DHFR-ligand complexes

Table 6.3 Dissociation constants (at 30°C) for various DHFR-ligand complexes... 

We will defer describing an example of an NMR determination of a macromolecule-ligand complex until Section 4.3, as part of a more general overview of DHFR-ligand complexes, but it suffices to say that there are now many examples in the literature of macromolecule-ligand complexes and some of these have recently been reviewed.2... 

The closed/occluded Met 20 loop conformations were also assigned to various DHFR ligand complexes in solution through observation of chemical shift changes associated with alanine resonances [29]. The findings are in close agree-... 

Fig. 13 CORCEMA-ST optimized structure of bovine DHFR/TMP complex. Protein residues within the binding pocket are aqua blue and ligand residues light purple. The hydrogens were omitted for clarity. Reprinted with permission from [75] 2005, American Chemical Society...

Multiple conformations have been detected in several other complexes of L. easel DHFR (for example, with NADP and trimethoprim, and with substituted pyrimethamines) and also in complexes with 5. faeelum DHFR and E. eoU DHFR it seems likely that many other protein ligand complexes will exist as mixtures of conformations. Of course, such conformations are more difficult to detect directly if they are in fast exchange. 

KarmaData contains information which the user enters, e.g., QSAR equations, congener set, as well as information about previously studied enzyme-ligand binding complexes. KarmaData contains several classes and subclasses. For example, in KarmaData, there is a class called proteins, a subclass in proteins called dehydrogenase, a particular member of dehydrogenase c led DHFR, and a specific instance of DHFR called chicken (vide ir a). Chicken DHFR contains those attributes which are specific to itself, and inherits properties from units DHFR, dehydrogenase, and proteins. 

Similarly, the techniques already described for determining the dynamics of ligands or macromolecules are also directly applicable to complexes. Again, specific examples are given in Section 4, including the use of relaxation data to study dynamics in HIV protease/inhibitor complexes and the use of dynamic lineshape studies for studying correlated ligand-protein dynamics in DHFR complexes. 

The power of NMR methods for studying dynamics of complexes is beautifully illustrated by an earlier study of the complex of DHFR with methotrexate.147 In this case a correlated dynamic rotation of a carboxylate group on the ligand and Arg57 of the protein was detected as illustrated in Fig. 28. 

Fig. 18.2-3 Y3H system, (a) Components of the Y3H system. A MTX-based hybrid ligand associates with a DBD-fusion protein and AD-fusion protein. Formation of a complex induces activation of a reporter gene. In the example shown here, the MTX-fusion compound (MFC) incorporates a PEG linker and the small molecule kinase inhibitor purvalanol B (PurvB). (b) Example of a Y3H interaction. The DNA-binding domain fusion protein is a LexA (DBD)-DHFR fusion. The AD-fusion protein is a GR -Gal4 (AD) fusion. GR represents...

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