Binding data

The equilibrium constant for a simple bimolecular association process 

This equilibrium constant is expressed as the association constant which has dimensions (concentration)-1, in molar terms M-1. The dissociation constant KDiss is the reciprocal of and has dimensions of concentration (M). The objective of the following derivation is to obtain an equation of the form cAB = f(cA tot, cBjtot, fCA ), in which ci tot are the total or stoichiometric concentrations of the components i (which are known), in contrast to the quantity c in Eqn. 9.19, which are the free concentrations of the species in solution, which are not known. An equation of this form will enable us to calculate theoretical data. 

Using the conservation conditions cAtot=cA + cAB and cBtot=cB + cAB Eqn. 9.19 can be written in the form  

The only unknown in this equation is the term cAB. Expanding and rearranging Eqn. 9.20 yields the following quadratic equation  

The solutions of a quadratic equation of the general form x2 + px + q=0 are given by the two roots and x2  

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Melatonin produces its effects via the GPCR, ML-1. A second lower affinity form, ML-2, has been described on the basis of binding data. Activation of melatonin receptors can inhibit DA release in the retina. 

GM Crippen. Distance geometry approach to rationalizing binding data. I Med Chem 22(8) 988-997, 1979. 

LG Boulu, GM Crippen. Voronoi binding site models Calculation of binding models and influence of drag binding data accuracy. I Comput Chem 10(5) 673-682, 1989. 

Koshland, D. E., Jr., Nemethy, G., and Filmer, D., 1966. Compari.son of experimental binding data and dieoretical models in proteins containing snbnnits. Biochemistry 5 365-385. The KNF model. 

Examples of these are shown for the saturation data in Figure 4.2. At first glance, these transformations may seem like ideal methods to analyze saturation data. However, transformation of binding data is not generally recommended. This is because transformed plots can distort experimental uncertainty, produce compression of data,... 

Scatchard analysis, a common linear transformation of saturation binding data used prevalently before the widespread availability of nonlinear fitting software. The Scatchard transformation (see Chapter 4.2.1), while easy to perform, can be misleading and lead to errors. 

Roche O, Kiyama R, Brooks CL 3rd. Ligand-protein database linking protein-ligand complex strnctnres to binding data. J Med Chem 2001 44 3592-8. 

Lombardo F, Obach RS, Shalaeva MY and Gao F. Prediction of volume of distribution values in humans for neutral and basic drugs using physicochemical measurements and plasma protein binding data. J Med Chem 2002 45 2867-76. 

In deciphering the role of the different NTs, or more precisely their antagonists, in the antischizophrenic action of neuroleptic drugs it must be remembered that published binding data and calculated dissociation constants vary considerably, which, of course, affects correlation coefficients made with clinical activity. Factors to bear in mind are ... 

The interpretation of much of the binding data given so far is based upon the assumption that the high affinity binding sites represent a population of independent sites. In the unphosphorylated II" " these sites would open up either to the periplas-mic or cytoplasmic side of the membrane independently of each other. The assumption ignores the evidence that the enzyme is, in fact, multimeric and that the data... 

Fig. 37.7. PLS biplot derived from the biochemical binding data in Table 37.10, after log doublecentering and analysis by two-block PLS [56]. The reading rules are the same as those indicated with Fig. 37.6. Reproduced with permission of E.J. Karjalainen.

Table 6.46 5,6-DIARYLPYRIDINE DERTVATTVES - IN VITRO BINDING DATA [319]...

Figure 12 Resynthesized library hits identified from the high throughput fluorescence-polarization assay along with their Src SH2 binding data.

These problems are provided to afford an opportunity for the reader to analyze binding data of different sorts. The problems do not require nonlinear least squares analysis, but this would be recommended to those with access to appropriate facilities. It must be emphasized that, while linearizing transformations allow binding data to be clearly visualized, parameter estimation should... 

To construct the Hill plot (Figure 5.10E), it was assumed that fimax was 0.654 fmol/mg dry wt., the Scatchard value. The slope of the plot is 1.138 with a standard deviation of 0.12, so it would not be unreasonable to suppose % was indeed 1 and so consistent with a simple bimolecular interaction. Figure 5.10B shows a nonlinear least-squares fit of Eq. (5.3) to the specific binding data (giving all points equal weight). The least-squares estimates are 0.676 fmol/mg dry wt. for fimax and... 

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