INDEX protein ligand, binding

Figure 6.6. Genomic information-driven drug discovery. The Initial Gene Index and Initial Protein Index are mined in a variety of ways to identify ligand-binding sites. These in turn can act as templates for structure-based design [Refs in 567].

Surface plasmon resonance spectroscopy provides both kinetic and thermodynamic data for the binding of small molecules and proteins to surfaces. One component of the binding interaction is attached to the surface and the refractive index near the surface is monitored as the other component is flowed across the surface. Surfaces that have been used include self-assembled monolayers which permit characterization of protein-ligand interactions, because the structure of the monolayer at the surface is well defined. ... 

SPR and ellipsometry are used to characterize the thickness and optical properties of membranes, whilst QCM provides information on the attachment of (bio)molecules to the membrane and their distribution on the surface. SPR is based on changes in the refractive index and is widely used as a label-free detection technique for studying molecular interactions, such as ligand binding to membrane proteins. QCM measures the change in frequency of a quartz crystal resonator and can be used to produce both qualitative and quantitative information on the protein in the membrane. Various IR techniques (FT-IT, ATR-IR, and PM-IRAS) provide information about sample composition, and whether or not biomolecules are attached to the surface. 

To date, three other APL-associated translocations of the RARa gene have been characterised at the molecular level. The t(5 17)(q35 q21) [96], t(ll 17)(q23 q21) [97, 98] and t(ll 17)(ql3 q21) [99] fuse RARa to Nucleophosmin (NPM), Promyelocytic Leukaemia Zinc Finger (PLZF), and Nuclear Mitotic Apparatus (NuMA) genes, respectively. These translocations result in the expression of chimeric RARa fusion proteins, which all retain the DNA and ligand binding domains of the receptor and gain a dimerization domain from the fusion partner (see Fig. 2 for a schematic representation). So far, the t(5 17)(q35 q21) and t(l I 17)(ql3 q21) have only been reported in index cases and, as with t(15 17)-associated APL, appeared to respond to treatment with ATRA [96,99]. In contrast, APL with t(l I 17)(q23 q21) has been reported on a recurrent basis, albeit at very low frequency, and has consistently been found unresponsive to ATRA therapy [100, 101]. 

The equilibrium association constant for this reaction is defined as ki/kj and provides an index of the affinity between the binding sites and the ligand. The inverse of the association constant (1/ a) is the equilibrium dissociation constant for the drug-protein complex ... 

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