Binding shift

We have previously calculated conformational free energy differences for a well-suited model system, the catalytic subunit of cAMP-dependent protein kinase (cAPK), which is the best characterized member of the protein kinase family. It has been crystallized in three different conformations and our main focus was on how ligand binding shifts the equilibrium among these ([Helms and McCammon 1997]). As an example using state-of-the-art computational techniques, we summarize the main conclusions of this study and discuss a variety of methods that may be used to extend this study into the dynamic regime of protein domain motion. 

The biochemical activity and accessibility of biomolecule-intercalated AMP clays to small molecules was retained in the hybrid nanocomposites. For example, the absorption spectrum of the intercalated Mb-AMP nanocomposite showed a characteristic soret band at 408 nm associated with the intact prosthetic heme group of the oxidised protein (Fe(III), met-myoglobin) (Figure 8.9). Treatment of Mb with sodium dithionite solution resulted in a red shift of the soret band from 408 to 427 nm, consistent with the formation of intercalated deoxy-Mb. Reversible binding of CO under argon to the deoxy-Mb-AMP lamellar nanocomposite was demonstrated by a shift in the soret band from 427 to 422 nm. Subsequent dissociation of CO from the heme centre due to competitive 02 binding shifted the soret band to 416nm on formation of intercalated oxy-Mb. 

In addition to the storage of iron in intestinal mucosal cells, iron is also stored, primarily as ferritin, in macrophages in the liver, spleen, and bone, and in parenchymal liver cells (Figure 33-1). Apoferritin synthesis is regulated by the levels of free iron. When these levels are low, apoferritin synthesis is inhibited and the balance of iron binding shifts toward transferrin. When free iron levels are high, more apoferritin is produced to sequester more iron and protect organs from the toxic effects of excess free iron. 

Scheme 2 Protein dynamics and ligand recognition. Fast motions are indicated by different shadings, slow motions by different (narrow vs. elongated) shape. Ligand binding shifts the population and is associated by changes in the fast dynamics.

Mechanism 2. Herbicide binding shifts the redox potential for B to more negative values, i.e., when the herbicide is bound,... 

Guszczynski, T. Copeland, T.D. A binding shift assay for the zinc-bound and zinc-free HIV-1 nucleocapsid... 

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