Binding-site mapping

Horak CE, et al. GATA-1 binding sites mapped in the heta-glohin 68. locus by using mammalian chip-chip analysis. Proc. Natl. Acad. 

Key words Structural biology, Database mining, Classification of protein structures, Pharmacophore, Hit finding, Binding site mapping, GRID/CPCA... 

The previous calculation assumed that the solvation energy of ammonium was equal the solvation energy of a single water molecule times the number of water binding sites. Is this a valid assumption Compare the electrostatic potential maps of ammonium ion and ammonium ion+water. For which are the exposed hydrogens more acidic Did the calculation underestimate or overestimate the difference in solvation energies ... 

The fact that the aliosterically preferred conformation may be relatively rare in the library of conformations available to the receptor may have kinetic implications. Specifically, if the binding site for the modulator appears only when the preferred conformation is formed spontaneously, then complete conversion to alios terically modified receptor may require a relatively long period of equilibration. For example, the allosteric p38 MAP kinase inhibitor BIRB 796 binds to a conformation of MAP kinase requiring movement of a Phe residue by 10 angstroms (so-called out conformation). The association rate for this modulator is 8.5 x 105 M-1 s-1, 50 times slower than that required for other inhibitors (4.3 x 107 M 1 s-1). The result is that while other inhibitors reach equilibrium within 30 minutes, BIRB 376 requires 2 full hours of equilibration time [8],... 

Both dynein and MAP2 interact with microtubules at the same binding sites, namely, the C termini of a- and p-tubulin. Also, MAP2 inhibits the microtubule-activated ATPase of dynein and prevents microtubule gliding on dynein-coated glass coverslips. Thus, MAP2 and other fibrous MAPs may be regulators of microtubule-based motility in vivo (Paschal et al., 1989). 

Viswanadhan VN, Ghose AK and Weinstein JN. Mapping the binding site of the nucleoside transporter protein a 3D-OSAR study. Biochim Biophys Acta 1990 1039 356-66. 

Although anosmias to these compounds occur at similar levels, some communicative value may arise from the persistence of signal emissions which are not enantiomerically pure (Carman, 1993 Wysocki et al., 1999). In secreted mixtures, the alternate versions of such compounds are produced in a constant ratio since they have identical volatility and hence provide stable informational content to the receiver. Support for this idea comes from the results of the NMR mapping of the BT binding site within the MUP1 carrier (Zidek et al., 1999). Here the protein-ligand complex does exist in the expected ratio, and for both enantiomers, although the orientation of the bound thiazole was interpreted as opposite to that indicated by previous X-ray analyses. 

Zidek L., Stone M., Lato S., Pagel M., et al. (1999). NMR-mapping of the recombi mouse major urinary protein-I binding site occupied by the pheromone 2-sec-bi 4,5-dihydrothiazole. Biochem 38, 9850-9861. 

Damaj BB, McColl SR, Neote K, et al. Identification of G-protein binding sites of the human interleukin-8 receptors by functional mapping of the intracellular loops. FASEB J 1996 10(12) 1426-1434. 

Miranker A, Karplus M. Functionality maps of binding sites a multiple copy simultaneous search method. Proteins 1991 11 29-34. 

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