determine how frequently the transcription event occurs. Mutations in these regions reduce the frequency of transcriptional starts tenfold to twentyfold. Typical of these DNA elements are the GC and CAAT boxes, so named because of the DNA sequences involved. As illustrated in Figure 37—7, each of these boxes binds a protein, Spl in the case of the GC box and CTF (or C/EPB,NF1,NFY) by the CAAT box both bind through their distinct DNA binding domains (DBDs). The frequency of transcription initiation is a consequence of these protein-DNA interactions and complex interactions between particular domains of the transcription factors (distinct from the DBD domains—so-called activation domains ADs) of these proteins and the rest of the transcription machinery (RNA polymerase II and the basal factors TFIIA, B, D, E, F). (See... 

The mDHFR protein complementation assay has been used to map a signal transduction network that controls the initiation of translation in eukaryotes (Remy and Michnick, 2001). A total of 35 different pairs of full-length proteins were analyzed and 14 interactions were identified using the survival selection of cells grown in the absence of nucleotides. In addition, the use of the fMTX reagent in combination with fluorescence microscopy was used to localize the protein complex within cells (Remy and Michnick, 2001). 

Figure 5.11. Generic approaches to identify interacting proteins within complexes. The complex is isolated from cells by affinity purification using a tag sequence attached to a protein known to be in the complex. Alternatively, the complex can be immunprecipitated with an antibody to one of the proteins in the complex. The proteins are resolved by polyacrylamide gel electrophoresis, proteolyzed, and the mass of the resulting peptides is determined by mass spectrometry. Alternatively, the proteins can be proteolyzed and the resulting peptides resolved by liquid chromatography. The peptide masses are then determined by mass spectrometry and used for database searching to identify the component proteins.

The experiments described above indicate that technology is available to couple SPR with mass spectrometry. These methods should be useful for protein-protein interaction mapping. For example, immobilized proteins can be used as hooks for fishing binding partners from complex protein mixtures under native conditions. The coupling of techniques can lead not only to the rapid identification of interacting proteins but will also provide information on the kinetic parameters of the interaction. This approach should serve as an excellent complement to the use of in vivo techniques such as the yeast two-hybrid system. 

A fascinating future area of study will be experimental and computational evaluation of the dynamics of protein networks. For example, how do protein complexes and interaction networks change in response to environmental signals or developmental states How do the networks of... 

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