Fatty acid binding pockets

Fig. 7. A stereo view of the n-hexyl moiety bound in the fatty acid-binding pocket in RmL.

Unesterified fatty acids within cells are commonly bound by fatty acid-binding proteins (FABPs), which belong to a group of small cytosolic proteins that facilitate the Intracellular movement of many lipids. These proteins contain a hydrophobic pocket lined by p sheets (Figure 18-3). A long-chain fatty acid can fit into this pocket and Interact noncovalently with the surrounding protein. 

Fig. 5 Models of cHSA and DHSA-G2. (a) Fatty acids bind on the surface of cHSA. (b) Fatty acids bind to the hydrophobic pockets of DHSA-G2...

Many of the picornavirus structures have been shown to have electron density in their VP1 pockets even in the absence of any added drug. These densities have been modeled as fatty acids or similar compounds [12,15,56,70-72]. The occurrence of these pocket factors have led some to hypothesize that these factors perform a similar function as do capsid-binding inhibitors, that is, to stabilize the virions [15,24,41,73,74]. 

The fluidity of the hydrogen-bond donation network at the pore could allow a large number of structurally distinct molecules to bind in this location. If the function of the pocket is to bind fatty acids or other structurally diverse pocket factors and thus stabilize the virion. The flexibility of the hydrogenbonding network at the pore seems ideally suited for such a purpose. 

The ligand binding pocket of USP is filled by a fortuitous phospholipid co-purified and co-crystallized with the USP LBD that was fiirther characterized by mass-spectroscopic and chemical analysis [57]. In a similar way, recent crystallographic investigations of the retinoid-acid related orphan receptor (3 (ROR (3) [58] and of the heterodimeric complex RARa/RXRa [30] revealed an E.coli endogeneous fatty acid in the ROR (3 and in the RXRa subunit, respectively. 

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