Kinases constructs

Proliferation of the BaF3 cells can be monitored rapidly by using standard techniques such as with Alamar blue or the commercially available CellTiter-Glo. These systems measure cell numbers by detecting intracellular ATP concentrations or by measuring intracellular reduction of the Alamar blue dye. The BaF3 system is excellent for looking at larger kinase constructions and receptor tyrosine kinases (Warmuth et al., 2007). 

The first technique is very intuitive. Out of the few proteins that could be crystallized in a number of different conformations, adenylate kinase is probably the best-studied example. By combining nine observed crystal structures and interpolating between them, a movie was constructed that visualized a hypothetical path of its hinge-bending transition (jVonrhein et al. 1995]). 

Of the 517 protein kinases in the human kinome [116], structures are publicly available for < 10% of the different enzymes. In the absence of experimental data, construction of homology models based on known structures has proven a reliable method for generating 3D information. How, then, are the models built and what are the limitations of the models especially as applied to the family of protein kinases ... 

Exposure of cells to interferon normally results in the induction of a protein kinase termed eIF-2a protein kinase. The enzyme, which is synthesized in a catalytically inactive form, is activated by exposure to dsRNA. The activated kinase then phosplorylates its substrate, i.e. eIF-2a, which is the smallest subunit of initiation factor 2 (eIF2). This, in turn, blocks construction of the smaller ribosomal subunit, thereby preventing translation of all viral (and cellular) mRNA (Figure 8.6). 

Replacement of the famesyl group by lipid analogues could be performed for full length Ras proteins in vitro by means of the enzyme famesyltrans-ferase. When such partially modified Ras constructs were applied in Xenopus oocytes the cellular machinery completed modification (endoprotease activity, carboxymethylation and palmitoylation). In these cases the H-Ras famesyl group could be stripped off most of its isoprenoid features that distinguish it from a fatty add without any apparent effect on its ability to induce oocyte maturation and activation of mitogen-activated protdn kinase In contrast, replacement by the less hydrophobic isoprenoid geranyl causes severely delayed oocyte activation. 

NMR and kinetic studies have been conducted with the hope of providing more details about the position and conformation of the polypeptide substrate in cAMP-dependent protein kinase. These have served to narrow down the possible spatial relationships between enzyme bound ATP and the phosphorylated serine. Thus, a picture of the active site that is consistent with the available data can be drawn (12,13,66,67). Although these studies have been largely successful at eliminating some classes of secondary polypeptide structure such as oi-hellces, 6-sheets or an obligatory 6-turn conformation 66), the precise conformation of the substrate is still not known. The data are consistent with a preference for certain 6-turn structures directly Involving the phosphorylated serine residue. However, they are also consistent with a preference or requirement for either a coil structure or some nonspecific type of secondary structure. Models of the ternary active-site complexes based on both the coil and the, turn conformations of one alternate peptide substrate have" been constructed (12). These two models are consistent with the available kinetic and NMR data. 

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