ATP analog 82,98

An ATP analog, /3, y-methylene-ATP, in which a —CHg— group replaces the oxygen atom between the /3- and y-phosphorns atoms, is a potent inhibitor of muscle contraction. At which step in the contraction cycle would you expect /3, y-methylene-ATP to block contraction ... 

The kinetically deduced existence of two classes of substrate sites may also account for the molar ratio between ATP analogs and inhibitors on the one hand and phosphoenzyme on the other hand. This ratio has been reported to be 2 1 for the ATP analogs adenylyl imido diphosphate (AMP-PNP) [135] and 2, 3 -0-(2,4,6-trinitrophenylcyclohexadienylidine)-ATP (TNP-ATP) [97], and also 2 1 for the ATP-site directed fluorescent inhibitors eosin [99] and FITC [49,50] and the transition-state inhibitor vanadate [126]. 

The insulin-like growth factor I receptor is closely related to the insulin receptor. The RTK activity of the IGF-I receptor is regulated by intermolecular autophosphorylation at three sites within the activation loop. The crystal structure of the trisphosphorylated form of IGF-I RTK domain with an ATP analog and a specific peptide substrate showed that autophosphorylation stabilizes the activation loop in a conformation that facilitates catalysis. Furthermore, the structure revealed how... 

Another group solved the crystal structure of the IGF-I RTK domain phosphorylated at two tyrosine residues within the activation loop and bound to an ATP analog. The ligand is not in a conformation compatible with phosphoryl transfer, and the activation loop is partially disordered. IGF-I RTK is trapped in a half-closed, previously unobserved conformation. This conformation may be intermediary between the open, inactive conformation and closed, active conformation of insulin and IGF-I RTKs. 

Hubbard, S. R., Crystal structure of the activated insulin receptor tyrosine kinase in complex with peptide substrate and ATP analog, EMBO J., 16, 5572-5581, 1997. 

Finally, a strategy to exploit protein engineering to mutate the ATP-binding pockets of protein kinases with the objective of enhancing selectivity for synthetic ATP analogs or inhibitors has been developed [66-68] using Src tyrosine kinase as a prototype model. In brief, mutation of a conserved amino acid in the ATP binding pocket was made to create a unique new site... 

In the Walker crystal structure of Fj-ATPase, the three non-catalytic a sites are liganded with the non-hydrolyzable ATP analog MgAMP-PNP. In contrast, the three catalytic (3 sites possess different conformations. One of the catalytic sites in the structure binds the analog MgAMP-PNP and is designated as Pjp another site binds MgADP and is denoted by (3dp, while the third site is empty and distorted and is called (3e [21]. In further contrast, the nucleotide-free subcomplex of ATP synthase is a symmetric trimer [36]. 

ATP and numerous ATP analogs have been extensively studied as substrates, inhibitors and as various other probes of the active sites of kinases. Efforts have been made to pinpoint the conformational and steric requirements of ATP at the active site of kinases in order to distinguish between general and specific characteristics of ATP binding. 

Non-hydrolyzable ATP analogs such as adenylyl imidodiphos-phate (AMP-PNP, Figure 2d) and B,Y-adenylyl methylene bisphospho-nate (CH.-ATP,Figure 2e) have been used as inhibitors of kinases because they can bind in a similar manner to the natural substrate... 

Although a very reliable radioligand binding assay with use The search for P2X receptor of a stable ATP analog (e.g. a, p-methylene ATP) and subtype selective ligands... 

Jacobsen, K.A., Fischer, B., Maillard, M. Biologically active ATP analogs, US5620676 (1995). 

Figure 19-12 (A) Stereoscopic views of computer-assisted reconstructions of images of myosin heads attached to an F-actin filament centered between two thick filaments. Atomic structures of actin (Fig. 7-10) and of myosin heads (Fig. 19-15) have been built into the reconstructed images obtained by electron microscopy. (A) With the nonhydrolyzable ATP analog ATPPNP bound in the active sites. (B) Rigor. Two myosin heads are apparently bound to a single actin filament in (A). If they belong to the same myosin molecule the two C-terminal ends must be pulled together from the location shown here. In (B) a third head is attached, presumably from another myosin rod. This configuration is often seen in rigor. From Winkler et al.13i Courtesy of K. A. Taylor.

As mentioned, AMP-PNP or ADP in the presence of glucose will bind only to the BII crystals at a site between the two subunits. Nucleotides bound at this site appear to be in a fully extended conformation (73). ATP analogs bound at this site make contact with amino acid residues from both subunits. The y-phosphate of ATP bound at this site is 20 A from the 6-hydroxyl of bound glucose on one subunit and 30 A from the glucose on the other subunit (73). It has been proposed that this site is an allosteric regulatory site for hexokinase and not the substrate site for ATP where phosphoryl transfer occurs (73). 

The first cluster consists of p38 in complex with pyridinylimidazole inhibitors. The second cluster consists mostly of human CDK2 in complex with different compounds with diverse chemical properties. The third cluster, which does not have a clear-cut boundary, is comprised of different kinases in complex with ATP or ATP analog inhibitors denoted ATPg (GTP, AMPPNP, AMPPCP, AMP, ADP, etc.). Besides these three major clusters, about one-third of the structures are either singletons or form tiny clusters. Interestingly, the three major clusters... 

Munson and Kyte (1981) used a similar analysis in a study of the labeling of Na,K-ATPase with an ATP analog. Of course the kinetic scheme can be complicated in a number of ways, for instance the rate of photolysis may be fast compared with the rate of attainment of the equilibria depicted. 

Elphick LM, Lee SE, Gouvemeur V et al (2007) Using chemical genetics and ATP analogs to dissect protein kinase function. ACS Chem Biol 2 299-314... 

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